From b55fcc33b66b5a4aa057d326deaa054d0ba9b562 Mon Sep 17 00:00:00 2001 From: Yaacov Date: Fri, 28 Aug 2026 16:07:13 +0300 Subject: [PATCH 1/5] docs: accept Scient documentation system --- docs/planning/README.md | 7 + ...ent-documentation-system-and-publishing.md | 1550 +++++++++++++++++ docs/research/spike-reports/README.md | 22 +- ...lity-and-reading-route-audit-2026-08-28.md | 516 ++++++ ...tation-system-markdown-audit-2026-08-28.md | 549 ++++++ ...oundation-architecture-audit-2026-08-28.md | 742 ++++++++ 6 files changed, 3385 insertions(+), 1 deletion(-) create mode 100644 docs/planning/scient-documentation-system-and-publishing.md create mode 100644 docs/research/spike-reports/documentation-system-maintainability-and-reading-route-audit-2026-08-28.md create mode 100644 docs/research/spike-reports/documentation-system-markdown-audit-2026-08-28.md create mode 100644 docs/research/spike-reports/scient-capability-to-foundation-architecture-audit-2026-08-28.md diff --git a/docs/planning/README.md b/docs/planning/README.md index ad0573a..0d4efa5 100644 --- a/docs/planning/README.md +++ b/docs/planning/README.md @@ -15,6 +15,13 @@ Do not use planning docs as product truth, accepted architecture, or current imp Current planning docs: +- `scient-documentation-system-and-publishing.md` - accepted cross-repository + documentation authority; docs/user/-backed, release-qualified public Scient + Docs publishing; internal capability and architecture structure; + feature-document lifecycle; minimal cross-repository governance promotion; + real-change maintenance tabletop; generated inventory and temporary + disposition/verification queues; first-principles architecture gates; + acceptance package; implementation start gate; and proof-first sequence. - `product-measurement-and-analytics-plan.md` - proposed product-measurement contract, privacy boundary, event catalog, KPI model, dashboard portfolio, cross-repository implementation sequence, and activation gates. diff --git a/docs/planning/scient-documentation-system-and-publishing.md b/docs/planning/scient-documentation-system-and-publishing.md new file mode 100644 index 0000000..3d7b88a --- /dev/null +++ b/docs/planning/scient-documentation-system-and-publishing.md @@ -0,0 +1,1550 @@ +# Scient Documentation System And Publishing + +Status: Accepted +Owner: Yaacov +Created: 2026-08-28 +Last updated: 2026-08-28 +Purpose: Defines the accepted sustainable cross-repository documentation system and staged implementation program for public Scient Docs, current capabilities, architecture, development, operations, upstream divergence, planning, research, and historical evidence. +Doc type: Planning note + +## Document Rules + +This document owns the accepted documentation information architecture, +cross-repository authority model, public publishing direction, update triggers, +and staged migration sequence for the Scient repository family. + +Yaacov explicitly accepted this documentation-system direction on 2026-08-28, +with the qualifications recorded in [Acceptance Record](#acceptance-record). +Acceptance authorizes staged implementation of the documentation system; it +does not authorize an indiscriminate file move, deploy an MCP server, change an +app release, or promote proposed product architecture into accepted direction. +Until each rule is promoted into its durable owner, the current +[Documentation Policy](../documentation-policy.md), repository AGENTS.md files, +and area indexes remain operationally authoritative. + +Current product behavior belongs beside the implementation that provides it. +Product direction and cross-product planning belong in this Scient repository. +Website deployment remains owned by the website repository. + +### Update Policy + +Update this plan while implementation changes the intended documentation +authorities, public publishing model, repository family, migration sequence, or +accepted qualifications. Promote durable rules into the documentation policy, +repository guidance, and owning indexes rather than leaving this plan as a +second competing authority. Mark this plan Superseded when the durable owners +and remaining roadmap fully replace its governing role. + +## Decision Summary + +Scient should maintain **two authored documentation systems** and publish them +through multiple delivery surfaces: + +1. **Scient Docs**: the complete public product-help corpus for people and + support agents learning or using released Scient behavior. +2. **Engineering knowledge**: the capability, architecture, development, + operations, upstream, planning, research, quality, and historical material + needed to build and maintain Scient correctly. + +The central rule is: + +> One authoritative fact, multiple linked or generated views. + +The accepted direction is: + +- use **Docs** as the public website label and /docs as the public route; +- keep the authored source for current app help with the app implementation in + ScientFactory/scient-desktop; +- keep the inherited docs/user/ path as the durable default source for that + public-help corpus and classify it logically as **Help**; +- publish only reviewed, release-qualified pages from docs/user/ rather than + treating directory membership as automatic public eligibility; +- make the website a renderer, navigator, search surface, and release selector + for the same corpus, not a second prose authority; +- build any later documentation MCP as a thin, version-aware retrieval adapter + over that same corpus, not as an independently maintained knowledge base; +- keep current implementation capability records and implementation + architecture in the repository that owns the code; +- keep product truth, philosophy, cross-product architecture, roadmaps, + research, quality doctrine, and cross-repository operating policy in this + Scient repository; +- preserve useful development, operational, upstream, philosophical, + first-principles, historical, and research documents throughout the + transition; and +- prove the authoring and update loop with a small vertical pilot before any + broad migration. + +## Why This System Is Needed + +The current repositories contain substantial useful documentation, but their +placement does not consistently explain authority or update responsibility. + +In scient-desktop, docs/user/ is already the established T3-compatible location +for user-facing guidance. Its folder name does not by itself say whether a page +is a tutorial, workflow, behavioral reference, candidate, or release-qualified +statement, but that ambiguity should be solved through logical classification, +indexing, and publication qualification rather than a second help directory. +The inherited docs/internals/ name groups current Scient capability records, +architecture, contributor reference, upstream receipts, proposals, and +historical plans under one broad label. + +The public website currently has a small hard-coded Docs page rather than a +complete documentation publishing system. Maintaining a second manually +written website corpus would create immediate drift from application behavior. + +The large scientific-platform plans preserve valuable current-state snapshots +and source context, but several plans repeat the same implementation facts. As +Scient advances, repeating current capability truth in every roadmap would make +ordinary changes expensive and allow those copies to disagree. + +The T3-derived desktop requires ongoing upstream integration. A physical +reorganization that ignores inherited paths could turn every upstream +documentation update into unnecessary conflict work. + +The current scient-agent repository is an OpenCode-derived fork checkout, +not an implemented native Scient agent or a Scient-owned documentation corpus. +Its Markdown should remain outside the initial inventory and migration. The +documentation model should extend to that repository when native Scient-agent +implementation begins, without treating inherited OpenCode pages as Scient +product guidance automatically. + +The target system must therefore improve clarity without requiring every +feature change to update many copies across several repositories. + +## Design Principles + +### 1. Nearest Authoritative Owner + +A fact belongs in the repository and document closest to the authority that can +verify and change it. + +- Shipped app behavior belongs with the app. +- Native-agent implementation behavior belongs with the native agent when it + exists. +- Website behavior belongs with the website. +- Product requirements and cross-product direction belong in Scient. +- T3 or OpenCode integration details belong with the fork that performs the + integration. + +Cross-repository documents link to that owner. They do not copy its complete +current state. + +### 2. Purpose Before Audience + +Folder and document names should explain what knowledge they own, not merely +who might read them. A user, support agent, developer, architecture agent, or +maintainer may read several areas for different purposes. + +This is a logical ownership rule, not a mandate to rename useful inherited +paths. The durable docs/user/ compatibility path can own the logical **Help** +role while its index and publishing manifest make purpose, release, and surface +qualification explicit. + +### 3. Public And Internal Documents Are Different Owners + +Scient Docs and capability records are related, but one is not an “internal +version” of the other. + +- A Docs page teaches a person how to use released behavior safely and + truthfully. +- A capability record describes implementation status, files, contracts, + tests, T3 seams, limitations, evolution, and roadmap relationships. + +They should link through a stable capability name or slug, but neither should +copy all of the other's content. + +### 4. Version-Aware Public Truth + +Public Docs should default to the current released product, not automatically +to development main. Candidate or unreleased material may appear in an explicit +preview, but it must not be presented as stable released behavior. + +### 5. Plans Describe Deltas + +Roadmaps own intended outcomes, dependencies, decisions, sequencing, and +acceptance gates. They should link to current capability truth rather than +maintain competing inventories of what is already implemented. + +### 6. History Remains Available Without Governing Current Work + +Forensic reports, migration plans, upstream receipts, retired capabilities, and +superseded proposals preserve important reasoning. Their status and placement +must prevent them from appearing current. + +### 7. Prove Maintainability Before Scaling + +The system should be exercised through representative capability changes and +an upstream integration before broad migration. If the update burden is high, +the model should be simplified before more documents are converted. + +## Repository Authority Model + +| Repository | Proposed documentation authority | +| ----------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| ScientFactory/Scient | Product truth, product philosophy, first principles, cross-product architecture and decisions, roadmaps, research, quality doctrine, documentation policy, cross-repository operating procedures, and the compact repository-family capability map. | +| ScientFactory/scient-desktop | Public app Docs source, current app capability records, implementation architecture, development guidance, desktop operations, T3 divergence and integration records, and desktop implementation history. | +| ScientFactory/scient-agent | Deferred from the initial documentation audit and migration. When native-agent implementation begins, this repository should own native-agent capability and implementation documentation, agent development and operations, and relevant OpenCode divergence and integration records. Its current inherited Markdown does not become Scient documentation automatically. | +| ScientFactory/ScientFactory-website | Docs rendering, navigation, search, stable public URLs, source-version selection, preview and production deployment, and website-specific behavior. It does not own a second copy of product-help prose. | + +The repositories remain independent. Cross-repository work uses separate +branches, commits, pull requests, and explicit dependency order under the +[GitHub Operating Model](../operations/github-operating-model.md). + +## Observed Markdown Baseline + +The 2026-08-28 audit found that a raw `.md` count does not describe the actual +documentation corpus. The refreshed remote heads inspected were Scient +`9a309d6bb952a3fae8c0dd3495139c7c0736b37a`, scient-desktop +`d5ff08e721086eec02a2a84ad1431b33da6f5269`, and the website +`f129246a9e59894c7bb19dc2d17b7c6ac3b0ce82`. Scient documentation alignment +[PR #99](https://github.com/ScientFactory/Scient/pull/99) and desktop upstream +alignment [PR #189](https://github.com/ScientFactory/scient-desktop/pull/189) +were merged at those heads. Desktop documentation alignment +[PR #188](https://github.com/ScientFactory/scient-desktop/pull/188) remained an +open draft and is not represented in desktop `origin/main`. Its branch was one +commit ahead and 28 commits behind current desktop main; a merge-tree check +found no textual conflict, but its existing checks predate PR #189 and do not +prove the combined baseline. + +Other open desktop work also carries documentation consequences that are not +current main: PR #179 adds a managed-provider-runtime proposal; PR #121 adds +Overleaf capability and help pages plus an index change; and PR #129 adds the +substantial ComputeSession implementation, a 3,398-line proposed foundation +record, candidate public computing help, and an index change. PR #188 separately +reconciles adjacent file, analysis, LaTeX, PDF, and Artifact Studio records, +including explicit in-flight compute boundaries. Treat these as independent +candidate surfaces, not one combined current corpus. + +| Repository area | Observed Markdown | +| --------------- | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | +| Scient | 118 tracked files: 85 under docs/, 27 under lab/, three project skills, and three root files. | +| scient-desktop | 1,070 tracked files, of which 928 are vendored under .repos/. The remaining 142 non-vendored tracked Markdown files include 113 under docs/. Three additional forensic reports under docs/reports/ were untracked in the audited checkout. | +| Website | Six tracked repository, contribution, and brand-support files; no authored Scient Docs corpus. | + +The scoped audit therefore contains 266 tracked non-vendored Markdown +files, or 269 when the three untracked forensic reports are included. Of these, +201 are in the primary Scient and desktop documentation trees when the reports +are included. This does not make all 201 files equally authoritative: fixtures, +historical records, proposals, current implementation, public guidance, and +repository orientation have different roles. + +The dated [file-by-file Markdown audit](../research/spike-reports/documentation-system-markdown-audit-2026-08-28.md) +records the purpose, authority, exact T3-base provenance, preliminary +disposition, active documentation-PR paths, metadata anomalies, and index gaps +behind these totals. It is audit evidence, not a permanent hand-maintained +registry or permission to perform its proposed dispositions. + +The desktop concentration explains the current ambiguity. Its 68 +docs/internals/ files contained 29 upstream or migration-history records, 20 +Scient capability or current-implementation documents, 14 inherited or shared +technical references, and five proposals, audits, or old plans. The problem is +therefore not merely naming. Several kinds of authority currently share one +folder and inconsistent status conventions. + +These counts are a dated planning snapshot, not a permanent registry. Refresh +the baseline after desktop documentation PR #188 or any later documentation or +upstream change lands. The current scient-agent source tree is deliberately +excluded until native Scient-agent work begins. + +A final readiness recheck found that desktop main subsequently advanced to +`c0baaab2cda29a84682b77b8384bb7542e59a8bd` through +[PR #190](https://github.com/ScientFactory/scient-desktop/pull/190). That pull +request changes seven non-Markdown files, so the audited Markdown counts remain +unchanged. It does change user-visible provider/settings defaults, sensitive +email display behavior, and default agent browser/Sources access without a +documentation update. Phase 0B must reconcile its documentation impact, and +P0-DESKTOP-FORENSICS must extend the capability/PR evidence through #190, +rather than rewriting the exact `d5ff08e7` audit snapshot as if it had included +the later change. + +## Proposed scient-desktop Documentation Areas + +The seven areas are a logical classification vocabulary. They are not seven +required directories, and the owner-selected default is to preserve useful +inherited paths: + +| Logical area | Current or default physical owner | Physical-path rule | +| ------------ | -------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------- | +| Help | docs/user/ | Keep as the durable authored source for public Scient Docs. Do not create a parallel docs/help/ tree. | +| Capabilities | Primarily Scient-owned records currently under docs/internals/ | Normalize ownership during pilots; move only when clarity gain exceeds T3 merge and link cost. | +| Architecture | docs/architecture/, focused ADRs, and current shared-foundation records under docs/internals/ | Preserve inherited architecture paths; separate capability detail only when a proven owner requires it. | +| Development | Existing contributor references, package READMEs, docs/internals/work-artifacts.md, and repository guidance | Keep useful guidance beside the workflow or package it owns. | +| Operations | docs/operations/ and focused runbooks | Keep the existing area and distinguish runbooks from product help. | +| Upstream | Root UPSTREAM.md, machine state, seam registries, and dated integration records | Preserve the operational entry point and history-preserving T3 integration surfaces. | +| Records | Dated reports, receipts, completed migrations, retirements, and superseded plans in their reviewed durable locations | Create or move records only through explicit disposition; do not build a cosmetic archive tree. | + +The repository docs/README.md is the compatibility map from these logical roles +to real paths. New physical areas may be proposed later only when pilots show a +durable authority benefit; completing the taxonomy is never a reason to create +empty or parallel directories. + +### Help — Authored Source For Scient Docs + +This area should answer how to use released Scient. The website presents it as +**Docs**. + +Its navigation may include: + +- getting started; +- concepts; +- workflows; +- features; +- providers and integrations; +- troubleshooting and recovery; and +- exact behavioral reference. + +The physical source remains docs/user/. It can remain relatively flat. Website +navigation, page selection, and generated metadata should not force deep +repository nesting before the corpus size requires it. + +A public Docs page should state only behavior appropriate to its documented +release or preview context. It may explain relevant limitations, local versus +remote behavior, platform differences, permissions, privacy and data-transfer +boundaries, recovery, and external continuation. It should not contain +implementation file maps, speculative roadmaps, unreviewed architecture, or +internal integration receipts. + +### Capabilities — Current Implementation Truth + +Each capability-family record should make the following questions answerable: + +- what user or system outcome the capability provides; +- which behavior exists on current main; +- whether it is released, unreleased, in flight, proposed, retired, or + platform-limited; +- which clients, providers, environments, and operating systems are qualified; +- which state or service is authoritative; +- important packages, contracts, services, UI roots, and tests; +- architecture dependencies and failure or recovery behavior; +- permissions, privacy, and local or external data-flow boundaries; +- T3 seams or other inherited-source relationships; +- open-source sources, donors, references, or compatibility oracles actually + used; +- current limitations and non-goals; +- related public Docs pages; +- related product requirements and roadmaps; +- important PR and evolution history; and +- retirement, replacement, or upstream-adoption conditions. + +Use one record per durable capability family, not one record per PR, button, +component, or minor variation. + +Capability status should not be compressed into one ambiguous word. The pilot +should test a small set of separate implementation, release, and qualification +fields before a mandatory schema is accepted. + +The list above is a completeness prompt, not a mandatory set of headings. The +pilot starts with only: + +- stable capability identity and accountable owner; +- implementation, release, and qualification status as separate facts; +- current implementation/source owner; +- related public help, architecture, and upstream owner when applicable; and +- the change that should trigger review of the record. + +Add detail only when the capability's authority, risk, dependencies, evolution, +or support needs justify it. + +### Architecture — Foundations And Invariants + +Architecture documents should describe shared authority, identity, lifecycle, +dependency direction, contracts, failure and recovery semantics, resource +bounds, security and privacy boundaries, and difficult decisions. + +They should not repeat complete public instructions or one capability dossier +per UI feature. Hard-to-reverse accepted choices should use focused ADRs. +Cross-product architecture belongs in Scient; desktop implementation +architecture belongs in scient-desktop. + +### Development + +This area should preserve contributor setup, source layout, commands, tests, +debugging, fixtures, APIs, configuration, and extension guidance. Useful +inherited T3 development documentation should remain available and should not +be moved merely to make the tree visually uniform. + +### Operations + +This area should preserve real runbooks for development instances, releases, +publication, migrations, observability, recovery, support, and maintenance. +Operational authority must remain distinct from product explanation. + +### Upstream + +This area should own the current T3 integration contract and navigable history: + +- current upstream base and process; +- protected Scient divergence registry; +- seam files and machine checks; +- why each divergence exists; +- conflict-resolution rules; +- upstream adoption or retirement conditions; and +- dated integration receipts. + +The current root UPSTREAM.md may remain a special compatibility and process +entry point. The migration should decide what it continues to own and what it +indexes rather than moving it automatically. + +### Records + +This area should contain immutable or historical evidence that remains useful +but does not govern current implementation: + +- forensic capability and PR reports; +- retired and removed capabilities; +- completed migrations; +- superseded implementation plans; +- historical upstream reviews and receipts; and +- dated architecture or implementation investigations. + +Records should identify their snapshot date, commit or range, authority limit, +and current successor where one exists. + +## Scient Repository Documentation Areas + +The current Scient categories remain useful and should not be replaced by the +desktop model: + +- product/ owns accepted or proposed product truth according to status; +- architecture/ and architecture/decisions/ own cross-product structure and + accepted difficult decisions; +- planning/ owns proposed direction and ordered future work; +- research/ owns source evidence and evaluations; +- quality/ owns quality and testing doctrine; +- development/ owns repository-specific contributor guidance; +- operations/ owns cross-repository operating procedures; and +- a later records area may receive completed or historical material when a + focused migration proves that placement useful. + +The [Product Philosophy](../product/product-philosophy.md), accepted +[Product Requirements](../product/PRD.md), quality doctrine, +source-adaptation strategy, and architecture decisions are governing context. +This documentation project must preserve their authority and must not flatten +them into capability pages or website help. + +## Cross-Product Capability Map + +Scient should eventually contain one compact repository-family capability map. +It should include only information needed to navigate ownership: + +- stable capability name or slug; +- owning implementation repository; +- current detailed capability record; +- related product requirement; +- related roadmap or accepted architecture; and +- major cross-repository dependencies. + +It should change when a capability is introduced, retired, renamed, or changes +ownership. It should not duplicate complete current implementation status, +source-file maps, or test evidence from the owning repository. + +## Public Publishing Model + +### Canonical Source + +The proposed authored source for current app help is +scient-desktop/docs/user/. The public label is **Scient Docs**, and the website +route is /docs. The physical path is deliberately retained as a useful T3 +compatibility surface; the public name does not need to match its source folder. + +Directory membership does not make a page public automatically. The publishing +pilot should prove a generated or reviewed manifest that selects pages from +docs/user/, records exact source identity, and excludes candidate, inherited, +platform-inapplicable, or unverified guidance. + +### Publication Qualification + +The first public corpus should be desktop-first. A page may be published only +when its documented behavior is verified for the applicable released version +and product surface. Inherited T3 pages remain useful source material, but are +not Scient product promises merely because they live under docs/user/. + +Publication metadata should support corpus-level defaults plus page-level +exceptions for desktop, web, mobile, provider, environment, or operating-system +scope. Do not require repetitive platform metadata on every page when one +qualified corpus default is accurate. + +### Website Responsibility + +The website should own: + +- rendering and visual design; +- navigation and search; +- stable public URLs and anchors; +- accessibility and responsive behavior; +- source-version selection; +- preview and production deployment; and +- website-specific analytics or operational behavior under their existing + privacy and activation rules. + +It should not maintain an independent prose copy of the same app instructions. + +### Version Selection + +Stable public Docs should be built from an exact released desktop commit, tag, +or equivalent release-proven source. A candidate Docs preview may render a +specific documentation or application PR head, but it must be labelled as a +preview and must not silently replace stable public guidance. + +The exact transport—multi-repository checkout, pinned source manifest, +release-owned documentation artifact, or another bounded mechanism—should be +selected during the publishing pilot. The decision must preserve exact source +identity, reproducible builds, preview support, failure visibility, and a +simple rollback path. It must also define: + +- the release or documentation event that triggers publication; +- the maximum acceptable lag between an applicable release or correction and + stable Docs; +- the owner and visibility of a failed or stale publication; +- a stable-Docs correction path that can repair public guidance without + requiring a new app binary; and +- how a corrected page remains truthfully associated with the app versions to + which it applies. + +### Agent-Readable Delivery + +Before building MCP, the public Docs surface should provide: + +- stable HTML pages; +- stable section anchors; +- raw Markdown or an equivalent structured representation; +- a generated page index containing title, summary, topic, version, and source + identity; and +- useful search. + +These delivery artifacts should be generated from the canonical corpus, not +maintained separately. + +### Future Documentation MCP + +A later public documentation MCP may provide version-aware topic search, +section retrieval, page listing, and source or version reporting. It should be +a thin retrieval adapter over the same public corpus. + +It must not: + +- become a second authored knowledge base; +- silently synthesize undocumented product claims; +- expose proposals as released behavior; +- mix private or internal operational information into public help; or +- require maintainers to update separate MCP answers after each feature. + +MCP implementation should wait until stable page identities, version semantics, +and the public corpus have been proven. + +## Agent Reading Routes + +Repository guidance should eventually route agents by question. These are +target logical routes, not instructions to create every target folder during +Phase 1. Until a path is deliberately migrated, each repository's documentation +index should map the logical role to its real current compatibility path. + +The full collaborator onboarding journey is occasional orientation, not a +per-change checklist. An already-oriented contributor or agent should normally +reach the actual content owner through no more than two governance or routing +surfaces: one family or repository front door and, when needed, one local +index. This is a design diagnostic rather than a CI limit, and it does not +reduce the source, code, test, history, or runtime investigation required after +the owner is found. + +| Question | Primary source | +| ------------------------------------------------------ | ------------------------------------------------------------------------------------------ | +| How does a person use released Scient? | scient-desktop/docs/user/ or the published Scient Docs version of a qualified page. | +| What does the current app implement? | The indexed capability-family owner at its current path and current source. | +| Why is the app structured this way? | Repo-local architecture and ADRs, plus cross-product architecture in Scient when relevant. | +| What should Scient become next? | Scient/docs/product/ and Scient/docs/planning/, honoring status. | +| How is an external source used or evaluated? | Scient/docs/research/ and the owning source-adaptation or upstream records. | +| How should the repository be built or tested? | The owning repository's development guidance and AGENTS.md. | +| How is it released, monitored, migrated, or recovered? | The owning repository's operations guidance. | +| Why does the fork differ from upstream? | The owning fork's upstream documentation and divergence registry. | +| What existed or was removed previously? | Capability evolution sections and historical records. | + +A route succeeds when it reaches the real owner or an explicit missing +decision while preserving repository, status, release or preview version, and +cross-repository dependency boundaries. A missing owner or undecided mechanism +must remain visible; agents must not fill the gap by copying prose or inventing +authority. + +The dated [maintainability and reading-route +audit](../research/spike-reports/documentation-system-maintainability-and-reading-route-audit-2026-08-28.md) +tests these routes against the current Scient, desktop, website, and open +documentation-candidate surfaces. It finds that upstream and temporary-work +routing are already strong, desktop routing is usable but incomplete, the +cross-repository documentation-impact rule is not yet operational, and website +Docs publishing correctly remains blocked on an explicit source-transport +pilot. + +## Governance Surfaces And Promotion Map + +The repository-family contract should be promoted through the smallest set of +surfaces that can make it usable. Policy, agent instructions, indexes, +contributor guides, pull-request templates, onboarding, and skills have +different jobs. Repeating the full taxonomy in all of them would create the +very drift this proposal is intended to remove. + +The current audit found a workable base with several boundaries that Phase 1 +must make explicit: + +- Scient/docs/documentation-policy.md is the active authority for durable + documentation inside Scient, but it currently says that it governs only that + repository; +- Scient's AGENTS.md, onboarding, documentation index, and stewardship skill + already route collaborators toward that policy, with some repeated guidance; +- scient-desktop's AGENTS.md owns local agent behavior and currently routes + user-visible behavior to docs/user/, architecture and contributor material to + docs/internals/, and runbooks to docs/operations/; +- scient-desktop/docs/internals/work-artifacts.md already owns the local rule + that durable facts belong in current documentation, active plans belong in + GitHub, and temporary agent artifacts stay outside the worktree; +- the desktop and website already have pull-request templates, while Scient + does not; and +- the website has repository, contribution, and deployment guidance but no + documentation-corpus policy or duplicate public-help corpus. + +Desktop documentation PR #188 changes docs/README.md and remains an open, +behind draft at the observed baseline. Its disposition is a bounded Phase 0B +decision: rebase, reverify, and merge it, or close it and carry its still-useful +reconciliations into the relevant pilot. Only the overlapping desktop index and +content edits should wait for that decision; it must not block truth repairs, +Scient policy work, website ownership work, or independent architecture review. + +### One Role Per Governance Surface + +| Surface | What it owns | What it must not own | +| ---------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- | +| Family documentation policy | Durable knowledge classes, statuses, evidence, canonical ownership, promotion, history, and family-level update principles. | Repository-specific commands, a copied map of every file, or current feature facts. | +| Shared contribution protocol | Cross-repository pull-request separation, documentation-impact evidence, dependent-PR ordering, and shared review expectations. | Local build commands, local paths, or the documentation taxonomy in full. | +| Repository AGENTS.md | Short, executable rules for agents in that repository, including which local owner to inspect and which changes trigger documentation review. | Product truth, a second documentation index, detailed publishing design, or long feature inventories. | +| Repository documentation index | The current local map from logical purpose to real path, including compatibility paths that have not moved. | Policy, implementation truth, or a manually maintained global inventory. | +| Owning help, capability, architecture, operations, upstream, product, planning, or research document | The actual durable fact and its evidence boundary. | Repository-wide routing rules unrelated to its subject. | +| CONTRIBUTING.md | Human and external-contributor expectations, proposal intake, local contribution workflow, and public-accessible minimum rules. | Internal product policy or a copy of every agent instruction. | +| Pull-request template | A concise prompt that makes documentation impact and cross-repository dependencies visible. | The explanation of how the documentation system works or a large checklist. | +| Project skill | Repeatable workflow for finding and updating the real owner, followed only when the skill applies. | Project authority, accepted decisions, or a private answer store. | +| Root README and onboarding | Human orientation and reading route into the governing sources. | Detailed policy, feature behavior, or implementation plans. | + +The current accepted local rule remains authoritative until a focused Phase 1 +change updates it. After promotion, the concern-specific owner above governs: +the policy classifies durable knowledge, the contribution protocol governs the +shared pull-request requirement, repository guidance makes that requirement +actionable locally, and the subject document owns the fact. An index or skill +cannot override a content owner. When two accepted sources disagree, agents +must report the conflict and route a reconciliation change; they must not infer +precedence from repository size, file age, or link order. + +### Phase 1 Owner Surfaces And Change Triggers + +This map identifies possible owners, not a checklist requiring every listed +file to change. Phase 1 should touch a surface only when its owned instruction +changes. + +The initially required promotion set is intentionally small: + +- Scient documentation policy, team contribution protocol, AGENTS.md, and + documentation index; +- desktop AGENTS.md, documentation index, work-artifacts guidance, + CONTRIBUTING.md, and pull-request template; and +- website AGENTS.md and pull-request template. + +Onboarding, skills, root READMEs, and contributor guides outside that required +set change only if the accepted route alters what they actually instruct a +reader to do. Phase 0 factual corrections remain independently justified and +do not make every corrected surface a recurring governance owner. + +| Repository and surface | Minimal Phase 1 responsibility | +| --------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| Scient/docs/documentation-policy.md | Add the accepted family-level nearest-owner, public-versus-engineering, update-before-create, temporary-artifact, status, history, and conflict rules. Keep Scient-specific placement rules clearly scoped rather than implying that desktop uses the same folders. | +| Scient/docs/operations/team-contribution-protocol.md | Own the concise `Documentation impact` declaration and dependent documentation-PR ordering as shared contribution evidence. | +| Scient/AGENTS.md | Route agents to the policy, protocol, owning repository, and documentation stewardship skill. Keep only the local actions an agent must perform; do not restate the entire target hierarchy. | +| Scient/docs/README.md | Map only Scient's current documentation areas and link the accepted family contract and cross-product capability map when they exist. | +| Scient/docs/onboarding.md | Change only if the accepted reading journey cannot reach the governing sources through the updated index and AGENTS.md. Preserve the existing journey otherwise. | +| Scient/skills/documentation/scient-documentation-stewardship/SKILL.md | Change only if its procedure or owner-selection workflow changes. The skill remains non-authoritative and returns agents to policy and content owners. Update skills/README.md only if the skill's identity, scope summary, or index route changes. | +| Scient pull-request surface | Do not create a new template merely for repository symmetry. Require the field through the shared protocol and agent guidance during the pilot; add a minimal template later only if omitted declarations become a repeated failure. | +| scient-desktop/AGENTS.md | Replace the audience-only documentation routing sentence with concise logical-role triggers and a link to the local index. Preserve the Scient safety override and inherited T3 guidance; do not copy the Scient policy. | +| scient-desktop/docs/README.md | Own the real local path map and logical classification, including docs/user/, docs/internals/, docs/operations/, root UPSTREAM.md, and package READMEs. This is the compatibility layer while physical paths remain mixed. Start from PR #188's explicit disposition for overlapping edits. | +| scient-desktop/docs/internals/work-artifacts.md | Remain the detailed local owner for feature plans, GitHub work, temporary artifacts, merged-PR records, new-file admission, and updating existing durable owners. Treat it logically as development guidance until a later move is justified. | +| scient-desktop/CONTRIBUTING.md | Keep external proposal and contribution expectations self-contained; add only the public minimum for documentation placement and impact reporting. | +| scient-desktop/.github/pull_request_template.md | Add one proportional documentation-impact field with `None`, `Updated`, or `Dependent PR`; do not add a taxonomy checklist. | +| website/AGENTS.md | Tell agents that app-help prose is owned in scient-desktop, website Docs work owns rendering and exact source/version behavior, and cross-repository changes use dependent pull requests. | +| website/README.md | Continue to own website role, build, deployment, and repository-family orientation. Correct factual repository-family wording in Phase 0A; document Docs transport only after the publishing pilot chooses it. | +| website/CONTRIBUTING.md | Change only if website-specific branch, check, preview, or human-review instructions change; link rather than repeat the source-ownership design. | +| website/.github/pull_request_template.md | Add one documentation/source-version impact field, preserving the existing validation and deployment evidence. | + +The current scient-agent repository is intentionally absent from this map. +Phase 1 should not inspect or change its inherited OpenCode documentation. Add +repo-local governance there only when native Scient-agent work begins and the +real implementation boundary can be documented. + +### Public-Repository Self-Sufficiency + +Scient is private while scient-desktop is public. A public contributor must not +need private repository access to understand the minimum rules for a desktop +change. The public repository should therefore state the small actionable rule +locally—where current help, implementation, operations, upstream, and temporary +work belong—and link to public local owners. It should not copy private product +plans, the complete family policy, or internal cross-product reasoning. + +This is deliberate bounded duplication of an instruction, not duplication of +the underlying product fact. The local sentence is updated only when the +action a public contributor must take changes. + +### Governance Update Triggers + +| Change | Required governance update | +| ---------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------- | +| Family-level document class, status, evidence, promotion, or history rule changes | Family policy; stewardship skill only if its procedure changes; local AGENTS.md only if an agent action changes. | +| Shared pull-request evidence or dependent-PR rule changes | Team contribution protocol and affected pull-request templates; do not rewrite content indexes. | +| A repository adds, renames, moves, or retires a documentation area | That repository's documentation index; AGENTS.md or CONTRIBUTING.md only if the route a contributor follows changes. | +| A feature or architecture fact changes | The owning subject document under the relevance test; no governance file merely because the topic is related. | +| Website source transport, version selection, preview, or rollback behavior changes | Website README or operations owner and affected agent rule; desktop release documentation only when its producer contract changes. | +| A new workflow repeatedly fails because agents cannot find the owner | First repair the nearest index or local instruction. Change family policy only if the rule itself is missing across repositories. | + +Phase 1 should validate these routes with a small set of question-based reading +tests: a public desktop contributor, an internal cross-repository feature +agent, a website publishing agent, an upstream-integration agent, and a +documentation-only agent should each reach the correct content owner without +reading every governance surface. + +## Documentation Update Contract + +Every implementation or documentation pull request should explicitly assess +documentation impact. A concise field is preferred over a large ritual: + + Documentation impact: + - None — + - Updated — + - Dependent PR — + +The expected owner depends on the change: + +| Change | Documentation consideration | +| ------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------------------------- | +| User steps, visible behavior, privacy, data flow, permissions, recovery, or terminology changes | Public Docs source in the owning implementation repository. | +| Capability availability, limits, platform support, provider support, or maturity changes | Capability record. | +| Authority, identity, lifecycle, dependency direction, shared foundation, or hard-to-reverse contract changes | Architecture document or ADR. | +| T3 or OpenCode seam, conflict rule, protected divergence, or upstream disposition changes | Owning fork's upstream documentation. | +| Build, test, configuration, debugging, fixture, or contributor workflow changes | Development documentation or repository guidance. | +| Release, migration, deployment, monitoring, support, or recovery procedure changes | Operations documentation. | +| Desired product outcome, scope, or sequence changes | Scient product or planning owner. | +| External dependency, source, license, donor, or research evidence changes | Scient research or source map and any accepted dependent decision. | +| Capability removal, replacement, or retirement | Capability disposition, public Docs change at the appropriate release, upstream disposition when relevant, and historical record. | + +A code change should update current implementation documentation in the same +repository and preferably the same pull request. A genuinely cross-repository +documentation consequence uses a separate dependent pull request with explicit +ordering. Matching branch names are not dependency evidence. + +Website publication should consume the approved source version. Maintainers +should not manually repeat the same product instructions in a website pull +request. + +## Feature Documentation Lifecycle + +Feature work does not receive a new Markdown file by default. An agent or +maintainer should first decide whether the information is temporary work, +whether an existing durable owner should change, and whether a new owner is +actually necessary. + +### During Investigation And Implementation + +- Keep agent scratch, transcripts, session handoffs, temporary research, and + implementation checklists outside the worktree. +- Track active outcome, constraints, acceptance criteria, and implementation + progress in the owning GitHub issue, project item, and pull request. +- Update an existing help, capability, architecture, upstream, development, or + operations owner before proposing a new document. +- Put reusable source evaluation or cross-product planning in Scient only when + it has durable evidence, scope, and an appropriate planning or research + owner. Do not copy ordinary feature implementation notes into Scient. + +### Admission Test For A New Durable File + +Create a new document only when all of the following are true: + +1. The knowledge will remain useful after the feature pull request closes. +2. No existing document can own it coherently without confusing authority. +3. It answers a distinct durable question for a defined audience. +4. Its accountable repository, owner, status, evidence boundary, and update + trigger can be stated. +5. It can be indexed from the appropriate documentation map without becoming + one record per PR, component, button, or minor state. + +A feature may update zero, one, or several existing documents. That is not a +requirement to create one file in every area. For example, a user-visible change +may update a public Docs page and its capability-family record while requiring +no architecture document because no shared invariant changed. + +### Relevance Test And Fan-Out Budget + +A document should change only when a fact it owns changed. Topical relation is +not enough: + +- update public Docs only when user behavior, availability, limitations, + privacy, permissions, recovery, or terminology changed; +- update a capability record when implementation, qualification, support, + limits, ownership, dependencies, or evolution changed; +- update architecture or an ADR only when a shared authority, lifecycle, + contract, invariant, or difficult decision changed; +- update a roadmap only when desired outcome, scope, dependency, sequence, or + acceptance gates changed; +- update an index only when navigation, placement, status, or page identity + changed; and +- do not rewrite a historical record merely because later work is related. + Add a successor or disposition only when its interpretation changed. + +As a pilot target, an ordinary bounded change should normally require zero to +two primary authoritative document updates. Three can be reasonable when the +same change genuinely spans public behavior, current capability truth, and a +shared architecture or operational contract. More than three primary owners +should trigger a relevance and ownership review, not an automatic failure. + +Large cross-cutting programs, retirements, and upstream integrations may +legitimately exceed that target. Their review should distinguish recurring +authority updates from one-time navigation, metadata, evidence, and historical +disposition work. This is a diagnostic budget, not a CI quota and not a reason +to omit a changed privacy, safety, recovery, or authority claim. + +### At Merge And Afterward + +- Update current implementation documentation in the implementation pull + request whenever practical. +- Use an explicitly ordered dependent pull request only for a genuine + cross-repository consequence. +- Treat the merged pull request as the implementation record. Do not preserve a + duplicate completed checklist or agent handoff in the repository. +- Promote durable decisions, evidence, or constraints into their existing + owners, then supersede or retain any predecessor according to its real + historical value. +- When a capability is removed, update its disposition and release-appropriate + public guidance; preserve a separate record only when the evolution or + reasoning remains useful. + +### Markdown That Is Not Product Documentation + +The inventory and agent rules must distinguish these classes rather than route +every Markdown file into the documentation hierarchy: + +| Class | Treatment | +| ------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------ | +| Durable project documentation | Classify by help, capability, architecture, development, operations, upstream, product, planning, research, quality, or records authority. | +| Package or source README | Keep beside the package or source it explains; index it only when broader navigation needs it. | +| Agent protocol or project skill | Keep in AGENTS.md or SKILL.md under its workflow rules; it must not become product or architecture authority. | +| Test or visual fixture | Keep with fixtures and label it non-authoritative; do not publish it as Docs. | +| Vendored or inherited source documentation | Preserve with its source boundary and exclude it from Scient-owned documentation counts unless deliberately adapted. | +| Temporary work artifact | Keep outside the worktree or in the owning GitHub work item; do not rename it to bypass the policy. | + +## Pre-Acceptance Maintenance Tabletop + +A read-only tabletop applied the proposed contract to five real merged desktop +changes. The observed documentation files below describe what the pull requests +actually changed; they are not assumed to be sufficient merely because they +exist. + +### User-Visible Feature: Voice Transcript Correction, [PR #164](https://github.com/ScientFactory/scient-desktop/pull/164) + +The 54-file feature changed only `docs/operations/local-dev-app.md`. It added an +optional, default-off setting that passes locally transcribed text to the +selected authenticated provider runtime for LLM correction and falls back to +the original local transcript on failure. The current public voice page still +states that recordings and transcripts are processed entirely by the bundled +local runtime, while the current voice architecture record does not describe +the correction path. + +Under the proposed model, the voice help page and voice capability record are +the two primary feature owners. The local-development runbook changes only if +the development-app lifecycle also changed; it does not substitute for either +feature owner. This is a material privacy and authority drift that the update +contract should have caught without requiring a new document. + +### Cross-Cutting Architecture: Provider Lifecycle, [PR #150](https://github.com/ScientFactory/scient-desktop/pull/150) + +The 100-file integration touched ten documentation files: three provider help +pages, current provider and lifecycle architecture, a Codex-specific deep dive, +an evidence audit, an implementation proposal, the glossary, and the index. +That breadth is defensible for a one-time multi-provider architecture program, +but it should not become the recurring cost of every provider fix. + +The target model keeps shared current behavior in one provider-lifecycle +capability and focused architecture owners, keeps provider-specific help only +where behavior genuinely differs, and treats the audit as evidence. The +implementation proposal currently still says final integration is open even +though PR #150 merged; it should receive a historical disposition rather than +continue as a living implementation owner. Index and glossary changes are +one-time navigation or vocabulary work, not recurring capability fan-out. + +### Retirement: Quick Chat And Projectless Threads, [PR #146](https://github.com/ScientFactory/scient-desktop/pull/146) + +The retirement updated `UPSTREAM.md`, fork divergence, and onboarding, and +deleted the 150-line current Quick Chat record plus a 45-line design-QA file. +The target model would update the capability disposition, released help if a +public page existed, the project-ownership or upstream invariant that changed, +and a historical record only where the reasoning remains useful. + +The retirement is summarized in current upstream documentation and described +in the forensic capability and divergence reports. Those reports were still +untracked at the audited baseline, so Phase 2 must give them an explicit durable +disposition before relying on them as the navigable retirement record. + +### Bounded Maintenance Change: HTML/PDF Freshness, [PR #187](https://github.com/ScientFactory/scient-desktop/pull/187) + +The 13-file change updated one current implementation document, +`scient-browser-pdf-export.md`. That is proportionate for the source identity, +automatic refresh, stale-revision rejection, and recovery contract. The public +Docs owner should also change if the visible Update/Retry workflow or its +limitations are part of the user contract; related roadmaps and historical PDF +plans should not change merely because they discuss PDF. + +### Upstream Integration: T3 Through c8aba2587d, [PR #189](https://github.com/ScientFactory/scient-desktop/pull/189) + +The 100-file merge updated the root upstream contract, added one dated +integration receipt, and updated the asset README for an actual asset-source +change. This matches the target model: one current upstream owner, one immutable +receipt, and a package-local README only when its own source boundary changed. +It did not require every affected capability or roadmap to repeat the adopted +upstream range. + +### Tabletop Conclusion + +The model survives the tabletop with bounded recurring fan-out. The failures +were not caused by too many proposed categories; they came from missing update +triggers, a completed plan that remained live, and retirement evidence without +a final durable disposition. The relevance test, feature lifecycle, and +logical-before-physical migration directly address those failures. The later +vertical pilots must still prove the model in normal authoring and publication +work; this tabletop is design evidence, not completion of Phase 5. + +## Migration Rules + +### Logical Classification Before Physical Movement + +The first migration should produce two complementary outputs. + +The **generated exhaustive inventory** should mechanically enumerate Markdown +paths in each in-scope repository and classify obvious structural boundaries, +including documentation trees, root protocols, package-local reference, +skills, fixtures, lab evidence, vendored material, and relevant untracked +candidate documents. Vendored files should be counted and excluded rather than +silently mixed into Scient-owned totals. This generated output is audit +evidence, not a manually maintained source of truth. + +The **human-reviewed disposition ledger** should cover the primary durable +documentation set and classify each current document by: + +- repository and accountable owner; +- path, title, and document class; +- purpose and doc type; +- current authority and status; +- intended audience and current consumers; +- related capability or foundation; +- update trigger; +- implementation, product, roadmap, research, or historical dependencies; +- intended logical area; +- public or internal delivery; +- keep, revise, merge, move, supersede, deprecate, or retain-as-record action; + and +- source evidence needed before rewriting factual claims. + +Review this inventory before moving files. + +The disposition ledger is a temporary migration authority. After the migration, +normal area indexes, document metadata, and proportional validation should make +the corpus navigable; maintainers should not have to keep a second exhaustive +manual spreadsheet or global status dashboard synchronized forever. + +### Preserve Upstream Compatibility Deliberately + +The T3-derived desktop receives upstream documentation in inherited docs/user/ +and docs/internals/ paths. Do not mass-rename inherited material for visual +purity. The logical documentation index may present clearer areas before every +physical path changes. + +Move Scient-owned documents only when the authority gain exceeds future merge +cost. Keep inherited paths when they remain useful compatibility surfaces, and +document their logical classification in the index. + +### Preserve History And Successors + +Moving or retiring a document must preserve its intent, Git history where +practical, inbound references, status, and current successor. Do not delete a +useful plan merely because its implementation landed or its source path is no +longer fashionable. + +## Overcomplication Constraints + +The accepted system should reject the following unless later evidence requires +them: + +- no docs/docs/ folder merely to match the public label; +- no parallel docs/help/ tree while docs/user/ remains the durable Help source; +- no automatic publication of every inherited docs/user/ page merely because + it is in the source directory; +- no separately authored website copy of app help; +- no separately authored MCP answer store; +- no one document per PR, component, button, or minor UI state; +- no global dashboard that duplicates every repository's detailed state; +- no requirement to update every roadmap after every implementation change; +- no mass movement of inherited T3 or OpenCode documentation for cosmetic + consistency; +- no deep folder hierarchy before corpus size proves it useful; +- no large mandatory metadata schema before the pilot proves which fields are + necessary; +- no repetitive platform field on every page when a qualified corpus default + plus explicit exceptions is truthful; +- no accepted proposal left as the recurring policy after its rules have been + promoted to durable owners; +- no automation that can mark a proposal accepted or claim implementation + maturity; and +- no deletion of philosophy, first-principles, quality, development, + operations, upstream, or historical evidence merely because it is not public + user help. + +## Implementation Sequence + +The accepted implementation goal authorizes this documentation program through +focused branches and pull requests. Each phase still receives proportional +review, validation, and collision checks. Merge, deployment, release, MCP, and +product-architecture authority remain separate where stated below. + +### Phase 0A — Repair Truth And Preserve Evidence + +Phase 0A contains factual corrections and preservation work that do not depend +on accepting the target documentation system: + +1. Correct the voice page and voice capability record so they distinguish + local audio/transcription from optional provider-based transcript-text + correction. +2. Reconcile the stale private-migration-candidate boundary in desktop + CONTRIBUTING.md with the active public released repository. +3. Correct or retire the stale provider-lifecycle implementation proposal while + preserving its useful rationale and current successor. +4. Correct the website repository-family description so `scient-agent` is the + planned home for future native-agent work, not an already implemented native + source foundation. This does not require reading or changing scient-agent. +5. Repair the three concrete Scient metadata anomalies identified by the + Markdown audit. +6. Preserve this accepted plan and its dated Draft audits on their isolated + Scient branch without claiming that acceptance proves implementation. +7. Preserve the three desktop forensic reports on an isolated branch based on + current desktop main, add appropriate metadata and an index route, and keep + their dated snapshot boundaries explicit. Do not commit them from the + behind canonical desktop checkout. + +Preservation does not settle final records placement or prove any migration. +Truth repairs may use separate focused pull requests where repository, review, +or collision boundaries require them. + +### Phase 0B — Reconcile The Moving Baseline + +1. Confirm any active upstream integration and its dependent documentation + rechecks are complete. +2. Confirm the exact merged heads in every affected repository. +3. Recheck cross-repository links and implementation snapshots. +4. Reconcile active documentation and feature candidates as candidate—not + merged-current—evidence, and reconcile merged PR #190's user-visible default + and privacy/display implications against current help and capability owners. +5. Decide the disposition of desktop documentation PR #188: either rebase, + reverify, and merge it, or close it and transfer still-useful reconciliations + into the relevant pilot. +6. Resolve the six missing public-help index routes, fourteen missing + non-receipt internal routes, and one historical migration route through + focused index or collection links rather than listing every upstream receipt + individually. + +Desktop upstream PR #189 is complete at the observed baseline. PR #188 affects +the desktop index and adjacent file, analysis, LaTeX, PDF, and Artifact Studio +records, but it is not a gate for unrelated repository work. Substantial +feature drafts remain in-flight evidence and do not require the inventory to +wait indefinitely for every open branch. + +These are targeted baseline repairs, not permission for a broad migration. + +### Phase 1 — Promote The Documentation Contract + +After explicit decision, promote only the accepted rules in dependency order: + +1. In Scient, update the documentation policy and team contribution protocol, + then update AGENTS.md and the documentation index. Change onboarding or the + stewardship skill only if their actual route or procedure changes. +2. After the overlapping disposition of desktop documentation PR #188 is + known, update desktop AGENTS.md, docs/README.md, the existing work-artifacts + guide, contributor guide, and pull-request template in one focused + repository-local change. +3. Update the website agent guidance and pull-request template, changing its + README or contributor guide only where the accepted source-ownership rule + changes their actual responsibility. +4. Run the question-based reading tests in the governance map and record any + ambiguous route before beginning the inventory. Include a public user or + support agent seeking version-correct released behavior, and use a fresh + contributor or agent that did not author the policy for at least one pass. + +Each repository uses its own branch, commit, pull request, checks, and review. +The Scient policy change lands first; the desktop and website changes identify +that dependency explicitly but remain self-contained for contributors who +cannot read Scient. Do not change scient-agent in this phase. + +Do not move the full corpus in this phase. + +Phase 1 is not complete until accepted rules have durable owners and this +proposal no longer competes with them. At the exit gate, mark this document's +real disposition, link to the promoted policy and repository-local owners, and +state which later pilot and migration choices remain open. Agents should not +need this planning document as recurring policy after promotion. + +### Phase 2 — Build The Cross-Repository Inventory + +Generate the exhaustive Markdown inventory and review the durable-document +disposition ledger across Scient, scient-desktop, and the website. Record the +scient-agent scope boundary but do not inspect or migrate its current inherited +OpenCode Markdown. Reconcile duplicate or conflicting authority before +rewriting prose. + +Use the dated file-by-file audit as the seed rather than repeating its work by +hand. Phase 2 still must refresh the exact merged heads after Phase 0, reconcile +the active candidate branches, and complete the human owner, audience, +dependency, update-trigger, and final-disposition review before the temporary +ledger can govern migration. + +Generate a temporary help-verification queue from docs/user/. It should record +publication eligibility, applicable release and surface, factual verification, +and any required correction or exclusion. Prioritize Getting Started, +Projects, Providers, Voice, file handling, PDF, and LaTeX. Retire this queue +after the corpus has durable page ownership and generated publication metadata; +do not turn it into a permanent second registry. + +### Phase 3 — Prove Three Vertical Pilots + +Use three representative app areas: + +1. **Projects and Getting Started**: public workflow and project-owned state. +2. **File viewing, PDF, and LaTeX**: Scient-owned capabilities, shared + architecture, generated documents, and cross-product roadmap links. +3. **Providers**: inherited T3 host behavior, Scient lifecycle divergence, + remote environments, provider-specific differences, and troubleshooting. + +For each pilot, produce only the necessary: + +- public Docs page or page set; +- capability record; +- shared architecture link or focused architecture update; +- upstream record when applicable; +- roadmap and product links; and +- historical disposition where prior material is superseded. + +### Phase 4 — Prove Website Publishing + +Render the pilot public Docs from an exact desktop source version in a website +preview. Verify navigation, links, search or index generation, accessibility, +responsive behavior, source or version display, preview versus stable +separation, failure behavior, and rollback. + +The pilot must also select and prove: + +- the manifest or other bounded page-selection mechanism over docs/user/; +- source transport without preselecting checkout, pinned manifest, or release + artifact before evidence; +- release and documentation-correction publication triggers; +- maximum acceptable freshness lag and visible stale/failure behavior; +- a correction path for stable Docs that does not require a new app binary; +- truthful version association after a correction; and +- corpus-level surface qualification with page-level exceptions. + +### Phase 5 — Prove The Maintenance Loop + +Process at least: + +- one real user-visible feature change; +- one architecture-affecting change; +- one feature retirement or supersession case; and +- one T3 upstream integration + +through the proposed update contract. Measure how many authored documents each +change truly requires. Simplify the model if ordinary work causes excessive +fan-out or ambiguous ownership. + +Use the next real retirement and upstream integration that occur during the +program. Do not manufacture product or upstream work merely to satisfy this +proof; those cases may remain pending while unrelated phases continue. + +### Phase 6 — Migrate The Remaining Corpus + +After the pilots and maintenance proof: + +- write the complete public Scient Docs corpus; +- normalize capability-family records; +- consolidate shared architecture and ADRs; +- preserve and clarify development and operations guidance; +- create the navigable upstream divergence system; +- place audits, retirements, migrations, and historical plans appropriately; +- reduce repeated current-state sections in roadmaps to links where safe; and +- update repository indexes and reading routes. + +### Phase 7 — Add Proportional Automation + +Only after the structure stabilizes, add checks that provide clear value: + +- local and cross-repository link validation; +- generated navigation and page indexes; +- source-version and release-pin validation; +- detection of missing documentation-impact declarations; +- checks for broken canonical-owner links; +- status or metadata validation for the small accepted schema; and +- reproducible website Docs builds. + +Automation supports human-auditable documentation. It does not decide truth or +acceptance. + +### Phase 8 — Evaluate Documentation MCP + +Evaluate actual agent retrieval failures against the mature public corpus. +Build the thin MCP only if it materially improves discoverability, version +selection, citation, or support-agent reliability beyond the website, raw +content, index, and search surfaces. + +## Relationship To The First-Principles Architecture Review + +The documentation program should supply evidence for the architecture review, +not become a reason to postpone it. The review can begin once the inventory and +a small representative set of capability records reliably describe current +authority, lifecycle, dependencies, seams, failure behavior, and limitations. +It does not need to wait for every public Docs page or historical record to be +polished. + +The dated +[capability-to-foundation architecture audit](../research/spike-reports/scient-capability-to-foundation-architecture-audit-2026-08-28.md) +completes the initial cross-capability evidence pass at the exact source and +in-flight identities it records. Its classifications remain research evidence; +they do not accept a foundation, authorize a rewrite, or replace the focused +workflow traces and decisions below. + +Documentation readiness must not serialize independent architecture work. With +focused authorization and current source evidence, the architecture track may: + +- decide proposed ADR-0006 before another canonical .scient/ namespace is + introduced; +- run the smallest accepted-operation-envelope proof and the end-to-end + file/resource/presentation trace as separate architecture slices; and +- require the F5 execution reconciliation between AnalysisRun, DocumentBuild, + ComputeSession, MATLAB, and Results before compute PR #129 can merge. + +These are decision and merge gates, not implementation authorization embedded +in this documentation proposal. Each architecture slice retains its own review, +branch, tests, migration safety, and acceptance decision. + +### Review Foundations, Not The Order Features Happened To Land + +The review should group current capabilities by the foundations they actually +share. It should not assume that a sequence of individually successful feature +pull requests produced the best long-term boundaries. For each foundation, +trace representative end-to-end workflows and ask: + +- Which product invariant or first principle requires this foundation? +- What object, identity, state, or service is authoritative? +- Who owns creation, mutation, persistence, synchronization, cleanup, and + recovery? +- Which contracts cross packages, processes, clients, providers, or + repositories, and is dependency direction coherent? +- Where do multiple features duplicate state, lifecycle, orchestration, + validation, presentation, provenance, or recovery logic? +- Which layers are intentional T3 seams, which are protected Scient + divergences, and which are accidental workarounds that no longer serve a + product need? +- What are the failure, cancellation, retry, resource-bound, permission, + privacy, and observability semantics? +- Which tests and operational evidence prove the foundation rather than only + one feature path? + +### Classify Findings Before Choosing A Rewrite + +Each finding should receive one explicit disposition: + +- keep the current boundary; +- simplify it in place; +- unify duplicated implementations behind one existing owner; +- extract a shared foundation because multiple real consumers and a distinct + lifecycle now prove the boundary; +- replace or rebuild a foundation whose authority or contracts are wrong; +- retire an obsolete layer or compatibility path; or +- defer because evidence is incomplete. + +The review should resist both extremes: preserving accidental structure merely +because it exists, and creating speculative shared infrastructure merely +because several features look related. Shared foundations should follow proven +common authority and lifecycle, not naming similarity. + +### Review And Migration Order + +1. Build the capability-to-foundation map from current source, tests, runtime + evidence, capability records, T3 seams, and source provenance. +2. Select the foundations with the highest duplication, authority ambiguity, + failure risk, upstream conflict cost, or roadmap leverage. +3. Trace representative workflows and write the current-state boundary before + recommending a target. +4. Compare keep, simplify, unify, extract, replace, and retire alternatives + against product principles, migration risk, update cost, and reversibility. +5. Accept focused architecture decisions only with evidence and a migration + path that preserves user value, project data, provenance, and rollback. +6. Implement incrementally where possible, update capability and architecture + owners with the code, and mark superseded paths clearly. + +Architecture findings should update the owning architecture or capability +record. Accepted rebuilds should preserve observable behavior unless a product +decision explicitly changes it. Public Docs should change only when user +behavior, availability, limitations, or recovery changes. + +## Requested Scope Coverage And Completion Boundary + +The documentation-system design is supported by complementary evidence rather +than one document that tries to own product history, current implementation, +architecture, policy, and public help simultaneously. + +| Requested concern | Evidence owner | Coverage at the observed baseline | +| --------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| Every Scient-specific capability, including small fixes, files, behavior, and why it exists | `scient-desktop/docs/reports/scient-specific-capabilities.md` plus the [capability-to-foundation audit](../research/spike-reports/scient-capability-to-foundation-architecture-audit-2026-08-28.md) | Complete dated inventory: 38 named capabilities plus the cross-cutting security/reliability family, reconciled to current desktop `d5ff08e7`. | +| Every desktop pull request, integration chain, quick timeline, and feature evolution | `scient-desktop/docs/reports/scient-pr-and-evolution-ledger.md` | All 183 live PR records through #189 are reconciled at the audit snapshot: 181 records through #187 plus the #188/#189 addendum. Later merged PR #190 is explicitly queued for P0-DESKTOP-FORENSICS before preservation. The six earlier absent numbers remain recorded rather than invented. | +| T3 ancestry, integration, conflicts, protected divergences, and why each category remains | `scient-desktop/docs/reports/scient-t3-divergence-integration-and-retirements.md`, current `UPSTREAM.md`, machine state, and dated receipts | Complete dated divergence narrative through #187 with a current-main #189 addendum; live operational authority remains `UPSTREAM.md` and `upstream-state.json`. | +| Features and implementation approaches built and later removed, replaced, renamed, rejected, superseded, or deferred | The divergence/retirement report and PR ledger | Twelve explicit retirement/replacement/defer cases plus current-versus-integration-only status. Capability records preserve evolution without making retired work current. | +| First-principles architecture, accidental layering, shared foundations, simplification, unification, extraction, replacement, and rebuild questions | [Capability-to-foundation architecture audit](../research/spike-reports/scient-capability-to-foundation-architecture-audit-2026-08-28.md) | Complete initial 39-item map, ten foundation findings, disposition ledger, deliberate non-unifications, evidence gates, and review order. It recommends focused foundation work rather than a wholesale rewrite. | +| Open-source donors, external services, versions, licenses, adaptation boundaries, and what remains Scient-owned | Forensic capability/divergence reports, architecture audit, and Scient source maps | Covered for T3, Effect, PDF.js, whisper.cpp, KaTeX, Mermaid, Vega, Plotly, Zotero and metadata APIs, citation tooling, MATLAB, TeX/TinyTeX/SyncTeX, Jupyter conventions, and Agent Skills. Source maps remain evidence, not automatic dependency selection. | +| Every existing Markdown file, what it currently does, authority, provenance, and preliminary disposition | [File-by-file Markdown audit](../research/spike-reports/documentation-system-markdown-audit-2026-08-28.md) | Every tracked path at the exact Scient, desktop, and website heads is accounted for; every non-vendored file is individually classified; vendored boundaries, open-PR Markdown, and three untracked forensic reports are explicit. The current scient-agent checkout is excluded by decision. | +| Where feature agents put plans, scratch notes, handoffs, research, current facts, and new durable Markdown | Feature-document lifecycle in this proposal plus desktop work-artifacts guidance | Complete proposed rule: GitHub owns active work; temporary material stays outside the tree; merged PRs are implementation records; existing durable owners are updated first; new files must pass the admission test. | +| Complete public documentation for users and support agents, website publication, versioning, and a possible MCP | Public publishing model and agent reading routes in this proposal | Complete design, not implemented corpus: docs/user/ remains the durable desktop Help source; a reviewed manifest selects release- and surface-qualified pages; website renders exact released/candidate sources and supports corrections; raw/structured delivery precedes a thin MCP. | +| Clean internal capability, architecture, development, operations, upstream, roadmap, research, quality, and historical documentation | Repository authority model, proposed desktop areas, Scient areas, and cross-product capability map | Complete logical target. The areas are classification and ownership roles, not mandatory physical folders or one-file-per-feature requirements. | +| Cross-repository ownership, dependency order, agent instructions, contributor guidance, indexes, templates, and update triggers | Governance promotion map and documentation update contract | Complete proposed contract with one concern per governance surface, public-repository self-sufficiency, separate dependent PRs only for genuine consequences, and a concise documentation-impact declaration. | +| Preservation of useful philosophy, first principles, development, quality, planning, research, upstream, and historical records | Migration rules, history/successor rules, and overcomplication constraints | Explicitly protected. Logical classification precedes movement; inherited compatibility paths may remain; temporary migration ledgers disappear after use; useful history is not deleted for cosmetic consistency. | +| Proof that the system can remain understandable and inexpensive to update | [Maintainability and reading-route audit](../research/spike-reports/documentation-system-maintainability-and-reading-route-audit-2026-08-28.md) | Six reading routes and seven representative update simulations pass the proposed target with bounded recurring fan-out and explicit unresolved publication transport. | +| Concurrent upstream and documentation work | Exact evidence identities and Phase 0 | Merged upstream PR #189 is reconciled; draft documentation PR #188 remains candidate evidence; later merged PR #190 advances desktop main without Markdown and requires documentation-impact and forensic-ledger reconciliation in Phase 0B. | +| Current `scient-agent` repository | Explicit exclusion throughout the proposal and audits | Deferred exactly as requested. No inherited OpenCode Markdown or source was inspected or classified; repository-local governance begins only when native Scient-agent implementation starts. | + +This matrix proves coverage of the **design and audit objective**. It does not +prove that the proposed documentation system has been accepted, migrated, +published, or maintained through live pilots. Those are deliberately separate +states: + +1. **Investigated and designed:** the proposal and dated evidence suite cover + the requested scope and expose their exact snapshots and unresolved risks. +2. **Accepted:** a human explicitly decides the acceptance questions below and + promotes only those choices into policy. +3. **Operational:** Phase 0A truth/preservation work, Phase 0B baseline + reconciliation, and Phase 1 repository-local governance changes land in + their owning repositories. +4. **Proven at scale:** vertical authoring, website publishing, maintenance, + migration, and automation phases pass their stated gates. + +The current evidence package has reached states 1 and 2. The implementation +program is responsible for proving states 3 and 4; acceptance must not be +misread as claiming that migration or publication is already complete. + +## Accepted Package + +The evidence supported accepting the core documentation contract without +settling the deferred implementation details. + +The accepted decisions are: + +- accept **Scient Docs** as the public label and /docs as the website route; +- accept scient-desktop/docs/user/ as the durable authored source for current + app help, with no parallel docs/help/ directory; +- accept a reviewed publication manifest, desktop-first qualification, stable + publication pinned to an exact released source, labelled candidate previews, + and a truthful stable-correction path; +- accept public Docs and internal capability records as separate but linked + owners; +- accept the federated nearest-owner model across Scient, scient-desktop, and + the website, with scient-agent deferred until native implementation begins; +- accept the seven-area desktop model as a logical classification target, not + a mass-move instruction; +- accept update-before-create, the concise documentation-impact declaration, + and the feature-document admission test; +- accept the one-role-per-governance-surface promotion map, including + a small required promotion set, conditional edits elsewhere, proposal + self-supersession, and self-contained minimum rules in public repositories + without copied private product or planning authority; +- accept generated exhaustive inventory plus a temporary reviewed disposition + ledger rather than a permanent manual catalog of every Markdown path; +- require logical classification and three vertical pilots before broad + migration; and +- defer MCP until the public corpus and retrieval model are proven. + +Acceptance should deliberately defer: + +- the exact website-to-desktop source transport; +- mandatory capability metadata beyond the small pilot schema; +- physical movement of inherited or Scient-owned files outside explicitly + reviewed dispositions; docs/user/ remains the durable default; +- the final automation and validation portfolio; +- any MCP interface or deployment choice; and +- any architecture simplification, extraction, replacement, or rebuild until + the first-principles review produces evidence and a focused decision. + +## Accepted Questions + +The explicit questions answered by the acceptance record are: + +1. Is the public label **Scient Docs** with website route /docs accepted? +2. Is scient-desktop accepted as the canonical authored source for current app + help? +3. Is docs/user/ accepted as the durable default Help source, with no parallel + docs/help/ tree and publication controlled by qualification rather than + directory membership? +4. Is the separation between public Docs and internal capability records + accepted? +5. Is the federated nearest-owner model across Scient, scient-desktop, and the + website accepted now, with scient-agent joining only when native + implementation begins? +6. Should stable public Docs default to an exact released app source, with + candidate documentation available only through labelled previews and a + version-truthful stable-correction path? +7. Is the seven-area logical desktop model—help, capabilities, architecture, + development, operations, upstream, and records—accepted as the target for + classification and pilots? +8. Is logical classification before physical movement accepted, including the + deliberate preservation of useful inherited paths? +9. Is the concise documentation-impact field accepted as the default pull + request coordination mechanism? +10. Is the feature-document lifecycle accepted, including update-before-create, + temporary work outside the source tree, and the new-file admission test? +11. Is the two-layer generated inventory and reviewed disposition ledger + accepted instead of a permanently hand-maintained list of every Markdown + path? +12. Is the three-pilot proof required before full migration? +13. Is MCP deferred until the public corpus, version model, and retrieval needs + are proven? +14. Is the governance promotion map accepted, including one concern-specific + owner, a small required file set, conditional edits elsewhere, thin routing + surfaces, proposal self-supersession, and self-contained minimum + instructions in public repositories? + +## Acceptance Record + +Yaacov accepted all fourteen questions on 2026-08-28, with these binding +clarifications: + +- **Public identity:** the public product-help surface is **Scient Docs** at + /docs. +- **Source ownership:** scient-desktop is the authored source for current app + help, and its inherited docs/user/ path remains the durable default. Do not + create a parallel docs/help/ tree. +- **Independent delivery:** the website and the desktop app have separate + release lifecycles. Publishing or correcting Docs must not require a new app + release, while stable pages must remain truthful about the app versions and + behavior they describe. +- **Separate but linked truth:** public help and internal capability or + architecture records answer different questions and must not become copied + prose authorities. +- **Repository family:** use nearest authoritative ownership across Scient, + scient-desktop, and the website. scient-agent remains excluded until native + Scient-agent work begins. +- **Logical areas:** Help, Capabilities, Architecture, Development, Operations, + Upstream, and Records are accepted roles, not mandatory folders or a reason + for cosmetic mass movement. +- **Minimal coordination:** trial one concise documentation-impact declaration. + Keep it useful and small; do not grow a broad metadata or pull-request + bureaucracy without repeated evidence that it is needed. +- **Gradual features:** feature work often lands in slices. Each slice should + update the stable owners for the same capability when their truth changes; + it should not create a new durable document merely because there is a new PR, + implementation phase, or partial milestone. +- **Inventory:** use generated exhaustive inventory plus a temporary reviewed + disposition ledger. Do not impose a permanently hand-maintained list of every + Markdown path. +- **Pilot boundary:** the three pilots happen inside this implementation + program. They gate broad remaining-corpus migration, final capability schemas, + and full public publishing—not Phase 0 truth repair, evidence preservation, + core governance, inventory, initial capability mapping, publishing + foundations, or other safe preparation that can be completed now. +- **Future MCP:** an agent-facing documentation MCP remains a later option. It + is not part of this implementation pass. +- **Anti-complexity rule:** every governance surface, field, file, and automated + check must earn its maintenance cost. Prefer existing owners, generated views, + links, and conditional updates; remove temporary migration machinery after it + has served its purpose. + +These decisions authorize the staged documentation implementation described +here. Repository merges, website deployment, app release, MCP implementation, +and separately proposed product-architecture changes retain their normal +review or authorization gates. + +## What Acceptance Would And Would Not Mean + +Acceptance would establish the intended information architecture, authority +model, public publishing direction, update contract, and staged order. + +Acceptance would not by itself: + +- move or delete documents; +- mark existing proposals as accepted architecture; +- publish unreleased behavior; +- merge or deploy website changes; +- create an MCP server; +- change T3 or OpenCode integration policy; +- accept every metadata field or publishing transport discussed here; or +- authorize the complete migration without phase-specific review. + +Phase 0A truth repairs and evidence preservation are part of the accepted +implementation program. They remain deliberately separate from policy +promotion so their factual evidence and review boundaries stay clear. + +## Implementation Start Gate + +The documentation program began after: + +1. the human acceptance answers above were recorded explicitly; +2. the accepted proposal and Draft audits were prepared for preservation and + the desktop forensic reports were queued for a current-base isolated branch; +3. exact repository heads and active overlapping pull requests were refreshed; +4. Phase 0A and Phase 0B work are separated from Phase 1 policy promotion; +5. each repository change has its own branch, scope, tests, review, and landing + order; +6. no corpus migration, website publication, MCP, or architecture + implementation is inferred from plan acceptance; and +7. scient-agent remains excluded until native Scient-agent implementation + begins. + +The accepted goal authorizes the in-scope documentation work through focused +repository-local branches and pull requests. It does not silently authorize +merging, deploying, releasing, MCP work, or product-architecture changes. + +### Prepared Initial Work Packages + +These are authorized initial scopes. Refresh their exact heads and collision +checks immediately before creating branches. + +| Package | Repository | Focused scope | Dependency and exit evidence | +| --------------------- | -------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------ | +| P0-SCIENT-EVIDENCE | Scient | Preserve this accepted plan, the three dated Draft audits, and their index entries without conflating acceptance with operational completion. | Current Scient main; formatting, metadata, local-link, and diff checks. No policy promotion. | +| P0-DESKTOP-FORENSICS | scient-desktop | Place the three forensic reports on an isolated current-main branch, reconcile the post-snapshot #190 change, add metadata and a discoverable index route, and preserve exact snapshot limits. | Current desktop main and refreshed capability/PR evidence; no claim that reports are live implementation authority. | +| P0A-DESKTOP-TRUTH | scient-desktop | Correct voice privacy/data flow, public contributor boundary, and stale provider-proposal disposition; reconcile index omissions only where the same focused owner is touched. | Current main plus collision review with PR #188 and other documentation candidates; targeted documentation checks and source verification. | +| P0A-SCIENT-TRUTH | Scient | Repair the three audited metadata anomalies without changing their evidence content or authority. | P0-SCIENT-EVIDENCE or a clean non-conflicting branch; metadata and link validation. | +| P0A-WEBSITE-TRUTH | Website | Correct repository-family wording for the planned scient-agent boundary. | Current website main; repository checks. No Docs transport or site construction. | +| P0B-DESKTOP-188 | scient-desktop | Rebase/reverify/merge PR #188 or close it and record where still-useful reconciliations will move. | Current desktop main and active feature-branch review; explicit human disposition. | +| P1-SCIENT-GOVERNANCE | Scient | Promote accepted family policy, contribution evidence, AGENTS.md route, and documentation index only. | Human acceptance; P0 truth complete; fresh-agent route tests; proposal disposition updated at exit. | +| P1-DESKTOP-GOVERNANCE | scient-desktop | Promote self-contained public rules through AGENTS.md, docs/README.md, work-artifacts, CONTRIBUTING.md, and the PR template. | Accepted Scient contract and known PR #188 disposition; public-contributor route test. | +| P1-WEBSITE-GOVERNANCE | Website | Promote app-help ownership, website rendering/version ownership, dependency rules, and the concise PR field. | Accepted Scient contract; website remains transport-neutral until the pilot. | + +Phase 2 inventory, the three vertical pilots, website publication, maintenance +proof, remaining-corpus normalization, automation, and possible MCP follow the +phase gates above. They should not be expanded into detailed pull-request lists +until the preceding pilots reveal the real owners and update cost. + +## Completion Criteria For The Documentation Program + +The documentation program is complete when: + +- users and support agents can reliably learn and troubleshoot released Scient + through one version-aware public Docs corpus; +- each current capability has one discoverable implementation owner and an + appropriately scoped record; +- shared architecture, authority, lifecycle, and divergence are explicit; +- product direction, current implementation, proposals, research, and history + remain distinguishable; +- plans no longer need to duplicate current implementation inventories; +- development, operations, philosophy, first principles, quality doctrine, and + upstream knowledge remain preserved and navigable; +- cross-repository update responsibility is clear to contributors and agents; +- feature agents update durable owners without leaving redundant plans, + transcripts, handoffs, or one-file-per-feature debris; +- website and any future MCP publish or retrieve canonical content rather than + maintaining separate prose; +- a real feature change, retirement, and upstream integration have proven the + maintenance loop; and +- the ongoing update cost is low enough that normal product work can keep the + system truthful. diff --git a/docs/research/spike-reports/README.md b/docs/research/spike-reports/README.md index 3658216..7536cf1 100644 --- a/docs/research/spike-reports/README.md +++ b/docs/research/spike-reports/README.md @@ -3,7 +3,7 @@ Status: Active Owner: Yaacov Created: 2026-06-27 -Last updated: 2026-08-06 +Last updated: 2026-08-28 Purpose: Indexes dated reports from technical or product spikes. Doc type: Research index @@ -11,6 +11,26 @@ Use this folder for short reports after a focused investigation or prototype. Current files: +- `documentation-system-maintainability-and-reading-route-audit-2026-08-28.md` - + question-based contributor and agent route tests, representative update + simulations, recurring fan-out analysis, overcomplication checks, and minimal + Phase 1 promotion guidance for the proposed cross-repository system, plus the + post-review docs/user/, truth-repair, publishing, and self-supersession + refinements; it excludes scient-agent and remains decision-readiness evidence + rather than accepted policy. +- `scient-capability-to-foundation-architecture-audit-2026-08-28.md` - + complete capability-to-foundation map and first-principles architecture + audit covering current authority, shared infrastructure, T3 seams, + open-source boundaries, in-flight work, deliberate separations, and focused + keep/simplify/unify/extract/replace/retire/defer recommendations; it excludes + scient-agent and remains dated evidence rather than rebuild authorization. +- `documentation-system-markdown-audit-2026-08-28.md` - exact-head, + file-by-file authority, provenance, discoverability, conflict, and + preliminary-disposition audit for the in-scope Scient, desktop, and website + Markdown corpus, including the post-review decision to retain docs/user/ as + the durable Help source; it deliberately excludes the current inherited + scient-agent checkout and remains dated evidence rather than a permanent + registry. - `t3-foundation-d4-bootstrap-2026-08-06.md` - exact D4 candidate ancestry, safety-envelope implementation, integration, verification, local development app, and remaining limitations. It records transition evidence, not release diff --git a/docs/research/spike-reports/documentation-system-maintainability-and-reading-route-audit-2026-08-28.md b/docs/research/spike-reports/documentation-system-maintainability-and-reading-route-audit-2026-08-28.md new file mode 100644 index 0000000..32ea265 --- /dev/null +++ b/docs/research/spike-reports/documentation-system-maintainability-and-reading-route-audit-2026-08-28.md @@ -0,0 +1,516 @@ +# Documentation System Maintainability And Reading-Route Audit + +Status: Draft +Owner: Yaacov +Created: 2026-08-28 +Last updated: 2026-08-28 +Purpose: Tests whether the proposed Scient documentation system gives contributors and agents short, unambiguous routes to the correct content owner without creating excessive recurring update work. +Doc type: Research evidence + +## Document Rules + +This report is dated decision-readiness evidence for the proposed [Scient +Documentation System And +Publishing](../../planning/scient-documentation-system-and-publishing.md). It +tests governance reading routes and representative update workflows against the +exact repository revisions below. + +It does not accept the proposal, replace current repository guidance, authorize +file moves, establish a website publishing transport, or make its suggested +limits into policy. Promote accepted rules into the concern-specific policy, +contribution, agent, index, and content owners described by the proposal. + +The current `scient-agent` repository is outside this investigation. No file in +that repository was read. It remains the planned home for future native Scient +agent work, while its current OpenCode-derived checkout is not treated as +implemented Scient-agent documentation. + +## Question + +Can the proposed system remain understandable and current when ordinary feature +agents, public contributors, internal cross-repository contributors, website +publishers, upstream integrators, and documentation stewards use it repeatedly? + +The test is deliberately narrower than another corpus audit. The [Markdown +audit](documentation-system-markdown-audit-2026-08-28.md) already enumerates +the files, and the [capability-to-foundation architecture +audit](scient-capability-to-foundation-architecture-audit-2026-08-28.md) +already maps the implementation. This report tests the missing operating +question: whether a person or agent can find and maintain those owners without +reading the whole governance system or creating one document per change. + +## Evidence Boundary + +The reading tests used these exact states on 2026-08-28: + +| Repository or candidate | Exact identity | Surfaces inspected | +| ------------------------------------ | ---------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `Scient` proposal candidate | `9a309d6bb952a3fae8c0dd3495139c7c0736b37a` plus the uncommitted proposal and dated audits in this worktree | `AGENTS.md`, documentation policy, documentation index, onboarding, team contribution protocol, project-skill index, and the complete relevant proposal sections | +| `scient-desktop` current remote main | `d5ff08e721086eec02a2a84ad1431b33da6f5269` | `AGENTS.md`, `CONTRIBUTING.md`, `docs/README.md`, work-artifacts guidance, pull-request template, and upstream-maintenance owner | +| Desktop documentation PR #188 | head `33cfee24` compared with current remote main | Its seven changed documents and especially the proposed desktop index additions; it remains open and behind current main | +| Website current remote main | `f129246a9e59894c7bb19dc2d17b7c6ac3b0ce82` | `AGENTS.md`, `README.md`, `CONTRIBUTING.md`, and pull-request template | + +The local canonical desktop and website checkouts were behind their remotes, so +the tests read `origin/main` objects rather than treating those local working +trees as current. The proposal candidate remains uncommitted and therefore is +not current policy. + +A later readiness recheck found desktop main at `c0baaab2` through merged PR +#190. It changes no Markdown or governance surface, so the route simulations +remain evidence for their exact `d5ff08e7` baseline. Its user-visible settings, +sensitive-display, and agent-access defaults must nevertheless pass the +proposed documentation-impact route during Phase 0B. + +## Method And Pass Conditions + +Each reading-route simulation begins with a real question rather than a folder +name. A route passes only when it lets an oriented contributor or agent: + +1. identify the repository that owns the fact; +2. reach a real content owner, or an explicit statement that the owner does not + exist yet; +3. distinguish current, candidate, proposed, and historical material; +4. know whether another repository has a genuine dependent change; and +5. avoid reading every policy, index, onboarding guide, skill, contributor + guide, and pull-request template before acting. + +This test separates three kinds of reading: + +- **Onboarding** is a deliberate, occasional deep journey through product, + authority, repository, and contribution context. +- **Task reorientation** is the short recurring path used by an already + oriented contributor before a specific change. +- **Content investigation** is the task-dependent reading of the actual help, + capability, architecture, source, code, tests, or history that owns the + subject. + +The proposed system becomes too expensive if it turns onboarding into a +per-pull-request ritual. Conversely, a short route does not excuse shallow +content investigation after the correct owner is found. + +## Outcome + +The proposed model is maintainable with several explicit safeguards. Its core +nearest-owner model, update-before-create rule, logical-before-physical +migration, and zero-to-two ordinary-update target survive the simulations. +Seven logical areas do not by themselves create seven files per feature. +Keeping docs/user/ as the durable physical Help source is consistent with this +finding and removes the need for a parallel target directory. + +The present repositories are not yet sufficient to operate the complete model: + +- desktop guidance can usually route an agent by audience, but its public + contributor boundary is stale, its indexes are incomplete, and it has no + documentation-impact declaration; +- Scient identifies repository ownership and has strong documentation policy, + but that policy explicitly governs only Scient and the shared contribution + protocol does not yet require documentation-impact evidence; +- the website identifies the repository family and deployment owner, but it + does not identify desktop documentation as the app-help source or define a + versioned publication route; and +- the current upstream and temporary-work routes are already strong and should + be preserved rather than redesigned. + +The proposal should therefore be tightened, not expanded. It needs a clear +one-time-onboarding versus recurring-route distinction, an explicit route +success criterion, current-path compatibility during migration, and one +additional factual baseline repair in the website repository-family wording. +It does not need another registry, another document category, mandatory +capability pages for every feature, or an MCP before publication is proven. + +## Current Front-Door Map + +| Surface | Current strength | Current limitation | +| ------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | +| `Scient/AGENTS.md` | Clearly identifies sibling repository ownership, independent pull requests, current product maturity, durable-document placement, and the stewardship skill. | It is an internal, broad orientation surface. It should route rather than become the recurring copy of family policy. | +| `Scient/docs/documentation-policy.md` | Strong metadata, status, placement, evidence, promotion, history, conflict, and truth rules. | It explicitly governs only the Scient repository and does not yet establish the proposed family nearest-owner contract. | +| `Scient/docs/onboarding.md` | Provides a careful shared reading journey and contribution-area routes. | Its depth is appropriate for onboarding, not for every ordinary feature update. | +| Shared team contribution protocol | Clearly owns separate pull requests, evidence, review, and dependency ordering across repositories. | It has no concise documentation-impact declaration or update responsibility yet. | +| Desktop `AGENTS.md` | Gives public local safety rules, direct documentation categories, upstream routing, and strong temporary-artifact rules before inherited T3 guidance. | The document is necessarily long because it preserves inherited guidance, and its documentation route remains audience-shaped rather than authority-shaped. | +| Desktop `CONTRIBUTING.md` | Gives a simple external proposal boundary. | It still describes the released repository as a private migration candidate and provides no documentation placement or impact route. | +| Desktop `docs/README.md` | Separates user and maintainer material and links many current owners. | The corpus audit found six public-help and fourteen non-receipt internal documents missing from current index routes; logical current-capability ownership is not explicit. | +| Desktop work-artifacts guidance | Already provides the right durable-facts, GitHub-plans, temporary-work, and merged-PR model. | It is labelled as an internal document rather than visibly presented as the local feature-document lifecycle owner. A move is not required to fix that. | +| Desktop pull-request template | Keeps contribution evidence concise. | It does not ask whether documentation changed or whether a dependent documentation pull request exists. | +| Website `AGENTS.md` | Correctly routes to local contribution rules and requires separate cross-repository pull requests. | It does not say who authors app-help prose or what source/version facts a Docs publisher must preserve. | +| Website `README.md` | Clearly owns the website, deployment, downloads, and current operational systems. | It has no public-Docs source contract. Its repository-family summary describes `scient-agent` as owning a native-agent source foundation without clarifying that native Scient-agent implementation has not begun. | +| Website pull-request template | Captures checks, human preview review, quality review, integration readiness, and deployment impact. | It does not expose documentation-source or version impact. | + +## Question-Based Reading Routes + +### Route 1: Public Desktop Contributor + +**Question:** “I changed behavior that a Scient user will notice. Where do I +document it?” + +Current route for an agent: + +1. Desktop `AGENTS.md` says user-visible behavior belongs in `docs/user/` and + points to the local documentation split. +2. Desktop `docs/README.md` should lead to the subject page. +3. The existing subject page and source own the actual behavior. + +Current verdict: **conditional pass**. This route is self-contained and does +not require private Scient access, which is essential. It fails when the page +is one of the currently unindexed documents, when a current capability fact is +mistaken for user instructions, or when a human contributor enters through the +stale `CONTRIBUTING.md` and never receives the documentation route. + +Target route after Phase 1: + +1. Desktop `AGENTS.md` or `CONTRIBUTING.md` gives one short trigger and links + the local index. +2. The desktop index maps the logical role—help, capability, architecture, + development, operations, upstream, or record—to the real current path. +3. The subject owner is updated; a new page is created only if no coherent + owner exists. + +During migration, the index must continue to identify `docs/user/` as the real +and durable help source. Phase 1 must not direct contributors to a parallel +help tree or cause a cosmetic mass move. A normal visible feature should reach +its owner after at most two routing surfaces. + +### Route 2: Internal Cross-Repository Feature Agent + +**Question:** “This feature changes desktop behavior and may affect product +planning. Which repositories and documents change?” + +Current route: + +1. Scient `AGENTS.md` identifies the repository owners and separate-pull-request + rule. +2. Scient policy classifies product, planning, architecture, research, and + current implementation material, but only inside Scient. +3. Desktop guidance and index route to local implementation documentation. +4. The team contribution protocol governs separate pull requests but does not + yet require an explicit documentation-impact result. + +Current verdict: **partial pass**. An informed agent can find the repositories, +but no accepted family contract says that ordinary current implementation facts +remain with desktop while Scient changes only when product direction, +cross-product architecture, planning, or research authority actually changes. +This leaves room for over-updating roadmaps or copying current behavior into the +private parent. + +Target route: + +1. An oriented internal agent uses the family rule in Scient `AGENTS.md` or the + accepted policy to identify the nearest repository owner. +2. The owning repository's local index leads to the content owner. +3. The pull request reports `None`, `Updated`, or `Dependent PR` for + documentation impact. +4. A Scient pull request is opened only when a fact Scient owns genuinely + changes, with explicit landing order. + +The stewardship skill is appropriate when documentation placement or +reconciliation is the task. It should not be mandatory machinery for every +ordinary code edit, and it cannot replace the policy or content owner. + +### Route 3: Website Docs Publisher + +**Question:** “Which app-help source and version should this website preview or +production build render?” + +Current route: + +1. Website `AGENTS.md` leads to website contribution guidance and the + repository-family section. +2. Website `README.md` explains deployment and desktop release metadata. +3. No current owner defines an app-help source, source transport, preview + identity, or stable documentation version. + +Current verdict: **fail, with an honest missing decision**. An agent cannot +safely implement canonical Docs publishing from current guidance. It should +report the gap rather than copy prose into the website or guess that branch +`main` equals the released desktop version. + +Target route: + +1. Website `AGENTS.md` states that desktop owns app-help prose and that website + work owns rendering plus exact source/version behavior. +2. Website `README.md` or a focused local operations owner records the + transport selected by the publishing pilot. +3. A reviewed manifest selects release- and surface-qualified pages from + desktop docs/user/; inherited directory membership is not publication + approval. +4. A preview identifies an exact candidate source; stable Docs identify an + exact released source and support version-truthful corrections. +5. Generated HTML, raw content, navigation, and page metadata come from that + source without a second authored website corpus. + +Phase 1 can establish ownership, but it must not pretend the transport has been +selected. The correct route ends at a visible “pilot decision required” boundary +until Phase 4 proves checkout, manifest, release artifact, or another bounded +transport. + +### Route 4: Upstream Integration Agent + +**Question:** “Why does this T3-derived fork differ, and what records change for +an upstream merge?” + +Current route: + +1. Desktop `AGENTS.md` directly requires `UPSTREAM.md`, + `upstream-state.json`, and the D4 bootstrap record before protected-divergence + work. +2. `UPSTREAM.md` identifies the owned repository, official source, current + verified ancestry, integration method, protected seams, and dated receipt. +3. The new integration receives one dated receipt and updates the current + upstream state. + +Current verdict: **pass**. The route is direct, repository-local, public, and +source-backed. The current owner plus machine state plus immutable receipts is +the strongest existing example of the proposed current-versus-history model. + +Target treatment: preserve the root `UPSTREAM.md` compatibility route. The +logical `upstream` area may index it without moving it. Do not make every +capability page repeat the integrated commit range; update a capability or +architecture owner only when its own Scient seam or behavior changed. + +### Route 5: Documentation-Only Or Feature-Planning Agent + +**Question:** “I have investigation notes, a plan, a handoff, and several +possible Markdown files. Which ones belong in Git?” + +Current desktop route: + +1. Desktop `AGENTS.md` says plans and scratch artifacts do not belong in the + source tree. +2. The work-artifacts owner distinguishes current durable facts, GitHub-owned + planned work, temporary work outside the tree, and the merged pull request + as implementation record. + +Current Scient route: + +1. Scient `AGENTS.md` routes to the documentation policy and stewardship skill. +2. The policy applies durable-knowledge, evidence, placement, status, + promotion, history, and conflict tests. +3. The relevant area index and existing owner are read before a new file is + admitted. + +Current verdict: **pass with repository-specific scope**. Desktop already has +the stronger feature-work rule; Scient already has the stronger durable +planning and research classification rule. The target system should connect +these without copying either one wholesale into the other repository. + +Target treatment: update an existing durable owner first. Keep active +implementation progress in the GitHub item and pull request. Keep scratch, +transcripts, temporary research, and session handoffs outside the worktree. +Create a new durable file only when it owns a distinct lasting question and can +state its repository, owner, status, evidence boundary, index route, and update +trigger. + +### Route 6: User Or Support Agent Seeking Released Behavior + +**Question:** “How do I do this in the version of Scient I actually have?” + +Current verdict: **fail as a complete public system**. Desktop has useful +`docs/user/` pages, but there is no complete version-selected public Scient Docs +surface and no public retrieval contract for support agents. + +Target route: + +1. The user or support agent enters the website's `/docs` surface. +2. Stable HTML, stable anchors, raw or structured content, generated page + metadata, search, and visible source/version identity all come from the same + released desktop documentation source. +3. Candidate behavior appears only in a labelled preview. + +This route does not require MCP. A future MCP is justified only if measured +retrieval failures remain after the public HTML, raw content, index, search, +anchors, and version model are stable. + +## Representative Update Simulations + +These simulations test recurring authoring cost. “Primary owners” means +documents whose own fact changed. Index, metadata, receipt, or navigation work +is counted separately when it is a one-time or structural consequence. + +| Change | Normal primary owners | Conditional owners | Expected recurring fan-out | +| -------------------------------------------------- | -------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------- | +| Ordinary user-visible feature or bounded fix | Existing help page; capability-family record when availability, limits, support, or maturity changed | Operations only for a real runbook change; architecture only for a changed invariant | Usually one or two | +| Privacy, permission, authority, or recovery change | Help and capability truth | Architecture or ADR when authority/lifecycle changed; website only if its own published claim or pipeline changed; Scient product truth only if product policy changed | Usually two or three because omission is high risk | +| Shared implementation foundation | Owning implementation architecture record | Affected capability-family records; ADR for a hard-to-reverse decision; Scient cross-product architecture only when the decision crosses repositories or product systems | One to three, proportional to real authority | +| T3 upstream integration | Current upstream owner and one dated receipt/machine-state update | Capability, help, architecture, or operations only where the integration changed a fact those documents own | Usually two upstream artifacts, without global fan-out | +| Capability retirement | Released help removal or replacement and capability disposition | Upstream record for a protected divergence; architecture for a removed invariant; historical record only when reasoning remains useful | Two to four; retirements legitimately exceed ordinary work | +| In-flight feature pull request | Candidate help/capability/architecture changes on the same branch when they are needed to review the candidate | A labelled website preview from that exact head; a proposed Scient decision only if the feature changes an owner there | No stable publication before merge/release; no repository plan merely to mirror the PR | +| Documentation-only correction | The document containing the wrong fact | Index only if navigation or identity changed; dependent repository only if its separately owned fact is also wrong | Usually one | + +### Simulation Findings + +1. **Current help and current capability are intentionally separate.** A help + page answers how a user performs a task; a capability record answers what is + implemented, where, with which limits, dependencies, support, and evolution. + They should link, not copy each other's full content. +2. **A roadmap is not a release ledger.** It changes only when desired outcome, + scope, dependency, sequence, or gates change. Landing another step does not + require rewriting every related plan if current implementation truth has a + nearer owner. +3. **Cross-repository does not mean multi-repository by default.** A desktop + behavior change can be complete in desktop. A dependent Scient or website + pull request exists only when that repository owns a changed fact or + publication mechanism. +4. **Stable publishing removes duplicate website updates.** Once the website + consumes an exact released desktop source, ordinary help changes should not + require a prose-edit pull request in the website. +5. **In-flight truth must remain visibly in flight.** Candidate documentation + can travel with a feature branch and power a labelled preview, while stable + Docs remain pinned to a released source. An abandoned branch should not + leave an implemented claim on stable Docs. +6. **Removal requires disposition, not unlimited history.** Preserve reasoning + when it remains useful, but do not keep a second living checklist for every + removed button or minor state. + +## Overcomplication And Drift Tests + +The proposed system should fail review if implementation introduces any of the +following maintenance burdens without new evidence: + +- contributors must read the full onboarding journey for every pull request; +- a feature must create one help, capability, architecture, roadmap, upstream, + and record file whether or not those owners changed; +- a parallel help directory is created while docs/user/ remains a usable + T3-compatible source merely to make the tree look complete; +- a global hand-maintained list must mirror every Markdown file after the + migration inventory has served its temporary purpose; +- private Scient documentation is required to make a valid public desktop or + website contribution; +- the website maintains an authored copy of desktop help; +- a support MCP maintains answers separately from the public corpus; +- every repository receives the same policy text or pull-request template for + visual symmetry; +- a missing publishing transport is hidden behind vague “source of truth” + language; or +- scient-agent governance is invented before native Scient-agent work gives it + a real owner and implementation boundary. + +Seven logical desktop areas are therefore a **classification vocabulary**, not +seven mandatory physical directories and not seven update obligations. A +repository index can map inherited `docs/user/`, `docs/internals/`, +`docs/operations/`, root `UPSTREAM.md`, package READMEs, and later target paths +into those roles while preserving useful T3 compatibility. + +## Required Proposal Tightening + +The evidence supports these focused changes to the proposal before acceptance: + +1. State explicitly that the deep onboarding journey is occasional, while an + oriented contributor's recurring route should normally use no more than two + governance/routing surfaces before the actual content owner. Treat this as + a design diagnostic, not CI or a substitute for task research. +2. Mark the question-based routes as target logical routes. Until migration, + the local index must map each role to real current paths, and agents must not + create missing target folders merely to satisfy the taxonomy. +3. Define route success as reaching the real owner **or an explicit missing + decision** with status, version, and repository boundary intact. Website + source transport is the important current example. +4. Keep the five original governance route tests and add the public user or + support-agent retrieval path as the publishing acceptance test. +5. Add a Phase 0 factual repair for the website repository-family wording so it + describes `scient-agent` as the planned native-agent home and does not imply + that native implementation already exists. This change does not require + reading or modifying the current scient-agent repository. +6. Preserve desktop's existing upstream and work-artifact models as foundations + to link and clarify, not replace. + +No new policy layer or acceptance question is needed for these refinements. +They clarify how the already-proposed governance and publishing choices should +operate. + +## Post-Review Proposal Refinements + +Subsequent independent reviews and owner discussion strengthened the proposal +without changing this audit's evidence boundary: + +- docs/user/ remains the durable Help source; no docs/help/ migration is a + target or acceptance requirement; +- Phase 0 is split into immediately justifiable truth/preservation work and + moving-baseline reconciliation; +- PR #188 receives a bounded disposition and blocks only overlapping desktop + documentation edits; +- Phase 1 distinguishes a small required promotion set from conditional + surfaces and requires the proposal to stop competing with promoted policy; +- the publishing pilot must prove page qualification, update triggers, + freshness, visible failure, and a stable-correction path; +- capability records start from a minimal schema, while the longer question + set remains a completeness prompt; and +- docs/user/ verification is a temporary generated queue, not a permanent + registry. + +These are proposed design dispositions, not accepted policy or implementation +evidence. + +## Minimal Phase 1 Promotion + +If the proposal is accepted, the smallest operational promotion remains: + +1. **Scient:** family policy owns nearest-owner and durable-knowledge rules; + the shared contribution protocol owns documentation-impact and dependent-PR + evidence; `AGENTS.md`, onboarding, indexes, and the skill remain thin routes. +2. **Desktop:** after PR #188's overlapping disposition is known, repair the + stale contributor boundary; make `AGENTS.md` route by logical role; make + `docs/README.md` the compatibility map to real paths; preserve and clarify + work-artifacts guidance; add one concise documentation-impact field to the + existing pull-request template. PR #188 does not block unrelated truth, + Scient, website, or architecture work. +3. **Website:** make `AGENTS.md` identify desktop app-help ownership and local + rendering/version ownership; correct the planned agent-repository wording; + add one source/version-impact field to the existing pull-request template. + Do not document a transport until the publishing pilot selects it. +4. **All repositories:** use separate branches and pull requests with explicit + dependency order. Do not move the full corpus and do not change + `scient-agent`. + +Scient does not need a pull-request template merely for symmetry during the +pilot. The shared protocol and local agent guidance can establish the field; +repeated omission would be evidence for adding a minimal template later. + +## Pilot Measurements + +The three documentation verticals and the maintenance-loop phase should record +only measurements that can help simplify the system: + +- routing surfaces read before reaching the content owner; +- primary authoritative documents updated; +- navigation, metadata, receipt, or historical files updated separately; +- dependent repository pull requests and why each was necessary; +- new durable files admitted and which admission criterion required them; +- owner ambiguity or conflicting current claims encountered; +- stable-versus-preview source identity and publication result; and +- documentation corrections required after implementation review or human use. + +Do not convert these measurements into a permanent per-feature dashboard unless +the pilot proves durable operational value. Their first purpose is to detect +unnecessary fan-out, missing owners, and false cross-repository dependencies. + +## Decision-Readiness Verdict + +**Ready for human decision on the core contract, not ready for broad +migration.** The model gives every tested question a coherent target route, +keeps ordinary authoring bounded, preserves strong existing local practices, +and exposes the website transport as a deliberate unresolved choice rather than +an invisible gap. + +The first implementation should remain Phase 0A truth/preservation work, +Phase 0B baseline reconciliation, and then the small Phase 1 governance +promotion. The vertical pilots must then prove real authoring, qualified +source-version publishing, stable correction, and maintenance cost before the +complete corpus is normalized or MCP is considered. + +## Remaining Risks + +- Desktop documentation PR #188 is open and behind current main; its final + disposition can change the exact Phase 1 index edit. +- Current indexes remain incomplete, so the migration ledger still needs a + refreshed exact-head review after active documentation work lands. +- Capability-family record shape is not yet proven. The pilots should begin + with only the fields needed to answer current behavior, ownership, support, + limits, evidence, dependencies, evolution, and update trigger. +- Website source transport, release/correction trigger, freshness expectation, + stable-correction mechanism, and rollback are intentionally undecided until + the publishing pilot. +- A good paper route can still fail in real agent use. Phase 1 should rerun + these questions with fresh agents or contributors who did not author the + policy and record where they hesitate. +- Public Docs cannot be called complete until released behavior, privacy, + limitations, troubleshooting, version identity, navigation, search, and + publication failure behavior are verified in a real website preview. diff --git a/docs/research/spike-reports/documentation-system-markdown-audit-2026-08-28.md b/docs/research/spike-reports/documentation-system-markdown-audit-2026-08-28.md new file mode 100644 index 0000000..78fb5be --- /dev/null +++ b/docs/research/spike-reports/documentation-system-markdown-audit-2026-08-28.md @@ -0,0 +1,549 @@ +# Scient Documentation Markdown Audit — 2026-08-28 + +Status: Draft +Owner: Yaacov +Created: 2026-08-28 +Last updated: 2026-08-28 +Purpose: Provides a dated, file-by-file authority and disposition audit of the in-scope Scient, Scient Desktop, and website Markdown corpus that grounds the proposed long-term documentation system. +Doc type: Research evidence + +## Document Rules + +This report is dated research evidence for the proposed documentation system. It owns the audited path inventory, observed role classification, provenance method, current conflicts, and preliminary disposition recommendations at the exact source identities below. It does not replace repository policy, product truth, current implementation source, public help, architecture decisions, pull requests, or the owning documentation indexes. + +Do not maintain this file as a permanent global registry. When the baseline materially changes, preserve this snapshot and generate a new dated audit or the temporary Phase 2 disposition ledger. A `keep`, `revise`, `merge`, `move`, or `retain` recommendation is planning evidence, not authorization to perform that action. + +The current scient-agent repository is excluded by explicit decision. Its inherited OpenCode Markdown was not inspected, counted, or classified. + +## Audit Question And Method + +The audit asks which Markdown files currently exist, what each one is for, what authority it has, whether it is Scient-created or inherited where that distinction can be proven, and what preliminary treatment the proposed system should consider. + +Evidence was gathered from: + +- Scient `origin/main` at `9a309d6bb952a3fae8c0dd3495139c7c0736b37a`; +- scient-desktop `origin/main` at `d5ff08e721086eec02a2a84ad1431b33da6f5269`; +- website `origin/main` at `f129246a9e59894c7bb19dc2d17b7c6ac3b0ce82`; +- desktop's recorded exact integrated T3 base `c8aba2587d56edbf3b7872987719a12b42031f48`; +- current GitHub pull-request metadata inspected on 2026-08-28; and +- the three untracked forensic reports in the audited desktop checkout. + +For desktop provenance, every non-vendored Markdown blob on scient-desktop main was compared with the same path at the exact integrated T3 base. `T3 unchanged at integrated base` means identical blobs at those two commits. `T3 path modified in Scient` proves a changed inherited path, but does not imply that every line is Scient-specific. `Scient-created path` means the path does not exist at that T3 base. Content-level ownership still requires reading the file and implementation evidence. + +## Count Reconciliation + +| Scope | Tracked Markdown | Authority treatment | +| ---------------------------- | ---------------: | ----------------------------------------------------------------------------------------------------------------------------------------------------- | +| Scient | 118 | File-by-file ledger below: 85 under docs/, 27 under lab/, three root files, and three project-skill files. | +| scient-desktop, non-vendored | 142 | File-by-file ledger below: 113 under docs/, five root files, and 24 protocol, skill, package, asset, application, infrastructure, or packaging files. | +| scient-desktop, vendored | 928 | Structurally excluded from Scient documentation authority: 872 under `.repos/effect-smol/` and 56 under `.repos/alchemy-effect/`. | +| Website | 6 | File-by-file ledger below; no authored Scient Docs corpus exists. | +| Total tracked | 1,194 | 266 non-vendored files receive individual authority classification; 928 vendored files are classified by read-only donor boundary. | +| Desktop forensic reports | 3 untracked | Candidate historical records; not current repository truth until deliberately placed and committed. | + +Of the 142 non-vendored desktop files, 84 are Scient-created paths, 21 are +inherited T3 paths whose blobs differ on Scient main, and 37 are unchanged from +the exact integrated T3 base. These are provenance counts, not a claim that all +content inside a modified file is Scient-owned. + +Before this report was written, the proposal worktree added one proposed planning path and modified the planning index. Open desktop PRs add five other candidate Markdown paths and modify existing files. Counting those independent candidates and the three untracked reports produces 275 unique non-vendored Markdown input paths in the observed main-plus-candidate universe. This report, the later [capability-to-foundation architecture audit](./scient-capability-to-foundation-architecture-audit-2026-08-28.md), and the later [maintainability and reading-route audit](./documentation-system-maintainability-and-reading-route-audit-2026-08-28.md) are evidence outputs and are deliberately excluded from that input count. The candidates are not one mergeable baseline and must not be presented as current main. + +A readiness recheck after the audit found desktop main at `c0baaab2` through merged PR #190. That pull request changes seven non-Markdown files, so the counts and file-by-file ledger below remain exact for the Markdown corpus. Its user-visible defaults and privacy/display implications still require Phase 0B documentation-impact review and a forensic-ledger addendum; this dated audit is not rewritten as though `d5ff08e7` contained the later code. + +## High-Confidence Findings + +### 1. A policy exists, but there is no accepted family-wide promotion contract + +Scient already has a strong active documentation policy, metadata system, area indexes, onboarding route, and documentation stewardship skill. Desktop already has a useful engineering-work-artifact rule. The missing layer is the accepted division of responsibility across repositories and governance surfaces described in the [documentation-system proposal](../../planning/scient-documentation-system-and-publishing.md). + +### 2. The `user` and `internals` ambiguity is structural, not cosmetic + +Desktop has 33 docs/user/ files and 68 docs/internals/ files. The internals folder combines dated upstream receipts, inherited architecture, current Scient capability records, evidence audits, implementation proposals, contributor reference, and historical plans. Renaming the folders without classification would preserve the ambiguity under new names and increase T3 merge cost. + +Post-audit review therefore retains docs/user/ as the durable physical Help source. Its pages still require release and surface qualification before public publication, but no parallel docs/help/ directory or cosmetic move is recommended. The `internals` corpus remains disposition-led because its mixed authorities—not its name alone—are the actual problem. + +### 3. Current, proposed, and historical desktop material conflict in several places + +- `CONTRIBUTING.md` still describes a private migration candidate, while AGENTS.md and the repository state describe the active public released desktop. +- `provider-lifecycle-unification-proposal.md` says final PR #150 integration remains open even though PR #150 merged. +- `scient-pdf-export-rendering-plan.md` begins by saying implementation has not started while later sections record landed foundations; draft PR #188 attempts part of this reconciliation. +- `scientific-artifact-studio.md` mixes desktop-current implementation with cross-product future direction that also has an owning Scient planning document. +- `scient-fork-pr-descriptions.md` preserves completed PR-drafting content already substantially owned by the fork-divergence record and merged PR history. + +### 4. Public-help discoverability and truth need a focused repair + +Six current docs/user/ pages are not linked from the desktop documentation index: `composer.md`, `content-direction.md`, `getting-started.md`, `latex.md`, `math-in-chat.md`, and `voice-dictation.md`. Fourteen non-receipt internal pages and the v0.6.0 migration rehearsal are also absent from that index. Twenty-seven dated upstream or qualification receipts are intentionally not listed individually, but the index needs a clear route to their collection. + +The voice page still claims entirely local recording and transcript processing even though optional provider-based transcript correction can transfer transcript text to the selected authenticated provider runtime. The install and updating pages also retain T3-facing titles that need an explicit compatibility-versus-product-identity decision. + +### 5. Scient metadata is mostly coherent, with three concrete anomalies + +`lab/external/upstream-reviews/2026-08-22-scient-desktop-t3.md` is missing four required metadata fields. `lab/notes/first-slice-source-trace-2026-07-18.md` and `lab/notes/t3-code-targeted-review-2026-07-18.md` use completion phrases as document statuses even though the active policy reserves status for authority and lifecycle. Completion should remain inside their evidence content while metadata uses a valid status. + +### 6. In-flight documentation must remain separate from merged truth + +- Desktop PR #188 is an open, behind draft changing seven existing documentation files; its checks predate the latest merged upstream range. +- Desktop PR #179 adds `docs/internals/managed-provider-runtime-latest-updates-proposal.md` as a 618-line proposal, not current capability truth. +- Desktop PR #129 adds the substantial in-flight ComputeSession implementation, `docs/internals/scient-compute-session-foundation.md`, `docs/user/scientific-computing.md`, and an index change. The two new pages are candidate architecture/help, not current main. PR #188 separately reconciles adjacent implementation records and labels the compute relationship as in flight. +- Desktop PR #121 adds `docs/internals/scient-overleaf.md` and `docs/user/overleaf-sync.md` plus an index change; none is current main. +- Scient has no open pull requests. Website PR #27 changes dependencies only and adds no Markdown. + +### 7. The vendored corpus is large but simple to govern + +All 928 vendored Markdown files live under two explicit `.repos/` donor boundaries. They are read-only implementation references, not Scient Docs, capability records, product truth, or project policy. A generated path inventory may enumerate them mechanically, but maintainers should not review or migrate them one by one unless a source is deliberately adapted. + +## Preliminary Repair And Migration Order + +1. Repair the current voice privacy/data-flow claim, stale desktop contributor boundary, stale provider-lifecycle proposal disposition, website repository-family wording, Scient metadata anomalies, and preservation of the three forensic reports. +2. Resolve or refresh desktop documentation PR #188 against current main as a bounded overlapping-documents decision; do not let it block unrelated truth or policy work. +3. Accept or revise the documentation-system contract before changing repository-wide guidance. +4. Build the temporary human disposition ledger and a generated docs/user/ publication-verification queue from the file-by-file evidence below; do not mass-move inherited T3 paths. +5. Use the three vertical pilots to prove help, capability, architecture, upstream, record, page-selection, version, and surface-qualification boundaries before broad migration. + +## In-Flight And Untracked Markdown + +| Surface | Paths | Current treatment | +| ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | +| This proposal worktree | `docs/planning/scient-documentation-system-and-publishing.md`; modified `docs/planning/README.md` | Proposed and uncommitted; not accepted policy. | +| Documentation-system audit outputs | `docs/research/spike-reports/documentation-system-markdown-audit-2026-08-28.md`, `docs/research/spike-reports/scient-capability-to-foundation-architecture-audit-2026-08-28.md`, `docs/research/spike-reports/documentation-system-maintainability-and-reading-route-audit-2026-08-28.md`; modified `docs/research/spike-reports/README.md` | Draft dated evidence created from the snapshot and later reviews; excluded from the input count. | +| Desktop PR #188 | `docs/README.md`, `docs/internals/scient-analysis-runtime-foundation.md`, `docs/internals/scient-latex.md`, `docs/internals/scient-pdf-export-rendering-plan.md`, `docs/internals/scient-universal-file-opening.md`, `docs/internals/scientific-artifact-studio.md`, and `docs/user/file-previews.md` | Open draft, behind current main; either rebase/reverify it or close it and transfer still-useful reconciliations into a pilot. | +| Desktop PR #179 | `docs/internals/managed-provider-runtime-latest-updates-proposal.md` | Open draft proposal; future direction, not current behavior. | +| Desktop PR #129 | `docs/internals/scient-compute-session-foundation.md`, `docs/user/scientific-computing.md`, and modified `docs/README.md` | Substantial compute implementation and its own candidate architecture/help remain in flight; none is current main or released truth. | +| Desktop PR #121 | `docs/internals/scient-overleaf.md`, `docs/user/overleaf-sync.md`, and modified `docs/README.md` | Open draft feature documentation; not current main or released help. | +| Desktop checkout | `docs/reports/scient-specific-capabilities.md`, `docs/reports/scient-pr-and-evolution-ledger.md`, and `docs/reports/scient-t3-divergence-integration-and-retirements.md` | Untracked dated forensic evidence; decide a durable records location before depending on it. | + +## File-By-File Ledger + +Each entry states the role and authority observed at the audited snapshot. Treatments are preliminary planning recommendations. They do not authorize movement, deletion, status promotion, or rewriting. + +### Scient + +Scient metadata provides the primary purpose and authority signal. Project skills and the minimal CLAUDE.md compatibility import are exempt from the ordinary metadata block. + +#### Root protocols and orientation + +- `AGENTS.md` — **Active / Agent protocol.** Defines how agents should work in this early Scient repository. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `CLAUDE.md` — **metadata-exempt / type missing.** Minimal compatibility file. **Treatment:** Keep as a minimal compatibility import; it is metadata-exempt and must not duplicate AGENTS.md. +- `README.md` — **Active / Repo orientation.** Entry point for the Scient product and project repository. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. + +#### Documentation governance and onboarding + +- `docs/documentation-policy.md` — **Active / Documentation policy.** Defines how Scient documentation should be created, classified, updated, and trusted. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/onboarding.md` — **Active / Repo orientation.** Gives new Scient collaborators a deliberate reading journey through the project, its repository, and its sources of truth before task-specific work begins. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/README.md` — **Active / Repo orientation.** Maps the Scient documentation structure and where each kind of information belongs. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. + +#### Scient docs/architecture + +- `docs/architecture/agent-runtime.md` — **Placeholder / Future home.** Defines what should be documented about Scient-agent and external-agent execution once implementation begins. **Treatment:** Retain only as a clearly reserved home; activate or remove only through a focused decision. +- `docs/architecture/collaboration-model.md` — **Placeholder / Future home.** Defines what should be documented about sharing and collaboration once the model is designed. **Treatment:** Retain only as a clearly reserved home; activate or remove only through a focused decision. +- `docs/architecture/decisions/ADR-0001-synara-opencode-foundation-and-scient-ownership-boundary.md` — **Superseded / Architecture decision.** Records the decision to use owned Synara-derived source as Scient's application foundation and owned OpenCode-derived source as the foundation for Scient while keeping external agents and canonical scientific state separately owned. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `docs/architecture/decisions/ADR-0002-standalone-source-ownership-and-upstream-authority.md` — **Accepted / Architecture decision.** Records ScientFactory's decision to own standalone desktop and agent repositories while treating original projects as read-only, selectively reviewed sources. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/architecture/decisions/ADR-0003-built-in-skills-portfolio-and-project-activation.md` — **Accepted / Architecture decision.** Records where Scient-maintained built-in skills live, how projects preserve exact activation identity, and how application and agent delivery remain subordinate to Scient authority. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/architecture/decisions/ADR-0004-scient-operation-capability-and-provenance-boundary.md` — **Accepted / Architecture decision.** Establishes one host-independent Scient operation boundary for the manual UI, agents, external MCP clients, automations, browser work, and scientific evidence capture. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/architecture/decisions/ADR-0005-t3-derived-desktop-foundation.md` — **Accepted / Architecture decision.** Selects the T3-derived foundation for Scient Desktop while preserving Scient ownership, scientific authority, user continuity, and the independent Scient agent boundary; records the completed repository cutover and predecessor retirement. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/architecture/decisions/ADR-0006-project-owned-scient-state-and-source-store.md` — **Proposed / Architecture decision.** Proposes `.scient/` as the durable project-owned Scient state boundary and documents the implemented source-store and Zotero-adapter contract inside it. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/architecture/decisions/ADR-template.md` — **Placeholder / Future home.** Defines what should become the standard architecture decision record template once agreed. **Treatment:** Retain only as a clearly reserved home; activate or remove only through a focused decision. +- `docs/architecture/decisions/README.md` — **Active / Repo orientation.** Indexes Scient's accepted and serious proposed architecture decision records and the rules for using them. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/architecture/local-first-sync.md` — **Placeholder / Future home.** Defines what should be documented about Scient local-first storage and cloud sync once the design is validated. **Treatment:** Retain only as a clearly reserved home; activate or remove only through a focused decision. +- `docs/architecture/project-format.md` — **Proposed / Architecture direction.** Maps the implemented minimum Scient project identity and source-store shape while keeping broader project-format choices explicit and unaccepted. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/architecture/README.md` — **Active / Repo orientation.** Defines where Scient architecture direction, future architecture homes, and decisions belong. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/architecture/security-and-permissions.md` — **Draft / Architecture direction.** Defines Scient's early security, trust-boundary, and permission principles before implementation-specific architecture exists. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/architecture/technology-stack.md` — **Proposed / Architecture direction.** Records Scient's current technology stack direction and open implementation decisions. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. + +#### Scient docs/design + +- `docs/design/chat-interface-ux.md` — **Draft / Planning note.** Captures early UX/UI notes for Scient chat and streaming conversation surfaces. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/design/product-design-principles.md` — **Placeholder / Future home.** Future home for Scient product design principles once there are real design decisions or prototypes to document. **Treatment:** Retain only as a clearly reserved home; activate or remove only through a focused decision. +- `docs/design/README.md` — **Active / Repo orientation.** Defines where Scient product design documentation should live. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/design/ux-ui-notes.md` — **Draft / Planning note.** Collects early UX/UI observations before they become product design principles, surface-specific guidance, research evidence, or implementation specifications. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. + +#### Scient docs/development + +- `docs/development/local-workspace-setup.md` — **Active / Operational procedure.** Provides the repeatable setup procedure for an internal contributor's local multi-repository ScientFactory workspace. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/development/README.md` — **Active / Repo orientation.** Indexes implemented contributor setup and future development documentation for Scient repositories. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/development/typescript.md` — **Placeholder / Future home.** Future home for Scient TypeScript conventions once implementation begins. **Treatment:** Retain only as a clearly reserved home; activate or remove only through a focused decision. + +#### Scient docs/operations + +- `docs/operations/github-operating-model.md` — **Active / Operational procedure.** Defines how ScientFactory repositories, branches, pull requests, releases, deployments, permissions, and local worktrees are operated. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/operations/README.md` — **Active / Repo orientation.** Indexes Scient's real monitoring, release-adjacent, support, and maintenance procedures. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/operations/team-contribution-protocol.md` — **Active / Operational procedure.** Defines the minimum shared workflow and verification evidence for contributions across maintained ScientFactory repositories. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/operations/upstream-intake.md` — **Active / Operational procedure.** Defines the repeatable process for detecting, reviewing, and selectively inheriting changes from Scient's original desktop and agent sources. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. + +#### Scient docs/planning + +- `docs/planning/desktop-fix-inbox.md` — **Active / Planning note.** Captures observed problems in the current T3-derived Scient desktop app that need a bounded diagnosis or fix but are not being implemented immediately. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/planning/file-resource-and-presentation-foundation.md` — **Proposed / Planning note.** Proposes the horizontal identity, resolution, revision, presentation, recovery, and broad-viewing foundation shared by Scient file, document, artifact, and scientific-data surfaces. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/first-scient-vertical-slice-implementation-plan.md` — **Superseded / Planning note.** Preserves the bounded Synara-specific source-tracing, implementation, and verification plan that preceded the active T3 foundation migration. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `docs/planning/gate-1-5-execution-plan.md` — **Historical / Planning note.** Defines the end-to-end preparation gate for owned Synara and OpenCode repositories, upstream updates, and Synara identity isolation. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `docs/planning/idea-inbox.md` — **Active / Planning note.** Provides one temporary intake surface for unprocessed Scient ideas and a compact index of ideas routed to durable homes or completed with verified evidence. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/planning/linux-distribution-hardening.md` — **Proposed / Implementation candidate.** Defines the proposed cross-repository migration from an insecure Ubuntu AppImage fallback to a supported, sandbox-preserving Linux distribution path. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/litrev-to-papilab-rename-execution-plan.md` — **Historical / Planning note.** Preserves the executed LitRev-to-PapiLab intermediate identity migration, evidence requirements, and rollback context. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `docs/planning/memory-architecture-discovery.md` — **Draft / Planning note.** Preserves the candidate scopes, vocabulary, product questions, trust boundaries, and investigation sequence required before Scient proposes or implements a memory architecture. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/model-access-and-routing-evolution.md` — **Draft / Planning note.** Tracks the rollout priorities and unresolved commercial choices for how Scient users access and select models. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/open-source-adaptation-build-strategy.md` — **Active / Planning note.** Defines the evergreen source-ownership, adaptation, upstream-update, and divergence strategy for the current T3-derived desktop, the still-open Scient-agent foundation, historical Synara evidence, and other open-source inputs used by Scient. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/planning/papilab-to-scient-rename-execution-plan.md` — **Historical / Planning note.** Preserves the executed PapiLab-to-Scient migration, compatibility contract, verification requirements, and later repository-visibility follow-ups. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `docs/planning/product-measurement-and-analytics-plan.md` — **Proposed / Planning note.** Defines the proposed product-measurement contract, privacy boundary, implementation sequence, event catalog, KPI model, dashboard portfolio, and activation gates for Scient. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/product-planning.md` — **Draft / Planning note.** Tracks current product planning after the accepted PRD, including candidate features, open product questions, and cross-document handoffs. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/product-roadmap.md` — **Active / Planning note.** Defines the current sequence of coherent Scient product outcomes without turning technology experiments into the product roadmap. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/planning/provider-connection-and-lifecycle-experience.md` — **Proposed / Implementation candidate.** Preserves the proposed provider-lifecycle direction, records which initial slices now exist, and identifies the remaining nontechnical connection work. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/README.md` — **Active / Repo orientation.** Defines where Scient planning documents live and how they relate to product truth, architecture, design, quality, and research documents. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/planning/repository-scope-and-company-memory.md` — **Proposed / Planning note.** Recommends how the Scient repository should relate to a broader connected company memory without mixing product authority with company-level authority. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/scient-and-external-agents-implementation-plan.md` — **Proposed / Planning note.** Defines the end-to-end implementation plan for one owned Scient agent, its still-open native-foundation selection, transitional specialist workers, and independently connected external agents. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/scientific-artifact-studio.md` — **Proposed / Planning note.** Proposes the product boundary, durable object model, experience, source strategy, capability envelope, quality gates, and staged growth path for Scient's scientific artifact inspection, composition, revision, and export workspace. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/scientific-computing-and-data-analysis-roadmap.md` — **Proposed / Planning note.** Proposes the product boundary, architecture direction, source-adaptation strategy, and ordered implementation path for manual code editing, Python, R, MATLAB, notebooks, executable documents, datasets, tables, figures, analysis runs, reproducible computational work, and the shared foundations it coordinates with Scient's document platform. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/scientific-document-platform-roadmap.md` — **Proposed / Planning note.** Proposes Scient's integrated product boundary, architecture direction, source-adaptation strategy, quality gates, and ordered implementation path for universal document viewing, scientific mathematics, source and visual authoring, typesetting, Office interoperability, review, collaboration, and publishing. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/scientific-python-environment-roadmap.md` — **Proposed / Planning note.** Proposes the full Python-specific scope Scient should support around an agentic platform where agents write and run Python inside a project, grounded in the everyday use cases scientists actually have for Python rather than in language-agnostic architecture. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/planning/t3-foundation-migration-plan.md` — **Historical / Planning note.** Preserves the proof-gated migration, cutover, compatibility, and predecessor-retirement record that produced the current T3-derived Scient Desktop. **Treatment:** Retain as a record with its successor and do not use it as current guidance. + +#### Scient docs/product + +- `docs/product/PRD.md` — **Accepted / Product truth.** Defines Scient's product direction, core capabilities, user experience principles, and product constraints. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/product/product-philosophy.md` — **Draft / Product truth.** Defines Scient's durable product principles across product, architecture, design, quality, and implementation. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/product/README.md` — **Active / Repo orientation.** Defines where Scient product documentation lives. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/product/scient-product-identity.md` — **Accepted / Product truth.** Defines the accepted company, product, agent, and external-agent naming system for Scient. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/product/skills-system.md` — **Draft / Product truth.** Defines the proposed product model, trust boundaries, candidate catalog, and validation order for reusable scientific skills in Scient. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. + +#### Scient docs/quality + +- `docs/quality/code-quality-principles.md` — **Draft / Engineering doctrine.** Defines Scient's code quality principles before implementation-specific standards and gates exist. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/quality/README.md` — **Active / Repo orientation.** Defines where Scient quality, testing, and engineering-standard documentation lives. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/quality/testing-philosophy.md` — **Draft / Testing doctrine.** Defines Scient's testing philosophy before implementation-specific commands, lanes, and CI gates exist. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. + +#### Scient docs/research + +- `docs/research/README.md` — **Active / Repo orientation.** Maps where Scient external research, source evaluations, and spike reports live. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/research/source-evaluations/anydoc-source-evaluation-2026-08-06.md` — **Proposed / Research evidence.** Evaluates AnyDoc as a lightweight local document-extraction source and defines the evidence required before Scient adopts it behind an ingestion adapter. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/source-evaluations/competitive-landscape.md` — **Draft / Research evidence.** Maps direct competitors, substitute workflows, specialized alternatives, and integration candidates against Scient's product scope. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/source-evaluations/model-benchmark-map.md` — **Draft / Research evidence.** Maps what external model benchmarks measure, how trustworthy they are, and how much weight Scient should give them. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/source-evaluations/model-portfolio-and-provider-routing.md` — **Draft / Research evidence.** Tracks Scient's candidate model portfolio and the distinct value each model must prove before selection. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/source-evaluations/open-source-adaptation-map.md` — **Proposed / Research evidence.** Maps which open-source systems Scient should study, prototype, adapt, or integrate, and which product boundaries Scient must keep owned. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/source-evaluations/README.md` — **Active / Repo orientation.** Maps evaluations of external sources and tools that may inform Scient product and architecture decisions. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. +- `docs/research/source-evaluations/scient-agent-foundation-and-capability-strategy-2026-08-06.md` — **Draft / Research evidence.** Records the current source-backed comparison of candidate Scient-agent foundations, specialist workers, and capability sources without selecting a final foundation or worker architecture. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/source-evaluations/scientific-document-platform-source-map.md` — **Proposed / Research evidence.** Records the inspected external sources, pinned evidence, candidate roles, exclusions, and acceptance gates that inform Scient's proposed Scientific Document Platform. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/source-evaluations/scientific-project-fixture-selection.md` — **Accepted / Research evidence.** Records Scient's selected validation projects, capability fixtures, agent-evaluation benchmarks, source evidence, and activation conditions. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `docs/research/source-evaluations/source-evaluation-template.md` — **Placeholder / Future home.** Defines what should become the source evaluation template once agreed. **Treatment:** Retain only as a clearly reserved home; activate or remove only through a focused decision. +- `docs/research/source-evaluations/t3-migration-capability-catalog.md` — **Draft / Research evidence.** Preserves a compact, repo-local research index of the capabilities evaluated for the accepted T3 foundation migration direction. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/spike-reports/coherence-report-2026-06-28.md` — **Draft / Research evidence.** Records a deep coherence, alignment, and consistency audit of the LitRev planning documents, a decision-by-decision architecture review, and a concrete set of proposed fixes, as a dated snapshot. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/spike-reports/litrev-2026-vnext-transfer-report-2026-06-27.md` — **Draft / Research evidence.** Synthesizes what the new LitRev repo should learn from LitRev_2026 and vNext planning without copying the old product shape. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/spike-reports/README.md` — **Active / Research index.** Indexes dated reports from technical or product spikes. **Treatment:** Keep as the current area index and update it when reports are added, moved, or retired. +- `docs/research/spike-reports/spike-report-template.md` — **Placeholder / Future home.** Defines what should become the spike report template once agreed. **Treatment:** Retain only as a clearly reserved home; activate or remove only through a focused decision. +- `docs/research/spike-reports/t3-foundation-d4-bootstrap-2026-08-06.md` — **Active / Research evidence.** Records the exact D4 candidate creation, literal T3 ancestry, bounded safety envelope, integration, local development path, verification, and remaining limitations. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `docs/research/spike-reports/t3-foundation-phase-zero-2026-08-02.md` — **Draft / Research evidence.** Records the refreshed T3 and owned-repository baseline, isolated untouched T3 verification, candidate identity risks, and evidence required before foundation acceptance or repository bootstrap. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `docs/research/visual-references/agent-workflows/README.md` — **Active / Research evidence.** Indexes visual patterns for agent task plans, step trackers, progress states, and workflow controls placed near a conversation composer. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `docs/research/visual-references/authentication/README.md` — **Active / Research evidence.** Indexes external and historical internal login, sign-up, account-entry, identity-provider, and authentication-consent UI references. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `docs/research/visual-references/dashboard-and-settings/README.md` — **Active / Research evidence.** Indexes external administrative dashboards and settings interfaces kept for later product-design comparison and inspiration. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `docs/research/visual-references/dialogs-and-overlays/README.md` — **Active / Research evidence.** Indexes external modal, dialog, warning, confirmation, and overlay patterns kept for later product-design comparison and inspiration. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `docs/research/visual-references/marketing-and-website/README.md` — **Active / Research evidence.** Indexes external public marketing and product-website surfaces — landing heroes, download and distribution flows, pricing, FAQ, and similar acquisition-facing pages — kept for later Scient website design comparison and inspiration. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `docs/research/visual-references/motion-and-interaction/README.md` — **Active / Research evidence.** Indexes external motion, hover, transition, and animated-state references that must be understood over time rather than from a still image alone. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `docs/research/visual-references/README.md` — **Active / Repo orientation.** Maps external and historical internal UI screenshots into retrieval-friendly categories for later product-design research. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. + +#### Lab orientation and experiments + +- `lab/README.md` — **Active / Repo orientation.** Defines the experimental lab area for early Scient source forks, adapters, and integration spikes. **Treatment:** Keep as the current lab index; its linked evidence retains its own dated authority boundary. +- `lab/scient-bridge/README.md` — **Draft / Planning note.** Holds Scient-owned adapter and integration experiments connecting lab source checkouts. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. + +#### Lab external-source boundaries + +- `lab/external/agent-forks/README.md` — **Draft / Planning note.** Organizes upstream agent engines and automation systems used in the Scient lab. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `lab/external/desktop-app-forks/goose-desktop.md` — **Draft / Planning note.** Records Goose's cross-role research status without implying a retained local checkout. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `lab/external/desktop-app-forks/README.md` — **Draft / Planning note.** Organizes upstream desktop and workbench apps used in the Scient lab. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `lab/external/README.md` — **Active / Repo orientation.** Explains how owned source repositories, external provenance, and optional reference checkouts are organized locally. **Treatment:** Keep as the current external-source route; do not let it make dated evaluations current. +- `lab/external/sources.lock.md` — **Active / Research evidence.** Records exact owned and external source provenance, tested owned revisions, and cross-repository upstream review evidence used by Scient. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. + +#### Lab upstream-review evidence + +- `lab/external/upstream-reviews/2026-07-18-scient-agent.md` — **Active / Research evidence.** Records the disposition review of official OpenCode changes published after Scient's current integrated agent-source base. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `lab/external/upstream-reviews/2026-07-18-scient-desktop.md` — **Active / Research evidence.** Records the disposition review of official Synara changes published after Scient's current integrated desktop base. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `lab/external/upstream-reviews/2026-07-26-scient-desktop.md` — **Active / Research evidence.** Records the complete Synara review from Scient's previous checkpoint through the official tip observed on 2026-07-26. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `lab/external/upstream-reviews/2026-07-28-scient-desktop.md` — **Active / Research evidence.** Records the complete Synara review from the accepted July 26 checkpoint through the official tip observed on July 29. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `lab/external/upstream-reviews/2026-07-30-scient-desktop.md` — **Active / Research evidence.** Records the complete Synara disposition review from the accepted July 29 checkpoint through the current official tip observed on July 31. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `lab/external/upstream-reviews/2026-07-30-t3-code.md` — **Draft / Research evidence.** Records the complete scheduled T3 Code research-donor scan from the durable targeted-review boundary through the official tip observed on July 31. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `lab/external/upstream-reviews/2026-07-31-scient-desktop-tail.md` — **Active / Research evidence.** Records the complete Synara disposition review after the merged July 30-31 evidence through the current official tip. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `lab/external/upstream-reviews/2026-07-31-t3-code-tail.md` — **Active / Research evidence.** Records the complete T3 Code research-donor tail after the merged July 30-31 scheduled scan. **Treatment:** Keep as dated evidence; reverify dependencies before reuse and do not promote it silently. +- `lab/external/upstream-reviews/2026-08-22-scient-desktop-t3.md` — **Accepted / type missing.** Title: Scient Desktop T3 Upstream Review Through `dedcd99a9d`. **Treatment:** Retain as dated upstream evidence; repair its missing Created, Last updated, Purpose, and Doc type metadata in a focused reconciliation. +- `lab/external/upstream-reviews/README.md` — **Active / Repo orientation.** Indexes dated evidence for reviews of changes in Scient's original desktop and agent sources. **Treatment:** Keep as the current review index while preserving each review's exact source and date boundary. +- `lab/external/upstream-reviews/review-template.md` — **Draft / Research evidence.** Records the inspected upstream range, dispositions, and any selected intake for one maintained Scient source. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. + +#### Lab investigation and execution evidence + +- `lab/notes/first-slice-source-trace-2026-07-18.md` — **Complete as source evidence; memory and package architecture not selected / Implementation evidence.** Maps the first scientific slice's current source seams and proven gaps without selecting memory layers, persistence technology, or permanent product architecture. **Treatment:** Retain as evidence, but normalize the non-policy status into a valid document status while preserving completion inside the content. +- `lab/notes/gate-1-5-execution-report-2026-07-11.md` — **Historical / Research evidence.** Records the executed Synara and OpenCode ownership, updateability, identity-isolation, and compatibility gate. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `lab/notes/goose-source-depth-inspection-2026-07-11.md` — **Draft / Research evidence.** Records research evidence on Goose integration seams, runtime boundaries, safety gaps, and its possible later role in Scient. **Treatment:** Keep non-canonical; revise, accept, supersede, or retain as evidence only through its accountable owner. +- `lab/notes/papilab-rename-execution-report-2026-07-16.md` — **Historical / Research evidence.** Records the executed PapiLab identity cutover, verification results, and remaining external cutover work. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `lab/notes/project-initiation-placement-trace-2026-07-16.md` — **Historical / Research evidence.** Records the source-backed placement and dependency decision for the first permanent PapiLab project-initiation package. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `lab/notes/README.md` — **Active / Repo orientation.** Maps temporary inspection notes and lab decisions before promotion into durable docs. **Treatment:** Keep as the current lab-note index and route promoted conclusions to their durable owners. +- `lab/notes/synara-first-inspection-2026-07-07.md` — **Historical / Research evidence.** Preserves the first technical inspection of Synara and the initial ownership plan that preceded the accepted foundation decision. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `lab/notes/synara-gate-1-baseline-2026-07-11.md` — **Historical / Research evidence.** Records the end-to-end Gate 1 run against the pinned Synara scaffold and the evidence for its go/no-go result. **Treatment:** Retain as a record with its successor and do not use it as current guidance. +- `lab/notes/t3-code-targeted-review-2026-07-18.md` — **Complete / Research evidence.** Records the bounded T3 Code inspection, accepted reliability intake, and explicit stop boundary for future T3-derived work. **Treatment:** Retain as evidence, but normalize the non-policy status into a valid document status while preserving completion inside the content. + +#### Project workflow skills + +- `skills/documentation/scient-documentation-stewardship/SKILL.md` — **metadata-exempt / Project skill.** Apply Scient's documentation policy to create, update, review, move, promote, retire, and reconcile repository documentation and progress records. Use for documentation audits, repository-scope and placement questions, AI-assisted durable knowledge capture, metadata or status changes, placeholder activation, index maintenance, conflict or drift reconciliation, and documentation resulting from product, architecture, research, implementation, or operations. Do not use for product analysis alone, code changes without documentation impact, or read-only status lookup. **Treatment:** Keep as a non-authoritative workflow helper and route back to governing documents. +- `skills/product/scient-product-stewardship/SKILL.md` — **metadata-exempt / Project skill.** Shape Scient product direction, feature choices, PRDs, roadmap priorities, and product research through first-principles reasoning grounded in researcher value, scientific trust, product quality, long-term ownership, coherence, and scale. **Treatment:** Keep as a non-authoritative workflow helper and route back to governing documents. +- `skills/README.md` — **Active / Repo orientation.** Indexes local workflow skills that help agents work on Scient without becoming project authority. **Treatment:** Keep at its current owner; update only when the fact, decision, route, or procedure it owns changes. + +### scient-desktop + +Desktop does not currently apply Scient's metadata schema. The ledger therefore uses path role, title, exact T3-base blob provenance, and content review for ambiguous files. + +#### Agent-operated testing or debugging workflow + +- `.agents/skills/ios-debugger-agent/SKILL.md` — Title: iOS Debugger Agent. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside agent tooling; it is not product or architecture authority. +- `.agents/skills/ios-simulator-browser/SKILL.md` — Title: iOS Simulator Browser. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside agent tooling; it is not product or architecture authority. +- `.agents/skills/test-t3-app/references/sqlite-fixtures.md` — Title: SQLite fixtures. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside agent tooling; it is not product or architecture authority. +- `.agents/skills/test-t3-app/SKILL.md` — Title: Test T3 App. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside agent tooling; it is not product or architecture authority. +- `.agents/skills/test-t3-mobile/SKILL.md` — Title: Test T3 Mobile. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside agent tooling; it is not product or architecture authority. + +#### Automated review-agent prompt or criterion + +- `.macroscope/approvability.md` — No H1 title at the audited snapshot. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep with the review tool; do not treat it as general project documentation. +- `.macroscope/check-run-agents/effect-service-conventions.md` — Title: Effect service review. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep with the review tool; do not treat it as general project documentation. +- `.macroscope/check-run-agents/ui-consistency.md` — Title: UI consistency review. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep with the review tool; do not treat it as general project documentation. + +#### Compatibility import + +- `CLAUDE.md` — No H1 title at the audited snapshot. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep minimal and subordinate to AGENTS.md. + +#### Completed pull-request drafting artifact + +- `docs/internals/scient-fork-pr-descriptions.md` — Title: Draft PR descriptions for Scient fork modernization. **Provenance:** Scient-created path. **Treatment:** Retire from current documentation unless unique reasoning is promoted to scient-fork-divergence.md; merged PRs are the implementation record. + +#### Contributor guidance with a stale migration-candidate boundary + +- `CONTRIBUTING.md` — Title: Contributing. **Provenance:** T3 path modified in Scient. **Treatment:** Reconcile its private-candidate wording with the active public released repository in Phase 0; keep external contribution rules self-contained. + +#### Current conversation-fork architecture and protected T3 divergence + +- `docs/internals/scient-fork-divergence.md` — Title: Scient conversation fork: design, provenance, and T3 divergence. **Provenance:** Scient-created path. **Treatment:** Keep as capability/upstream truth; avoid duplicate PR drafting artifacts. + +#### Current getting-started capability architecture + +- `docs/internals/scient-onboarding.md` — Title: Scient getting started. **Provenance:** Scient-created path. **Treatment:** Keep as capability truth and link it to public getting-started help; avoid duplicating product direction. + +#### Current operational runbook + +- `docs/operations/local-dev-app.md` — Title: Scient Local Dev App. **Provenance:** Scient-created path. **Treatment:** Keep logically under operations and update with the procedure it owns. +- `docs/operations/mobile-app-store-screenshots.md` — Title: Mobile app-store screenshot harness. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under operations and update with the procedure it owns. +- `docs/operations/observability.md` — Title: Observability. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under operations and update with the procedure it owns. +- `docs/operations/relay-observability.md` — Title: Relay observability. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under operations and update with the procedure it owns. +- `docs/operations/release.md` — Title: Scient desktop release runbook. **Provenance:** T3 path modified in Scient. **Treatment:** Keep logically under operations and update with the procedure it owns. + +#### Current public/help candidate + +- `docs/user/background-service.md` — Title: Running Scient in the Background. **Provenance:** T3 path modified in Scient. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/charts-in-chat.md` — Title: Interactive charts in chat. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/composer.md` — Title: Message composer. **Provenance:** T3 path modified in Scient. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/content-direction.md` — Title: Conversation text direction. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/conversation-forks.md` — Title: Fork a conversation. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/diagrams-in-chat.md` — Title: Diagrams in chat. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/file-previews.md` — Title: File previews. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/getting-started.md` — Title: Getting started with Scient. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/images-in-chat.md` — Title: Images in chat. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/keybindings.md` — Title: Keybindings. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/latex.md` — Title: LaTeX. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/math-in-chat.md` — Title: Math in chat. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/matlab-run-file.md` — Title: Run a MATLAB file. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/mobile-appearance.md` — Title: Mobile appearance. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/pdf-reader.md` — Title: PDF reader. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/permission-modes.md` — Title: Permission Modes. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/project-settings.md` — Title: Project settings. **Provenance:** T3 path modified in Scient. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/projects.md` — Title: Starting a project. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/providers-antigravity.md` — Title: Antigravity in Scient. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/providers-claude.md` — Title: Claude in Scient. **Provenance:** T3 path modified in Scient. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/providers-codex.md` — Title: Codex in Scient. **Provenance:** T3 path modified in Scient. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/providers-cursor.md` — Title: Cursor in Scient. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/providers-droid.md` — Title: Droid (Factory) in Scient. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/providers-grok.md` — Title: Grok in Scient. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/providers.md` — Title: Providers in Scient. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/remote-access.md` — Title: Remote Access. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/source-control.md` — Title: Source Control Integrations. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/sources.md` — Title: Sources and PDF import. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/thread-sidebar.md` — Title: Organizing threads. **Provenance:** T3 path modified in Scient. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. +- `docs/user/usage.md` — Title: Review usage. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep in docs/user/ as the durable Help source and verify against released Scient behavior before publication. + +#### Current queue capability, T3 seams, and retirement contract + +- `docs/internals/scient-thread-queue.md` — Title: Scient thread queue: design, seams, and retirement plan. **Provenance:** Scient-created path. **Treatment:** Keep as capability plus upstream-seam truth; update when queue semantics or upstream retirement conditions change. + +#### Current Scient capability or implementation record + +- `docs/internals/scient-analysis-runtime-foundation.md` — Title: Scient analysis runtime foundation. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-browser-pdf-export.md` — Title: Scient browser HTML → PDF export. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-chat-diagrams.md` — Title: Scient rich chat diagrams. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-chat-images.md` — Title: Scient inline workspace images. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-chat-visualizations.md` — Title: Scient rich chat visualizations. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-codex-runtime-auth.md` — Title: Scient Codex runtime and authentication. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-content-direction.md` — Title: Scient content direction. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-latex.md` — Title: Scient LaTeX build. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-math.md` — Title: Scient math rendering. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-pdf-reader.md` — Title: Scient PDF reader. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-project-initialization.md` — Title: Scient project initialization. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-skills.md` — Title: Scient skills core. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-sources.md` — Title: Scient Sources foundation. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-typography.md` — Title: Scient typography profile. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-universal-file-opening.md` — Title: Scient universal file opening. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. +- `docs/internals/scient-voice.md` — Title: Scient local voice architecture. **Provenance:** Scient-created path. **Treatment:** Normalize into a capability-family owner, separating shared architecture and historical evolution where necessary. + +#### Current shared or inherited implementation architecture + +- `docs/internals/connection-runtime.md` — Title: Connection Runtime. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. +- `docs/internals/environment-auth.md` — Title: Environment Authentication Profile. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. +- `docs/internals/overview.md` — Title: Architecture. **Provenance:** T3 path modified in Scient. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. +- `docs/internals/provider-lifecycle.md` — Title: Provider lifecycle architecture. **Provenance:** Scient-created path. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. +- `docs/internals/providers.md` — Title: Provider architecture. **Provenance:** T3 path modified in Scient. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. +- `docs/internals/remote.md` — Title: Remote Architecture. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. +- `docs/internals/resource-telemetry.md` — Title: Resource telemetry architecture. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. +- `docs/internals/server-updates.md` — Title: Server Update Architecture. **Provenance:** T3 path modified in Scient. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. +- `docs/internals/t3-connect.md` — Title: T3 Connect. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under architecture; preserve inherited paths unless a move produces clear authority value. + +#### Current T3 integration and protected-divergence contract + +- `UPSTREAM.md` — Title: Upstream maintenance. **Provenance:** Scient-created path. **Treatment:** Keep as the special root upstream entry point and index historical receipts from it or the documentation map. + +#### Current What's New capability and authoring contract + +- `docs/internals/scient-release-notes.md` — Title: Scient release notes. **Provenance:** Scient-created path. **Treatment:** Keep as a capability/operations boundary; public release content should be release-qualified. + +#### Dated T3 integration, bootstrap, or qualification record + +- `docs/internals/2026-08-17-upstream-sync-cd096b9ad5.md` — Title: Upstream sync through `c7e6d711d3`. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-19-upstream-sync-f2d5fc91e3.md` — Title: Upstream sync through `f2d5fc91e3`. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-20-upstream-sync-beab6886f4.md` — Title: Upstream sync through `beab6886f4`. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-21-upstream-sync-be7d35aaeb.md` — Title: Upstream sync through `be7d35aaeb`. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-22-upstream-sync-dedcd99a9d.md` — Title: Upstream sync through `dedcd99a9d`. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-23-upstream-sync-b1670ac7d9.md` — Title: T3 upstream sync through b1670ac7d9. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-24-upstream-sync-e6a109b9f7.md` — Title: T3 upstream sync through e6a109b9f7. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-25-upstream-sync-082e6ea521.md` — Title: T3 upstream sync through 082e6ea521. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-25-upstream-sync-1a4a7596c2.md` — Title: T3 upstream sync through 1a4a7596c2. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-25-upstream-sync-99960383d0.md` — Title: T3 upstream sync through 99960383d0. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/2026-08-28-upstream-sync-c8aba2587d.md` — Title: T3 upstream sync through c8aba2587d. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/scient-next-d4-bootstrap.md` — Title: Scient Next D4 bootstrap record. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-foundation-refresh-20260807-b.md` — Title: T3 foundation refresh — 2026-08-07 (second range). **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-foundation-refresh-20260807.md` — Title: T3 foundation refresh — 2026-08-07. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-foundation-refresh-20260809-1a003e38.md` — Title: T3 foundation refresh — 2026-08-09 through `1a003e38`. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-foundation-refresh-20260809.md` — Title: T3 foundation refresh — 2026-08-09. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-foundation-refresh-20260811-78f462c4.md` — Title: T3 foundation refresh — 2026-08-11 through `78f462c4`. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-phase-2-gates-2-3-20260811.md` — Title: T3 phase two Gates 2 and 3. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260811-2db08457f.md` — Title: T3 upstream sync through 2db08457f. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260811-65b005f1.md` — Title: T3 upstream sync through 65b005f1. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260811-ac4780f4.md` — Title: T3 upstream sync through ac4780f4. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260812-849bac894.md` — Title: T3 upstream sync through 849bac894. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260813-5015d7cf.md` — Title: T3 upstream sync through 5015d7cf. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260813-97db94c9.md` — Title: T3 upstream sync through 97db94c9. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260814-5304f3e9.md` — Title: T3 upstream sync through 5304f3e9. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260814-7e01d33f.md` — Title: T3 upstream sync through 7e01d33f. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260815-6ae9662d8e.md` — Title: T3 upstream sync through 6ae9662d8e. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260815-8c628f14.md` — Title: T3 upstream sync through 8c628f14. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. +- `docs/internals/t3-upstream-sync-20260816-bab4b6f02b.md` — Title: T3 upstream sync through bab4b6f02b. **Provenance:** Scient-created path. **Treatment:** Retain immutably under the logical upstream/records area; do not use as current behavior. + +#### Desktop copy of a cross-product roadmap with current-state material + +- `docs/internals/scientific-artifact-studio.md` — Title: Scientific Artifact Studio roadmap. **Provenance:** Scient-created path. **Treatment:** After PR #188, keep desktop implementation truth locally and let Scient's planning document own future cross-product direction. + +#### Desktop documentation index + +- `docs/README.md` — Title: Scient Desktop documentation. **Provenance:** T3 path modified in Scient. **Treatment:** Make it the compatibility map from logical roles to current physical paths; begin from PR #188's explicit disposition for overlapping edits. + +#### Development or contributor reference + +- `docs/internals/ci.md` — Title: CI quality gates. **Provenance:** T3 path modified in Scient. **Treatment:** Keep logically under development; update only when the local workflow or vocabulary changes. +- `docs/internals/glossary.md` — Title: Glossary. **Provenance:** T3 path modified in Scient. **Treatment:** Keep logically under development; update only when the local workflow or vocabulary changes. +- `docs/internals/scripts.md` — Title: Scripts. **Provenance:** T3 path modified in Scient. **Treatment:** Keep logically under development; update only when the local workflow or vocabulary changes. +- `docs/internals/work-artifacts.md` — Title: Engineering work artifacts. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under development; update only when the local workflow or vocabulary changes. +- `docs/internals/workspace-layout.md` — Title: Workspace layout. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under development; update only when the local workflow or vocabulary changes. + +#### Historical migration rehearsal + +- `docs/operations/v060-migration-rehearsal.md` — Title: v0.6.0 migration rehearsal. **Provenance:** Scient-created path. **Treatment:** Retain as a record rather than a current runbook once no supported migration path depends on it. + +#### Historical provider-lifecycle implementation proposal with stale completion text + +- `docs/internals/provider-lifecycle-unification-proposal.md` — Title: Provider Lifecycle Unification Proposal. **Provenance:** Scient-created path. **Treatment:** Correct its disposition after merged PR #150; current behavior belongs in provider-lifecycle.md and capability records. + +#### Inherited/shared implementation architecture + +- `docs/architecture/terminal-renderers.md` — Title: Terminal renderers. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep logically under architecture; preserve the upstream path while it remains a useful merge surface. + +#### Mixed implementation plan and landed-progress ledger + +- `docs/internals/scient-pdf-export-rendering-plan.md` — Title: Scient PDF Export And Rendering Implementation Plan. **Provenance:** Scient-created path. **Treatment:** After PR #188 is resolved, separate current capability truth from remaining proposed deltas and retain useful completed-plan reasoning as a record. + +#### Non-authoritative rendering or visual fixture + +- `docs/fixtures/scient-chat-diagrams.md` — Title: Scient chat diagram visual fixtures. **Provenance:** Scient-created path. **Treatment:** Keep with fixtures and exclude from public Docs and capability authority. +- `docs/fixtures/scient-chat-images.md` — Title: Scient inline image fixtures. **Provenance:** Scient-created path. **Treatment:** Keep with fixtures and exclude from public Docs and capability authority. +- `docs/fixtures/scient-chat-plotly.md` — Title: Scient Plotly chat fixtures. **Provenance:** Scient-created path. **Treatment:** Keep with fixtures and exclude from public Docs and capability authority. +- `docs/fixtures/scient-chat-visualizations.md` — Title: Scient chat visualization fixtures. **Provenance:** Scient-created path. **Treatment:** Keep with fixtures and exclude from public Docs and capability authority. + +#### Package-, asset-, or source-local reference + +- `apps/marketing/tweets.md` — No H1 title at the audited snapshot. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. +- `apps/mobile/modules/t3-markdown-text/UPSTREAM.md` — Title: Upstream Attribution. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. +- `apps/mobile/modules/t3-terminal/README.md` — Title: T3 Mobile Terminal Native Module. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. +- `apps/mobile/README.md` — Title: T3 Code Mobile. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. +- `apps/web/src/terminal/ghostty/README.md` — Title: Ghostty web terminal. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. +- `assets/README.md` — Title: Brand icons. **Provenance:** T3 path modified in Scient. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. +- `infra/relay/README.md` — Title: T3 Connect Relay. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. +- `packages/client-runtime/README.md` — Title: Client Runtime. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. +- `packaging/aur/README.md` — Title: AUR packaging. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the code or asset it explains; index only when broader navigation needs it. + +#### Package-local license and attribution notice + +- `apps/mobile/modules/t3-terminal/THIRD_PARTY_NOTICES.md` — Title: Third-Party Notices. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep beside the distributed package and update with dependency provenance. +- `apps/web/THIRD_PARTY_NOTICES.md` — Title: Third-Party Notices. **Provenance:** T3 path modified in Scient. **Treatment:** Keep beside the distributed package and update with dependency provenance. + +#### Provider capability evidence audit + +- `docs/internals/provider-lifecycle-capability-audit.md` — Title: Provider Lifecycle Capability Audit. **Provenance:** Scient-created path. **Treatment:** Retain as evidence, but distinguish observations from current architecture and reverify before reuse. + +#### Public help with a material privacy/data-flow drift + +- `docs/user/voice-dictation.md` — Title: Voice dictation. **Provenance:** Scient-created path. **Treatment:** Keep in docs/user/; correct the claim that all transcript processing is local when optional provider-based correction is enabled, then release-qualify it before publication. + +#### Public installation help retaining a T3 title + +- `docs/user/install.md` — Title: Install T3 Code. **Provenance:** T3 path modified in Scient. **Treatment:** Keep in docs/user/; reconcile product identity and release qualification, preserving only compatibility terms that users genuinely encounter. + +#### Public update help retaining T3 identity + +- `docs/user/updating.md` — Title: Keeping T3 Code in Sync. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep in docs/user/; reconcile Scient product wording while preserving real T3 server/CLI compatibility vocabulary where technically required. + +#### Pull-request evidence prompt + +- `.github/pull_request_template.md` — No H1 title at the audited snapshot. **Provenance:** T3 unchanged at integrated base. **Treatment:** Keep concise and add the accepted documentation-impact field in Phase 1. + +#### Repository and product orientation + +- `README.md` — Title: Scient desktop. **Provenance:** T3 path modified in Scient. **Treatment:** Keep as the human entry point; preserve the Scient override above inherited T3 orientation. + +#### Repository triage operations + +- `.github/triage/PLAYBOOK.md` — Title: Scient triage playbook. **Provenance:** T3 path modified in Scient. **Treatment:** Keep as repository-specific operations guidance. + +#### Repository-local agent protocol + +- `AGENTS.md` — Title: Scient desktop instructions. **Provenance:** T3 path modified in Scient. **Treatment:** Keep as the executable local rule surface and route to the documentation index rather than duplicating policy. + +#### Shipped built-in Scient skill definition + +- `apps/server/src/scient/skills/built-ins/improve-workspace-readiness/SKILL.md` — Title: Improve Workspace Readiness. **Provenance:** Scient-created path. **Treatment:** Keep with runtime source; this is product content, not project documentation. +- `apps/server/src/scient/skills/built-ins/scient-skill-authoring/SKILL.md` — Title: Scient Skill Authoring. **Provenance:** Scient-created path. **Treatment:** Keep with runtime source; this is product content, not project documentation. +- `apps/server/src/scient/skills/built-ins/workspace-readiness-review/SKILL.md` — Title: Workspace Readiness Review. **Provenance:** Scient-created path. **Treatment:** Keep with runtime source; this is product content, not project documentation. + +### Website + +The website has no product-help corpus. Its six files own repository operation, contribution, compatibility routing, pull-request evidence, and brand-asset support. + +- `.github/pull_request_template.md` — **Pull-request evidence prompt.** No H1 title at the audited snapshot. **Treatment:** Keep website validation/deployment evidence and add one source/version documentation-impact field after acceptance. +- `AGENTS.md` — **Website agent protocol.** Title: AGENTS.md. **Treatment:** Keep concise; route app-help prose to desktop and website work to rendering/version ownership. +- `assets/brand/README.md` — **Brand asset source and generation reference.** Title: Scient brand assets. **Treatment:** Keep beside brand assets; it is not product-help prose. +- `CLAUDE.md` — **Compatibility import.** No H1 title at the audited snapshot. **Treatment:** Keep minimal and subordinate to AGENTS.md. +- `CONTRIBUTING.md` — **Website contribution and human-preview procedure.** Title: Contributing. **Treatment:** Keep website-specific; link rather than copy family documentation policy. +- `README.md` — **Website repository, deployment, and analytics orientation.** Title: ScientFactory Website. **Treatment:** Keep as the human entry point; record Docs source transport only after the publishing pilot selects it. + +## Coverage Conclusion + +The audit accounts for every tracked Markdown path in the three in-scope repositories at the exact heads above, every non-vendored file individually, both vendored donor boundaries, the three untracked forensic reports, and every Markdown path in the four open desktop pull requests. It deliberately does not claim that every proposal is correct, every help page is release-qualified, or every file should remain where it is. + +The evidence supports the proposed logical areas and update-before-create policy. It also shows why migration must be disposition-led: the immediate quality problems are stale authority, mixed lifecycle states, missing index routes, and privacy or product-identity drift, not merely folder names. diff --git a/docs/research/spike-reports/scient-capability-to-foundation-architecture-audit-2026-08-28.md b/docs/research/spike-reports/scient-capability-to-foundation-architecture-audit-2026-08-28.md new file mode 100644 index 0000000..620d29f --- /dev/null +++ b/docs/research/spike-reports/scient-capability-to-foundation-architecture-audit-2026-08-28.md @@ -0,0 +1,742 @@ +# Scient Capability-To-Foundation Architecture Audit — 2026-08-28 + +Status: Draft +Owner: Yaacov +Created: 2026-08-28 +Last updated: 2026-08-28 +Purpose: Maps every catalogued Scient-specific desktop capability to its current authority, shared foundations, T3 seams, source anchors, architectural disposition, and highest-value first-principles review questions. +Doc type: Research evidence + +## Document Rules + +This is a dated architecture audit, not accepted architecture and not a rebuild +authorization. It records what the inspected code, current implementation +records, accepted product principles, accepted ADRs, proposed plans, Git +ancestry, and in-flight branches support at the exact identities below. + +Use this report to decide which foundations deserve a focused trace, ADR, or +incremental simplification. Do not use a `unify`, `extract`, `replace`, or +`retire` classification as permission to change code, move project data, merge +an open pull request, rewrite documentation authority, or publish a capability. + +Current product behavior remains owned by the implementation and its repository- +local maintenance records. Accepted product truth and architecture remain owned +by the PRD and accepted ADRs. Proposed plans remain proposals. The three local +forensic reports used as the coverage baseline remain untracked candidate +records until deliberately placed and committed. + +The current `scient-agent` repository is excluded by explicit decision. It is +an inherited OpenCode-derived starting repository on which native Scient agent +work has not begun. Its Markdown, source architecture, and inherited capability +surface were not inspected, counted, classified, or used to propose a shared +foundation here. + +## Question, Scope, And Evidence + +The audit asks: + +> Which foundations do Scient's current desktop capabilities actually share, +> where are their authorities and lifecycle boundaries coherent, where has +> implementation accumulated avoidable duplication or incompatible concepts, +> and what—if anything—should be kept, simplified, unified, extracted, +> replaced, retired, or deferred? + +### Exact evidence identities + +| Evidence scope | Identity inspected | Treatment | +| -------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------- | +| Scient product/planning repository | `origin/main` `9a309d6bb952a3fae8c0dd3495139c7c0736b37a` | Current accepted/proposed product, architecture, planning, research, and operating authority at the audit point. | +| Documentation-system candidate | branch `codex/documentation-system-20260828` at the same base, with this report and the proposal/audit changes uncommitted | Candidate output only. | +| Scient Desktop current main | `origin/main` `d5ff08e721086eec02a2a84ad1431b33da6f5269` | Current source truth after merged upstream PR #189. | +| Capability, PR, and divergence reports | local desktop checkout at `aa23f1d3b96f6904dcc1a114cc33415fa267315a` | Coverage baseline. The `aa23f1d3..d5ff08e7` delta was reviewed separately. | +| Exact current T3 integration base | `c8aba2587d56edbf3b7872987719a12b42031f48` | Donor comparison and current ancestry boundary, not Scient product authority. | +| In-flight desktop documentation | draft PR #188, head `33cfee24d6551ec4fee701587b414bb7a60f6ca2` | Documentation reconciliation evidence; not current main. | +| In-flight stateful compute | draft PR #129, head `4955966dc6731a262d839a13ced8faf40390384c` | Substantial implementation plus candidate foundation/help documentation; not a shipped capability. | +| In-flight Overleaf sync | draft PR #121, head `3bdf7486fc9ced9491168333e4daca67b7dc8d28` | Separate proposed integration; not current product truth. | +| In-flight provider-update proposal | draft PR #179, head `02695010b6b13688bf3341ae5532ba0560fc0ffe` | Proposal only; no current runtime behavior. | + +Desktop PR #189 merged the official T3 range through `c8aba2587d` after the +capability catalog snapshot. Its 128-file delta is an upstream-host refresh and +protected-seam reconciliation, not a new Scient capability family. It advanced +the exact integrated T3 base, improved inherited provider, projection, mobile, +usage, Git, preview, and release behavior, and preserved Scient release, +provider-lifecycle, awareness, voice, sidebar, migration, and privacy seams. +The 38 named capability subsections plus the catalog's top-level cross-cutting +security/reliability family therefore remain a 39-item architecture coverage +baseline for current Scient-specific product behavior at `d5ff08e7`. + +A later readiness recheck found desktop main at `c0baaab2` through merged PR +#190. Its seven-file settings/defaults change adds no new architecture family or +Markdown, so this report preserves the exact `d5ff08e7` map. The capability and +PR reports still require a post-snapshot #190 addendum before durable placement. + +Scient's planning alignment is partly merged on current main through docs PRs +#99 and #100. The separate local planning branch diverges from their common +base with equivalent and follow-up documentation commits; it is not additional +accepted architecture. Desktop's seven-file implementation-record +reconciliation remains open as PR #188. This audit uses those branches only to +avoid proposing foundations that their evidence already shows as present or +deliberately separate. + +### Method + +1. Reconcile all 39 mapped items in the local capability catalog—38 named + capability subsections plus its cross-cutting security/reliability family; + 37 are current, one is retired, and one is integration-only—with the PR and + divergence ledgers. +2. Read the PRD, product philosophy, accepted ADRs 0002–0005, proposed ADR-0006, + project-format and security direction, current upstream policy, and the + relevant current implementation records. +3. Inspect representative contracts and implementation seams for project + identity, Sources, skills, forks, queueing, provider lifecycle, file + opening, right-panel identity, PDF/document artifacts, LaTeX, analysis, + execution, voice, and in-flight compute. +4. Separate project-owned canonical records, ordinary files, app-private + policy, server-derived execution state, external-system state, and UI + projections. +5. Classify architecture findings only after identifying common authority, + lifecycle, failure, recovery, retention, and T3-maintenance semantics. +6. Reconcile every proposed extraction with a concrete second consumer. Naming + similarity alone is not evidence of a shared foundation. + +## First-Principles Evaluation Criteria + +The accepted PRD and architecture decisions produce the following tests: + +1. **The project is the durable center of scientific work.** Host threads, + provider sessions, browser tabs, runtime processes, and app databases may be + useful projections or execution state; they are not automatically + scientific truth. +2. **Scient owns authority and acceptance.** A model, provider, client path, + page, prompt, runtime, external source, or upstream host cannot widen + authority or define an accepted scientific record. +3. **Inspectability, provenance, review, and recovery are product behavior.** + Failure and uncertainty must remain visible; last-success output must not be + confused with the latest failed attempt. +4. **One authority may have several representations.** A file, source record, + generated document, analysis artifact, or future manuscript may be opened + through common presentation infrastructure without becoming one generic + record type. +5. **Shared foundations require shared lifecycle.** Similar state names or + download steps do not justify one manager when creation, authority, + mutation, retention, and recovery differ. +6. **T3 is the maintained generic host, not product authority.** Prefer narrow + Scient-owned packages and marked mounts while allowing justified direct + inherited-core changes. Every divergence must remain explicit and tested. +7. **Agents use the same owned operations as manual flows.** Agent or automation + execution must not bypass project scope, capabilities, authority generation, + idempotency, provenance, or effect receipts. +8. **Extraction follows evidence.** Co-location is acceptable until a real + independent consumer, release, security, deployment, or operational + lifecycle proves a separate package, service, or repository. + +## Current Architectural Shape + +The current desktop is not one monolithic Scient subsystem. It is a layered +thin fork: + +```text +official T3 ancestry and generic host + Electron / React / Effect server / provider sessions / threads / files / browser + | + narrow protected mounts + | + Scient-owned packages and server/web/desktop modules + | + project records derived execution state app policy + .scient/* /analysis settings + project files /latex trust receipts + promoted results document-artifacts provider overlays + | + external adapters and engines remain replaceable + Zotero / metadata APIs / provider CLIs / MATLAB / TeX / whisper.cpp +``` + +The structure is directionally coherent: most scientific behavior lives in +`packages/scient-*`, `apps/server/src/scient`, `apps/web/src/scient`, and +bounded desktop modules. The largest long-term risk is not that everything is +inside one repository. It is that several horizontal concerns—resource +identity, presentation selection, currentness, operation authority, derived- +state cleanup, and verified installation—are currently repeated at feature +boundaries or only partly generalized. + +## Complete Capability-To-Foundation Map + +All paths in the following tables are relative to `ScientFactory/scient-desktop` +unless stated otherwise. `Keep separate` means keep the domain authority or +lifecycle distinct; it does not forbid sharing lower-level utilities. + +### Product, delivery, project entry, and navigation + +| # | Capability and state | Authority and shared foundation | T3 seam and primary anchors | Disposition | +| --: | -------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| 1 | Scient identity and fork boundary — current | Scient product/release policy; literal Git ancestry and recorded integration state | `UPSTREAM.md`, `upstream-state.json`, product metadata, `apps/web/src/assets/scient-*` | **Keep.** This boundary is the reason generic host updates remain possible without surrendering product authority. | +| 2 | Isolated development app and release lanes — current | Candidate/stable process and state isolation; exact artifact promotion and release receipts | `scripts/`, `.github/workflows/`, `apps/desktop/`, release docs; inherited package/build seams | **Keep; simplify only locally.** Release authority must remain separate from T3 publication. Reuse shared verification helpers where evidence supports it. | +| 3 | Scient What's New — current | Version-pinned local release communication; last-handled version is UI state | `apps/web/src/scient/releaseNotes/`, sidebar mount, `docs/internals/scient-release-notes.md` | **Keep.** It is a bounded product surface, not a release generator or documentation authority. Link its approved entries to public Docs later. | +| 4 | Safe project initialization — current | `@scientfactory/project-init` owns `.scient/project.json`, known-file inspection, recovery, and exact preservation | `packages/scient-project-init/`, `apps/server/src/scientProject/`, initialization dialog/hook; T3 still owns project registration and navigation | **Keep and treat as foundational.** Its identity reader is already reused by Sources, skills, and analysis. Do not widen initialization into feature activation. | +| 5 | Compact getting-started flow — current | UI orchestration over canonical provider/project state plus small app-private preferences | `apps/web/src/scient/onboarding/` and three narrow host mounts | **Keep.** This is presentation policy, not a new provider, compute, or project state machine. | +| 6 | Editorial thread titles — current | Product-level title rules; thread title remains host thread state | `packages/shared/src/scientForkTitle.ts`, fork title logic, provider title seam | **Keep; share editorial rules only.** Do not create a second thread identity. | +| 7 | File breadcrumbs, path copy, and viewer layout — current | Presentation affordances over current file/environment identity | `apps/web/src/scient/layout/`, file-surface modules, `FilePreviewPanel.tsx`, tabs/sidebar mounts | **Unify with the viewer shell.** Path display/copy/reveal should consume the same resolved file reference and action contract, not remain entry-point-specific. | + +### Conversation and thread lifecycle + +| # | Capability and state | Authority and shared foundation | T3 seam and primary anchors | Disposition | +| --: | ------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| 8 | Durable assistant-boundary conversation forks — current | Server-resolved transcript boundary, independent Scient migration ledger, durable lineage/saga, provider-neutral bootstrap | `apps/server/src/orchestration/scient-fork/`, fork reactor layers, web fork UI; narrow T3 command/projection/provider seams | **Keep.** It has a real durable lifecycle and restart model. Continue reducing host conflicts, but do not flatten it into client navigation. | +| 9 | Fork continuation with another provider — current | Same fork authority plus explicit provider/runtime choice through current lifecycle contracts | fork bootstrap/provider-selection modules and provider lifecycle | **Keep as a composition.** Provider choice must remain explicit and must not become silent queue steering or transcript mutation. | +| 10 | General Chat / Quick Chat — retired | Historical product experiment; migration removes projectless current authority | migration 043, historical migration 010, PR and divergence records; live feature modules removed | **Retire completely in current docs and code.** Preserve provenance and compatibility decoding only where immutable history requires it. | +| 11 | Per-thread queue and steer — current | Server file store owns pending composer payloads; ordinary `thread.turn.start` owns actual dispatch | `packages/contracts/src/scientThreadQueue.ts`, server/threadQueue, client/web queue modules, small composer/ChatView mounts | **Keep as a bounded removable layer.** It deliberately avoids orchestration state. Re-evaluate and retire when a qualified T3 queue supplies equivalent product behavior. | + +### Provider lifecycle and local runtime setup + +| # | Capability and state | Authority and shared foundation | T3 seam and primary anchors | Disposition | +| --: | ---------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| 12 | Capability-driven provider lifecycle — current | Provider snapshots remain authoritative; Scient managers coordinate advertised connection/runtime operations and transient overlays | `packages/scient-provider-runtime/`, `apps/server/src/scient/providerLifecycle/`, web provider connection; T3 owns instances, drivers, sessions, model discovery, enablement | **Keep.** This area has already undergone the justified cross-provider unification. Avoid another rewrite; make targeted corrections against evidence. | +| 13 | Codex runtime selection and authentication — current | Codex app-server/account API and fresh-process verification; Scient owns runtime-source selection and safe orchestration, not credentials | Codex lifecycle modules and inherited Codex driver seam | **Keep provider-specific policy above shared managers.** A generic `connected` state would lose real credential and package semantics. | +| 14 | Assisted provider connections — current | Shared setup host and manager lifecycle; each provider owns its protocol, credential ownership, URL/code semantics, and verification | provider-specific action modules plus `AssistedProviderSetupHost` | **Keep the shared host and explicit provider adapters.** Do not pursue button parity or a dynamic adapter that silently inherits unsupported behavior. | +| 15 | Capability-aware Scient context — current | Server advertises only delivery seams a provider can actually receive | `apps/server/src/provider/ScientAwareness.ts`, skills/source/rendering awareness modules, provider adapters | **Keep and connect to capability records.** This is delivery, not proof of feature use or scientific authority. | +| 16 | Local Whisper transcription — current | Desktop model selection and native lifecycle; host-independent voice package; web capture; optional provider correction is a separate data-flow step | `packages/scient-voice/`, desktop/web/server voice modules, staging scripts, composer mount | **Keep domain lifecycle separate; investigate shared verified-asset primitives.** Voice model selection, audio limits, and helper lifecycle must not be forced into provider or TeX managers. Correct public privacy documentation. | + +### Skills, sources, citations, and agent-facing scientific access + +| # | Capability and state | Authority and shared foundation | T3 seam and primary anchors | Disposition | +| --: | ----------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| 17 | Reviewed built-in and project-scoped skills — current | Exact release/project identity, digest, trust receipt, activation policy, and immutable per-turn snapshot; skills are data, not authority | `packages/scient-skills/`, server/web skills modules, provider MCP/awareness seams, `.scient/skills*` | **Keep.** Preserve the distinction between portable project activation, app-private trust/policy, provider-native inventory, and actual invocation evidence. | +| 18 | Local-first project source library — current | Canonical project-owned records and content-addressed PDFs under `.scient/sources`; `.scient/project.json` is project identity | `packages/scient-sources/`, server/web Sources modules, source-PDF adapter into existing reader | **Keep as a distinct scientific authority.** Do not collapse source records into ordinary files, Zotero items, host SQLite, or a universal artifact store. | +| 19 | Source intake and enrichment — current | Adapter candidates are normalized into Scient source truth; exact identifiers and field-level provenance constrain enrichment | Zotero adapter, PDF intake, metadata resolver, NCBI/Crossref/Europe PMC seams | **Keep as adapters.** A provider or API response must remain provenance, not authority. Shared bounded-network utilities may be extracted only without weakening per-source evidence rules. | +| 20 | Notes, citation formatting, and source agent operations — current | One project-owned source note with optimistic revision; citation strings are derived; current agent operations are Sources-specific | `packages/scient-citations/`, source note/edit operations, `scient_sources_*` delivery | **Keep domain semantics; route future mutation through the accepted Scient operation envelope.** Citation rendering must remain derived and agent access must not bypass project scope. | + +### Chat content, rich rendering, and presentation + +| # | Capability and state | Authority and shared foundation | T3 seam and primary anchors | Disposition | +| --: | ------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| 21 | Math rendering — current | Authored Markdown remains canonical; local KaTeX rendering is a bounded representation | `apps/web/src/scient/math/`, one `ChatMarkdown.tsx` seam | **Keep.** Share presentation loading/fallback conventions, not mathematical source identity. | +| 22 | BiDi/RTL direction — current | Structural direction metadata over authored content and composer state | `apps/web/src/scient/bidi/`, ChatMarkdown/composer seams | **Keep as cross-cutting presentation policy.** Reuse direction-aware title/action primitives in the shared viewer shell and public Docs. | +| 23 | Scient typography — current | Small token profile over T3 appearance pipeline | `apps/web/src/scient/typography/` and theme/CSS seams | **Keep and minimize.** Do not fork the renderer or spread one-off sizes through inherited components. | +| 24 | Mermaid diagrams — current | Authored fence is canonical; local sanitized renderer/card is disposable presentation | `apps/web/src/scient/diagrams/`, `ScientRichFence.tsx`, ChatMarkdown settled-fence seam | **Keep inside a static renderer registry.** Durable artifact identity begins only when content is deliberately captured/promoted. | +| 25 | Vega-Lite charts — current | Authored bounded JSON/JSONC is canonical; current view state is UI projection | `apps/web/src/scient/visualizations/`, `presentation/ScientRichFence.tsx` | **Keep; share renderer capability descriptors and export actions.** Do not make the Vega view a project record. | +| 26 | Plotly charts — current | Authored bounded figure spec is canonical; WebGL/activity state is disposable runtime state | visualization modules and shared rich-fence seam | **Keep; share lifecycle/resource-budget primitives where semantics match.** Preserve explicit network-resource labeling. | +| 27 | Workspace image cards — current | Workspace/project file is canonical; signed URL and card state are renewable presentation | `apps/web/src/scient/images/`, asset policy, ChatMarkdown image seam | **Unify with resource identity and viewer actions.** Do not turn every opened image into an analysis or document artifact. | +| 28 | Static artifacts and generated-document foundation — current | Producer-owned artifact identity; immutable revisions; explicit provenance; generated-document binding preserves last success | `packages/scient-document-artifacts/`, server/desktop documentArtifacts, web artifacts | **Keep authority families distinct; unify representation/resource vocabulary cautiously.** This is the strongest current shared document-output foundation. | +| 29 | Scient right-panel surface registry — current | Typed logical tab descriptors for Sources, source PDFs, artifacts, generated PDFs, and environment files | `apps/web/src/scient/rightPanel/surfaces.ts` and inherited right-panel host | **Extend into the file/presentation convergence, not a universal scientific record.** Stable IDs should consume durable resource identity rather than raw paths. | + +### Files, PDF, generated documents, and typesetting + +| # | Capability and state | Authority and shared foundation | T3 seam and primary anchors | Disposition | +| --: | ---------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| 30 | Universal file opening — current | Owning environment server canonicalizes and classifies the path; presenters own viewing; source file remains authoritative | server `scient/fileOpening`, web fileOpening/fileSurfaces, `EnvironmentFilePresentation`, five inherited host mounts | **Unify direct and workspace dispatch behind `FileReference`, one registry, and a shared shell.** Preserve environment authority and existing specialist presenters. | +| 31 | Preview and workspace-file freshness — current | Exact-file watchers are hints; authoritative rereads and conditional-save revisions decide truth | web fileOpening/fileSurfaces, workspace read/write/watch contracts, `FilePreviewPanel` seam | **Unify currentness vocabulary and observer plumbing where proven.** Rename/move recovery needs a stable file reference; dirty-buffer conflict semantics stay editor-specific. | +| 32 | Scient PDF reader — current | Logical source descriptor owns identity; renewable URL is transport; reader session is bounded UI state | `packages/scient-pdf-validation/`, web PDF modules, server asset routes, desktop Save Copy | **Keep as the polished PDF presenter.** Generalize its source adapter through resource/presentation contracts; do not create another PDF viewer per producer. | +| 33 | Browser HTML-to-PDF export — current | Live Browser tab is renderer binding; generated-document store owns immutable PDF revision and last-success binding; local source identity is environment + canonical path | desktop documentExport, server documentArtifacts, web export lifecycle, Browser/PDF mounts | **Keep producer and artifact lifecycles separate.** Reuse a future `DocumentBuild`/conversion receipt vocabulary without relabeling a live-page export as a typesetting build. | +| 34 | Local LaTeX build workflow — current | `LatexBuildService` owns root/build state; `GeneratedDocumentStore` owns published revision; project `.tex` and dependency hashes own source truth | server/web LaTeX modules, `@scientfactory/execution` process port, document-artifact contracts, file-panel mount | **Keep `DocumentBuild` distinct from analysis and compute.** Generalize only shared process, cancellation, diagnostic, artifact, and receipt primitives after concrete consumers prove them. | +| 35 | SyncTeX forward/inverse navigation — current | Exact generated PDF revision plus retained index and workspace-contained source locations | LaTeX SyncTeX modules, verified helper staging, PDF/editor navigation mounts | **Keep as a document-build auxiliary capability.** Share stable source/document anchors later; never navigate against a newer or evicted revision. | + +### Scientific execution and measurement + +| # | Capability and state | Authority and shared foundation | T3 seam and primary anchors | Disposition | +| --: | --------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | +| 36 | Analysis/execution runtime foundation — current, deliberately bounded | `@scientfactory/execution` owns a language-neutral run/process vocabulary; `@scientfactory/analysis` and server services own `AnalysisRun`, receipts, artifacts, recovery, and promotion | `packages/scient-execution`, `packages/scient-analysis`, server/web analysis, file auxiliary mount | **Keep the specialization and existing execution kernel.** Add adapters and shared coordinator behavior only when real workflows prove it; do not turn all work into `AnalysisRun`. | +| 37 | Stateful compute and rich output — integration-only | PR #129 owns persistent `ComputeSession`, execution requests/results, Jupyter-compatible representation bundles, resources, variables, and history | `packages/scient-compute`, server/web compute modules on head `4955966d`; no mainline product authority | **Keep as a sibling lifecycle and reconcile before merge.** Preserve `languageId` versus `transportKind`, project files versus submitted bytes, and `ComputeSession` versus `AnalysisRun`/`DocumentBuild`. Reuse Results/presentation seams without merging the records. | +| 38 | First-party analytics runtime — current but disabled by default | Bounded event schemas, local outbox/worker, and privacy policy; enablement is explicit product/user state | `packages/scient-analytics/`, server/web analytics, settings/release seams | **Keep disabled and isolated.** Product analytics is neither scientific provenance nor an authority for user projects. Enablement requires its separate rollout and privacy gates. | + +### Cross-cutting security, reliability, and maintenance + +| # | Capability and state | Authority and shared foundation | T3 seam and primary anchors | Disposition | +| --: | ----------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| 39 | Security, reliability, CI, release, and seam safeguards — current | Feature owners retain their safety contracts; exact artifact checks, bounded resources, race isolation, deterministic tests, provenance manifests, and static seam audits preserve them across release and upstream change | `.github/workflows/scient-*`, `scient-*-seams.json`, co-located adversarial/restart/race tests, release scripts, and small inherited corrections | **Keep as owned invariants and verification, not one generic reliability service.** Extract only proven lower-level helpers; keep security tests and seam ownership beside the capability they protect. | + +## Foundation Findings + +### F1. Project identity is already a real shared foundation — keep and formalize + +`@scientfactory/project-init` is not merely an onboarding helper. Its exact +identity reader is imported by Sources and skills, and the analysis server uses +the same identity after initialization inspection. This is appropriate shared +infrastructure because the consumers agree on authority: `.scient/project.json` +is the stable project identity and none may redefine it. + +The remaining decision is architectural authority, not code extraction. +Proposed ADR-0006 accurately describes the implemented Sources store and the +current one-`.scient/` direction, but it is still proposed. Before adding +evidence, manuscript, analysis, sync, or collaboration namespaces, accept, +revise, or replace ADR-0006. Do not let implementation-by-accumulation silently +make every future `.scient/*` representation canonical. + +Keep these state families explicit: + +| State family | Current authority | Portability/retention consequence | +| ------------------------------------------------------- | ---------------------------------------------- | ------------------------------------------------------------------------------------ | +| Ordinary project files | Current authorized path and file revision | Mutable, user-owned, editor conflict semantics; future relocation identity needed. | +| Project identity | `.scient/project.json` | Durable and shared by scientific namespaces. | +| Source records and imported PDFs | `.scient/sources/*` | Canonical project-owned scientific records and immutable attachments. | +| Reviewed skill lock and project skill files | `.scient/skills.lock.json`, `.scient/skills/*` | Portable activation/content; app-private trust and preferences still gate delivery. | +| Analysis run history | server `/analysis`, keyed by project ID | Derived execution evidence; promoted `results/*` is the portable deliberate handoff. | +| Generated document revisions | server `/document-artifacts` | Derived immutable revisions with bounded retention and producer bindings. | +| LaTeX aux/evidence/SyncTeX | server `/latex` | Rebuild/navigation support, not canonical source; needs coherent cleanup. | +| Thread queue | server `/scient/thread-queue` | Pending composer state tied to host thread lifecycle; deliberately easy to retire. | +| Provider, onboarding, analytics, and skill trust policy | app/server-private settings and caches | Product/runtime policy, not project scientific truth. | + +### F2. The accepted Scient operation boundary is not yet the common execution path — implement before widening agent effects + +Accepted ADR-0004 defines one host-independent operation envelope with actor, +project scope, capabilities, authority generation, idempotency, lineage, and an +effect receipt. Current source has strong feature-local authorization and +recovery, but no common `ScientOperation`/operation-envelope implementation was +found across the inspected mainline scientific packages and server services. +The analysis implementation record also explicitly defers actor identity until +that accepted envelope exists. + +This is the most important authority gap because future agent, external MCP, +automation, browser, source, analysis, document, and Studio mutations otherwise +risk receiving separate authorization and provenance models. + +Recommended next proof: + +1. Implement the smallest operation core for one existing low-risk read and one + protected project mutation. +2. Resolve actor and project capability on the host; do not accept them from + the request payload. +3. Bind idempotency to actor, project, operation, canonical payload, and + authority generation. +4. Commit protected state and effect receipt atomically where the state owner + permits it; classify uncertain external effects without automatic retry. +5. Adapt the manual UI and one agent-facing path to the same operation. +6. Preserve current domain stores and services behind the operation; this is an + authority seam, not a rewrite of Sources or analysis. + +Do not wait for the native Scient agent repository. The boundary is a desktop +product responsibility and is also required for external providers and future +automations. + +### F3. File identity and presentation are the clearest justified unification + +Four present-day dispatch families overlap without sharing one owner: + +- direct file classification through `EnvironmentFilePresentation`; +- workspace preview's narrower format switch and inherited file panel; +- the typed `ScientRightPanelSurface` union; +- chat rich-fence, workspace-image, PDF-source, and analysis-artifact selection + helpers. + +These implementations share opening, title, freshness, retry, save/copy, +reveal, fallback, and view-state concerns. They do **not** share canonical +record identity. The proposed File, Resource, And Presentation Foundation has +the correct boundary: + +- stable `FileReference` above path-based I/O; +- bounded, evidence-based relocation resolution; +- deterministic static presentation registry; +- compact shared viewer shell; and +- specialized adapters preserving current editor, PDF, Browser, LaTeX, + analysis, and artifact behavior. + +The first slice should migrate logical open-surface identity while continuing +to call current path-based preparation and asset APIs. It should not replace +all path parameters, invent a universal artifact union, or weaken environment +authorization. Direct and workspace entry points should converge only after a +fixture proves no regression in editing, PDF state, interactive HTML, RTL, +freshness, or failure recovery. + +### F4. Currentness is cross-cutting, but staleness semantics remain producer-owned + +Scient now has several strong currentness mechanisms: + +- workspace files: content revision, conditional save, watcher hint, and + dirty-buffer conflict; +- direct files: canonical path, size/mtime revision, signed exact-resource + renewal, and explicit refresh; +- generated documents: binding generation, immutable revision, `current`/ + `stale`/`failed-production`, and last success; +- LaTeX: exact dependency SHA-256 evidence plus build attempt and PDF binding; +- Browser HTML export: source generation, Browser binding, update coalescing, + and last successful PDF; +- analysis: source revision, run receipt, artifact hash, selected/current run, + and promoted result capsule; and +- compute candidate: submitted code hash, source buffer state/revision, + append-only display facts, and content-addressed resources. + +The shared opportunity is a small revision/currentness vocabulary and a +dependency-edge contract used by presentation and future staleness graphs. +The source owner must still decide what a change means. A dirty editor buffer, +a failed LaTeX build, an outdated MATLAB figure, and an evicted generated PDF +cannot share one state machine merely because all can be called `stale`. + +### F5. Execution has a proven low-level core; its three product lifecycles should remain siblings + +`@scientfactory/execution` and `apps/server/src/scient/execution/LocalExecutionProcess.ts` +already provide a no-shell process port, output stream, exit observation, and +process-tree cancellation. Both the MATLAB analysis service and the real LaTeX +build service consume that foundation. This is a genuine shared layer, not a +future abstraction. + +Above it, preserve separate product records: + +| Product object | Lifecycle that makes it distinct | +| ---------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | +| `AnalysisRun` | Bounded run action against a saved source revision; runtime profile; stdout/stderr; diagnostics; run-owned artifacts; history and promotion. | +| `DocumentBuild` | Resolved document root and dependencies; coalescing/supersession; compiler passes; diagnostics; last successful render; source-output navigation. | +| `ComputeSession` | Persistent language namespace; generation; queued executions; interrupt/restart; variables; submitted code; append-only rich display facts. | + +Share process control, normalized diagnostic primitives, bounded output/resource +transport, cancellation language, and base provenance only where the existing +consumers agree. A future execution coordinator may emerge from repeated +server orchestration, but neither LaTeX nor compute should depend on +`AnalysisService`, and no universal `Task` should erase specialized receipts. + +PR #129 should be reviewed as an in-flight foundation integration, not rebuilt +from its feature labels. Its `languageId`/`transportKind` separation, durable +request/result split, source buffer truth, and Jupyter-compatible but Scient- +owned representation bundles are sound directions. The integration decision +must reconcile current main's MATLAB/AnalysisRun and result presentation rather +than keeping two long-term MATLAB execution authorities. + +### F6. Representation selection can share a vocabulary without sharing artifact identity + +Current code has: + +- generated PDF descriptors and immutable document revisions; +- analysis artifacts with `static`/`interactive`/`native` representations; +- static artifact surface descriptors; +- chat fence renderer aliases; +- compute candidate MIME bundles and surface-owned priority selection; and +- resource URLs whose expiry never defines identity. + +These are enough real consumers to justify a common representation descriptor +and renderer-capability vocabulary. They are not enough to justify one +artifact database. The shared layer should describe media type, content or +resource identity, byte bounds, interactivity, fidelity, required capability, +fallback, and selected presenter. Producer-specific provenance, revisions, +retention, and staleness stay with generated documents, analysis, compute, +Sources, or Studio. + +### F7. Verified installation is repeated enough for a focused extraction spike + +Provider runtimes, Whisper models, TinyTeX, SyncTeX staging, and whisper.cpp +staging independently implement combinations of: + +- compile-time manifests and exact target selection; +- bounded HTTPS/redirect policy; +- expected size and digest verification; +- private staging and partial-download handling; +- archive traversal/link/duplicate/expansion defenses; +- required-file or magic-header checks; +- smoke tests and executable permissions; +- atomic activation and last-known-good preservation; +- interruption, superseded-root cleanup, receipts, and diagnostics. + +The duplication is real, but the managers should remain separate: provider +selection includes credentials and runtime instances; voice installs large +resumable single-file models and coordinates a helper; TinyTeX performs +collections and package repair; build-time native staging produces release +assets rather than user-installed state. + +Run a focused extraction spike for lower-level verified-asset primitives only. +Characterize the current threat and cancellation tests first. A neutral package +may own URL policy, streamed bounded download, digest/size verification, safe +archive extraction, receipt generation, and atomic directory activation. Each +domain should retain its manifest schema, selection, progress language, smoke +contract, credentials, repair, and removal semantics. Do not make LaTeX or +voice depend on a package named for providers. + +### F8. Derived-state retention and cleanup need one operating contract, not one store + +The generated-document store has bounded revision/byte retention and protects +active bindings. Analysis has explicit metadata-preserving cleanup and no +automatic deletion. LaTeX documents known orphan risks for build directories, +evidence, and SyncTeX indexes. Provider/TinyTeX installers clean superseded +roots under their own rules. Queue files are deleted with the last item and +quarantined on corruption. + +Create a common operational contract for every server-derived state owner: + +- authoritative versus rebuildable contents; +- measured bytes and item counts; +- automatic versus user-confirmed retention; +- pin/lease/protection rules; +- safe sweep and orphan reconciliation; +- corruption and partial-recovery behavior; +- project/worktree identity and deletion semantics; and +- user-visible storage summary and cleanup receipts. + +Do not put all state into one database or one directory. A shared storage +dashboard and cleanup operation may coordinate owners while each owner keeps +its correct store and retention policy. + +### F9. Provider lifecycle is a recent successful unification — do not restart it + +The provider program already replaced provider-by-provider UI and operation +duplication with shared connection/runtime managers, a coordinator, truthful +capabilities, transient overlays, strict verification, a common setup host, +and provider-specific policy adapters. PR #150 is the integration parent. + +The architecture review should therefore focus on evidence gaps, action +currentness, target qualification, and upstream conflict cost—not on another +generic provider framework. Draft PR #179 is planning for safe managed updates +and must be reconciled with current manifests and the landed manager before it +can become direction. + +### F10. Thread queue separation is deliberate technical debt with an exit path + +The queue is not an accidental failure to use orchestration. It intentionally +stores pending composer payloads outside thread events so a later T3-native +queue can replace it without event migration. Its hashed filenames, atomic +writes, limits, quarantine, serialized mutation lanes, and explicit dispatch +acknowledgement are proportionate. + +Keep the current boundary while monitoring upstream. Architecture work should +not generalize this store into a universal work queue or silently steer queued +messages. Its maintenance document already contains a complete retirement +procedure. + +## Architecture Disposition Ledger + +| Finding | Disposition | Confidence | Decision or proof required | +| ------------------------------------------------------------------------- | ---------------------------------------------- | ----------: | ---------------------------------------------------------------------------------------------- | +| Literal T3 ancestry, fetch-only upstream, and protected seams | Keep | High | Continue exact-range upstream receipts and hostile-merge rehearsal. | +| Shared `.scient/project.json` identity reader | Keep/formalize | High | Decide proposed ADR-0006 before new canonical namespaces. | +| Sources as project-owned records | Keep separate | High | Accept/revise source-store architecture; add sync/conflict design only when required. | +| Skills activation/trust/turn snapshots | Keep separate | High | Add invocation receipts only through an accepted operation/provenance path. | +| Direct/workspace file identity and presentation dispatch | Unify incrementally | High | Accept a focused file-foundation slice and migration fixtures. | +| Viewer titles, freshness, failure, retry, locate, save/copy, reveal | Unify in shared shell | High | Prove no regression across editor, PDF, HTML, image, media, remote, and RTL cases. | +| Generated document, analysis artifact, compute representation descriptors | Unify vocabulary only | Medium-high | Define a minimal media/resource/capability contract against real producers. | +| `AnalysisRun`, `DocumentBuild`, `ComputeSession` | Keep as siblings | High | Reconcile PR #129 with mainline analysis before integration. | +| No-shell process control and tree cancellation | Keep/extract where already shared | High | Preserve current `@scientfactory/execution` and local process adapter tests. | +| Higher-level execution coordinator | Defer/selectively extract | Medium | Require repeated orchestration across at least two real product lifecycles. | +| Scient operation envelope | Implement focused core | High | Produce actor/project/capability/idempotency/effect-receipt proof before agent effects expand. | +| Provider lifecycle managers and setup host | Keep; simplify locally | High | Reconcile current proposals and close target/live qualification gaps. | +| Verified download/extract/activate mechanics | Investigate lower-level extraction | Medium-high | Side-by-side threat, cancellation, restart, and rollback characterization. | +| Derived-state retention and cleanup | Unify operating contract | High | Inventory all state owners; design measured cleanup and receipts without one universal store. | +| Rich-fence registry | Keep and extend as presentation adapter family | High | Keep authored source canonical and streaming fallback readable. | +| Right-panel Scient surface registry | Extend toward shared presentation identity | High | Migrate path-based IDs through compatibility decoding. | +| Quick Chat | Retire | High | Preserve only migration/provenance/immutable decoding requirements. | +| Thread queue | Keep with retirement trigger | High | Replace only after qualified T3-native behavior and data handoff. | +| Wholesale desktop or scientific-core rewrite | Defer/reject on current evidence | High | No authority failure currently justifies it; use focused traces and migrations. | +| Separate Scient core repository/service now | Defer | High | Require a real independent consumer, release, security, deployment, or operational lifecycle. | + +## Deliberate Boundaries That Must Not Be “Simplified” Away + +1. T3 host state versus Scient scientific truth. +2. Project identity versus environment, thread, provider session, worktree, or + absolute path identity. +3. Mutable ordinary files versus immutable source attachments. +4. Source records versus citation strings, extracted metadata, or Zotero + records. +5. Generated document revisions versus analysis artifacts and Studio + compositions. +6. `AnalysisRun` versus `DocumentBuild` versus `ComputeSession`. +7. Provider enablement, runtime health, authentication, entitlement, + readiness, and operation state. +8. Skill availability, activation, trust, selection, loading, invocation, and + authority. +9. Authored chat fence source versus its disposable rendered card. +10. Manual UI, provider transport, external MCP, and automation ingress versus + the common Scient operation semantics they should call. +11. Public product help versus internal capability, architecture, roadmap, + evidence, and upstream records. +12. Current main versus open PR, local candidate, proposed plan, retired code, + and historical evidence. + +## Open-Source And External-Source Architecture Map + +| Source | Current use or evidence | Scient-owned boundary | +| ----------------------------------------- | ------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | +| T3 | Maintained Electron/React/Effect host, provider sessions, threads, files, Browser, release/runtime foundation | Git ancestry and generic host only; Scient owns product, scientific records, privacy, release, and accepted divergence. | +| Effect | Typed schemas, services, layers, streams, process/filesystem primitives | Implementation substrate; does not define scientific domain records or authority. | +| PDF.js 6.2.108 | Local PDF parse/render/search/outline/range validation and generated-PDF structural qualification | Scient owns source descriptors, authorization, reader sessions, save/copy, freshness, and product quality. | +| whisper.cpp 1.9.1 | Local speech inference helper and pinned native runtime | Scient owns model manifest, download/verification, lifecycle, IPC, cancellation, privacy boundary, and optional correction flow. | +| KaTeX and remark-math | Local mathematical parsing/rendering | Scient owns delimiter policy, safety bounds, fallback, source copy, streaming behavior, and mobile boundary. | +| Mermaid | Local diagram renderer | Scient owns settled-fence gating, sanitization, resource limits, source/error states, export, and identity rebasing. | +| Vega, Vega-Lite, vega-embed, vega-tooltip | Declarative chart runtime | Scient owns schema/value bounds, CSP-safe expression path, network labeling, lifecycle, export, and renderer activation. | +| Plotly strict and MathJax | Broad interactive chart rendering and labels | Scient owns trace/value/frame bounds, WebGL pool, mutation queue, network disclosure, export, and failure fallback. | +| Zotero local API | Read-only local intake adapter | Scient source schema, project record identity, duplicate decisions, provenance, and notes remain canonical. | +| NCBI E-utilities, Crossref, Europe PMC | Exact-identifier metadata enrichment | Only exact identifiers leave the project; responses are bounded evidence and never overwrite stronger source/user truth. | +| parse5 | Bounded HTML/abstract parsing | Provider markup is normalized into Scient's plain-text/section source representation. | +| Citation.js, citeproc, CSL styles | Derived citation formatting | Rendered references are not persisted as source truth. | +| MATLAB | First external analysis engine | Scient owns discovery/verification, process safety, source revision, run receipt, artifacts, history, and result promotion. | +| `latexmk`, Tectonic, TinyTeX | Replaceable local typesetting engines/distribution | Scient owns root resolution, build lifecycle, dependency evidence, diagnostics, last-success publication, and managed-install consent. | +| SyncTeX and zlib | Exact-revision source/PDF navigation helper | Scient pins, builds, receipts, packages, confines, and refuses stale or unsafe navigation. | +| Jupyter protocol and MIME conventions | In-flight compute transport/representation compatibility | PR #129 keeps language, transport, session, durable records, resources, authority, and retention Scient-owned. | +| Agent Skills specification | Portable skill document shape | Scient owns reviewed release metadata, exact digest/origin, project trust, activation, per-turn delivery, and capabilities. | + +These are adaptation inputs and replaceable engines, not a single dependency +stack to expose as product authority. Future source maps should record exact +versions, commits, licenses, receipt paths, evaluation dates, and the boundary +between adopted code, adapted pattern, protocol compatibility, and research +reference. + +## Architecture Evolution Timeline + +| Period | Foundation evolution | Long-term interpretation | +| ------------------- | ---------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | +| 2026-08-06 to 08-09 | Literal T3 bootstrap, Scient identity/isolation/release guards, safe project initialization, durable fork, local voice | Established the thin-fork and project-boundary pattern before scientific breadth. | +| 2026-08-10 to 08-14 | Sources, PDF, universal opening, analysis/MATLAB, generated artifacts, math, LaTeX, diagrams, Vega, Plotly | Added several strong vertical slices, each correctly owning domain behavior but creating horizontal presentation/currentness pressure. | +| 2026-08-15 to 08-23 | Repeated T3 refreshes, file/image/browser convergence, release cutover, onboarding, provider additions | Proved that marked seams and owned modules can survive upstream movement; also exposed duplicated provider and viewer dispatch. | +| 2026-08-24 to 08-27 | Provider lifecycle integration, skills core/project skills, queue, SyncTeX, file/PDF freshness | Provider duplication was intentionally unified; currentness and trust became explicit cross-cutting concerns. | +| 2026-08-28 | T3 alignment through `c8aba2587d`, file/document/artifact planning alignment, capability/Markdown/architecture audits | The correct next step is selective foundation work with accepted boundaries, not feature replay or wholesale rewrite. | + +## Recommended First-Principles Review Order + +### 0. Stabilize documentation authority + +Accept or revise the documentation-system proposal, then run its three logical +pilots without a mass move. Promote the forensic capability/divergence/PR +reports into the appropriate permanent records only after current/open/retired +status and source anchors are refreshed against `d5ff08e7` and PR #188. + +### 1. Trace file/resource/presentation end to end + +Use at least these workflows: + +- open the same workspace file from tree and chat; +- open an external or remote-environment file; +- rename/move/delete/recreate and resolve ambiguity; +- edit while an external write arrives; +- open PDF, interactive HTML, image, Markdown/math, unknown binary, and a + generated PDF; +- lose/renew an asset URL and restart the app; and +- preserve RTL title, view state, last success, and recovery actions. + +If the trace supports the current proposal, accept a focused ADR/slice for +`FileReference`, relocation, the static registry, and the viewer shell. This +has the highest roadmap leverage across Documents, Computing, and Artifact +Studio. + +### 2. Implement the smallest operation-authority proof + +Choose an existing manual operation with a real project mutation—such as a +source note update—plus a read. Route manual and one agent-facing call through +the same host-resolved envelope and effect receipt. Prove revocation, +idempotency conflict, stale expected version, retry, and receipt redaction. +Do not broaden external MCP or automation authority in the same slice. + +### 3. Reconcile execution before integrating PR #129 + +Map mainline MATLAB `AnalysisRun`, LaTeX `DocumentBuild`, and candidate +`ComputeSession` against: + +- project/source identity; +- adapter/runtime identity; +- process and cancellation ownership; +- event/output/diagnostic vocabulary; +- artifact/representation identity; +- storage, cleanup, recovery, and promotion; +- operation actor/provenance; and +- UI Results and figure-following surfaces. + +Decide which MATLAB behavior moves into or consumes the compute foundation, +which analysis-run behavior remains for isolated reproducible runs, and how +project results link both. Avoid two long-term MATLAB authorities. + +### 4. Characterize verified-install duplication + +Compare provider runtime, Whisper model, TinyTeX, and native staging threat +models and tests. Extract only the lower-level primitives whose cancellation, +rollback, archive, progress, and receipt behavior can be represented without +domain conditionals. + +### 5. Define derived-state storage operations + +Inventory actual bytes and cleanup/recovery behavior for analysis, LaTeX, +document artifacts, compute candidate, provider runtimes, voice models, queue, +and caches. Design one storage summary and cleanup coordination contract while +leaving each store authoritative for its own data. + +### 6. Review provider and thread foundations only for measured pain + +Provider lifecycle is newly unified and the queue has an explicit retirement +plan. Revisit them only for a reproduced root-cause failure, repeated upstream +conflict, unsupported provider state, or qualified T3 replacement. + +## Required Evidence Before Any Rebuild + +A foundation should not be replaced or extracted without: + +1. a current workflow trace and source-of-truth diagram; +2. the exact authority, lifecycle, data, and T3 seams being changed; +3. at least two real consumers for a proposed shared foundation; +4. a concrete failure, duplication, maintenance, security, or roadmap cost; +5. preserved behavior and explicit intended behavior changes; +6. data/state compatibility, migration, rollback, and cleanup plans; +7. focused contract, adversarial, restart, cancellation, and upstream-merge + tests; +8. current/open/retired documentation updates in the owning repositories; and +9. an accepted ADR when the change is hard to reverse or establishes durable + authority. + +A clean package graph or shorter file list is not enough. The target must make +authority, recovery, provenance, upstream maintenance, and future workflows +better. + +## Documentation Consequences + +The proposed long-term capability record should make this map maintainable +without preserving this dated report as a hand-edited registry. Each current +capability page should state: + +- user-visible behavior and limitations; +- current/open/retired status and release availability; +- authoritative state and lifecycle owner; +- primary packages/services/surfaces and narrow inherited T3 mounts; +- operations, permissions, failure, cancellation, retry, recovery, retention, + and privacy behavior; +- open-source/adapted sources and exact provenance route; +- verification evidence and unqualified platforms/scenarios; +- related architecture decisions, proposals, roadmap stages, and retirement + triggers; and +- update triggers naming which code/contract/PR changes require the page to be + reviewed. + +Architecture pages should own shared foundations, not repeat feature manuals. +Public Scient Docs should explain how to use released behavior and recover +from failure, not expose internal package topology. Roadmaps should link to +current capability records instead of repeating large current-state snapshots. +Upstream receipts should record each integration range and conflict decision +without becoming permanent capability descriptions. + +The [documentation-system proposal](../../planning/scient-documentation-system-and-publishing.md) +and [Markdown audit](./documentation-system-markdown-audit-2026-08-28.md) +define how those owners should be classified, published, indexed, and kept +current across repositories. + +## Review Conclusion + +Scient's current architecture is not fundamentally misaligned. The strongest +foundations—thin-fork governance, project identity, Sources, skills trust, +provider lifecycle, generated document revisions, PDF presentation, and the +low-level execution process boundary—should be preserved. + +The evidence does justify focused foundation work in four places: + +1. file identity, relocation, presentation selection, and the shared viewer + shell; +2. the accepted but not yet implemented Scient operation-authority envelope; +3. execution/representation reconciliation before stateful compute merges; and +4. lower-level verified-install plus derived-state lifecycle primitives after + focused characterization. + +It does not justify a wholesale desktop rewrite, one universal scientific +object, one universal lifecycle manager, a new Scient core repository, or +rebuilding current providers, Sources, skills, PDF, LaTeX, or analysis from +zero. The intelligent path is to preserve the vertical slices that already +prove product value, make their common seams explicit, and migrate one +foundation at a time behind compatibility and recovery gates. + +## Completeness And Re-Review Record + +The final coverage pass must continue to prove: + +- all 39 mapped catalog items—38 named capability subsections plus the + cross-cutting security/reliability family—appear exactly once in the + numbered map; +- current, integration-only, retired, proposed, and disabled states are not + collapsed; +- the `aa23f1d3..d5ff08e7` desktop delta and merged PR #189 are reconciled; +- open PRs #121, #129, #179, and #188 remain non-current; +- project files, source records, generated documents, analysis artifacts, + build records, and compute sessions remain distinct authorities; +- every cited desktop path exists at its stated main or candidate revision; +- accepted ADRs, proposed ADR-0006, and planning proposals retain their actual + authority status; +- no scient-agent Markdown or source was inspected or classified; and +- recommendations remain evidence and require separate acceptance and change + authorization. From fc45cf91ee4cbcee7e1e12fce9f50a0d8e448ced Mon Sep 17 00:00:00 2001 From: Yaacov Date: Fri, 28 Aug 2026 16:18:28 +0300 Subject: [PATCH 2/5] docs: repair audited metadata anomalies --- lab/external/upstream-reviews/2026-08-22-scient-desktop-t3.md | 4 ++++ lab/notes/first-slice-source-trace-2026-07-18.md | 3 ++- lab/notes/t3-code-targeted-review-2026-07-18.md | 3 ++- 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/lab/external/upstream-reviews/2026-08-22-scient-desktop-t3.md b/lab/external/upstream-reviews/2026-08-22-scient-desktop-t3.md index 9f1b1c7..5ef10cb 100644 --- a/lab/external/upstream-reviews/2026-08-22-scient-desktop-t3.md +++ b/lab/external/upstream-reviews/2026-08-22-scient-desktop-t3.md @@ -2,6 +2,10 @@ Status: Accepted Owner: Yaacov +Created: 2026-08-22 +Last updated: 2026-08-22 +Purpose: Records the accepted bounded T3 upstream review, exact integration range, owned merge, protected Scient seams, and qualification evidence through dedcd99a9d. +Doc type: Research evidence Reviewed at: 2026-08-22 Reviewed through: `dedcd99a9d16240327ce763b885b326aff607bdb` Integration base: `dedcd99a9d16240327ce763b885b326aff607bdb` diff --git a/lab/notes/first-slice-source-trace-2026-07-18.md b/lab/notes/first-slice-source-trace-2026-07-18.md index 04d38f9..eeb8517 100644 --- a/lab/notes/first-slice-source-trace-2026-07-18.md +++ b/lab/notes/first-slice-source-trace-2026-07-18.md @@ -1,11 +1,12 @@ # First Scientific Slice Source Trace -Status: Complete as source evidence; memory and package architecture not selected +Status: Historical Owner: Yaacov Created: 2026-07-18 Last updated: 2026-07-18 Purpose: Maps the first scientific slice's current source seams and proven gaps without selecting memory layers, persistence technology, or permanent product architecture. Doc type: Implementation evidence +Completion: Complete as source evidence; memory and package architecture not selected ## Verdict diff --git a/lab/notes/t3-code-targeted-review-2026-07-18.md b/lab/notes/t3-code-targeted-review-2026-07-18.md index bf284d8..d5df881 100644 --- a/lab/notes/t3-code-targeted-review-2026-07-18.md +++ b/lab/notes/t3-code-targeted-review-2026-07-18.md @@ -1,11 +1,12 @@ # T3 Code Targeted Review -Status: Complete +Status: Historical Owner: Yaacov Created: 2026-07-18 Last updated: 2026-07-18 Purpose: Records the bounded T3 Code inspection, accepted reliability intake, and explicit stop boundary for future T3-derived work. Doc type: Research evidence +Completion: Complete through the recorded donor revision and accepted reliability intake ## Verdict From fbac4a473b870f43662905a1443a439da56ee197 Mon Sep 17 00:00:00 2001 From: Yaacov Date: Fri, 28 Aug 2026 16:27:56 +0300 Subject: [PATCH 3/5] docs: promote documentation governance --- AGENTS.md | 18 +++++ docs/README.md | 1 + docs/documentation-policy.md | 72 +++++++++++++++++++ docs/operations/team-contribution-protocol.md | 21 +++++- ...ent-documentation-system-and-publishing.md | 9 +++ 5 files changed, 119 insertions(+), 2 deletions(-) diff --git a/AGENTS.md b/AGENTS.md index f825342..e379004 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -106,6 +106,13 @@ Optimize for long-term quality. Prefer the correct, maintainable solution even w Place documentation deliberately. Before creating a new document, decide where the information belongs in the existing documentation structure. Prefer updating the canonical existing document over creating a duplicate. If a new document is needed, give it the required metadata and link it from the relevant index. +Use the nearest authoritative repository and classify the fact by the question +it answers: Help, Capabilities, Architecture, Development, Operations, +Upstream, Product/Planning/Research, or Records. These are logical roles, not a +requirement to rename inherited folders. Current app Help belongs in +`scient-desktop/docs/user/`; the website renders approved, version-aware Scient +Docs from that source instead of owning a second prose copy. + Capture durable future context, not documentation volume. Preserve consequential decisions, constraints, interfaces, evidence, hard-won lessons, and repeated explanations. Do not promote every chat, meeting, transcript, or generated summary into repository knowledge. AI may draft documentation, but it is not the accountable owner and cannot confer acceptance. Preserve uncertainty and specific reasoning for human review. When authoritative sources conflict, surface the contradiction and route it to the owning person or document instead of smoothing it into false agreement. @@ -118,6 +125,10 @@ Current important documents: - `docs/README.md` - documentation map and current repo structure. - `docs/documentation-policy.md` - rules for creating, updating, and classifying documentation. +- `docs/planning/scient-documentation-system-and-publishing.md` - accepted + documentation-system decisions, implementation sequence, pilot gates, and + deferred choices; durable recurring rules live in the policy and repository- + local guidance rather than in that plan. - `docs/product/PRD.md` - product direction, core capabilities, user experience principles, and technical requirements. - `docs/product/skills-system.md` - draft product model, trust boundaries, candidate catalog, and validation order for reusable scientific skills; the @@ -167,6 +178,13 @@ Be honest about the repo's maturity. Do not describe planned architecture as imp When adding documentation, prefer clear current-state wording over polished but vague language. +For the same capability, update existing durable owners as implementation lands +gradually. Keep scratch, transcripts, temporary checklists, and handoffs outside +the worktree or in the owning GitHub item. Create a new durable file only when +it answers a distinct lasting question with a clear owner, evidence boundary, +update trigger, and index route. In every pull request, include the concise +`Documentation impact` declaration defined by the team contribution protocol. + If a document is useful now but does not yet have an obvious permanent home, it may be left in the repo temporarily. Later, as the repo architecture settles, documents should be moved into the right structure. When moving or reorganizing documents, preserve their intent and history. Do not delete planning material just because it is rough. diff --git a/docs/README.md b/docs/README.md index 400b883..c9abc51 100644 --- a/docs/README.md +++ b/docs/README.md @@ -26,6 +26,7 @@ Start here: - [Collaborator onboarding](onboarding.md) - ordered project journey, repository tour, and contribution-area reading routes. - [Documentation policy](documentation-policy.md) - documentation rules, metadata, statuses, and placement policy. +- [Scient documentation system and publishing](planning/scient-documentation-system-and-publishing.md) - accepted repository-family authority, public Docs direction, implementation sequence, pilot gates, and deferred choices; recurring rules are promoted into the documentation policy and repository-local guidance. - [Product requirements](product/PRD.md) - canonical product direction. - [Scient skills system](product/skills-system.md) - draft product model, trust boundaries, candidate catalog, and validation order for reusable scientific diff --git a/docs/documentation-policy.md b/docs/documentation-policy.md index eed2b69..459809c 100644 --- a/docs/documentation-policy.md +++ b/docs/documentation-policy.md @@ -118,6 +118,60 @@ A broader company memory may connect to Scient through links and shared conventi The current scope recommendation and unresolved structural choices live in `docs/planning/repository-scope-and-company-memory.md`. +## Repository-Family Authority + +Scient documentation uses the nearest authoritative owner across independent +repositories: + +- `Scient` owns product truth, philosophy, cross-product architecture and + decisions, roadmaps, cross-repository operations, research, and this family + policy; +- `scient-desktop` owns current desktop Help, implementation capability and + architecture records, development guidance, runbooks, and T3 divergence; +- the website owns Docs rendering, navigation, search, deployment, and the + exact source/version it publishes; and +- `scient-agent` joins this model only when native Scient-agent implementation + begins. Its current inherited starting repository is outside the present + documentation migration. + +Repositories remain independent. A cross-repository consequence uses a +separate, explicitly ordered dependent pull request; matching branch names do +not establish dependency or authority. Each public repository must state the +minimum local rule a contributor needs without requiring access to this +repository or copying private planning authority. + +Current desktop product help is authored under `scient-desktop/docs/user/`. +The public **Scient Docs** website at `/docs` publishes a reviewed, +version-aware selection from that source; the website must not maintain a +second prose copy. Website documentation can be corrected and deployed without +an app release, but stable pages must remain truthful about the app versions +and behavior they describe. A future documentation MCP, if justified, must +retrieve this same corpus rather than become another authored authority. + +## Documentation Roles + +Classify durable knowledge by the question it answers, not by a vague audience +label or a required folder name: + +- **Help** explains how people and support agents use released behavior. +- **Capabilities** records what implementation exists, its limits, maturity, + source anchors, evolution, and related plans. +- **Architecture** owns authorities, boundaries, invariants, dependencies, and + hard-to-reverse decisions. +- **Development** owns build, test, configuration, contributor, and debugging + guidance. +- **Operations** owns release, deployment, migration, monitoring, support, and + recovery procedures. +- **Upstream** owns donor ancestry, protected divergences, conflicts, and + selective-intake decisions. +- **Records** preserves useful historical evidence, superseded plans, + retirements, and delivery context without governing current behavior. + +These are logical roles. Repositories may retain inherited paths such as +`docs/user/` and `docs/internals/` when moving files would add merge or link +cost without improving authority. Repository indexes map the logical role to +the real current path. + ## Knowledge Selection Rules Create durable documentation when it will provide future context: an important decision and its reasoning, a durable principle or constraint, an owned interface or process, source-backed research, a hard-won lesson, a repeated explanation, or knowledge at real risk of disappearing. @@ -126,6 +180,24 @@ Do not preserve every meeting, chat, transcript, task trace, or generated summar Documentation volume is not a quality measure. Prefer a small coherent knowledge system over a large archive that obscures authority. +Update an existing durable owner before creating a new file. Feature work often +lands in slices; later slices update the same capability, Help, or architecture +owner when its truth changes rather than creating one document per pull +request, milestone, component, or implementation phase. + +Create a new durable document only when the knowledge remains useful after the +pull request, no existing owner can hold it coherently, it answers a distinct +durable question, its repository/status/evidence/update trigger are clear, and +the appropriate index can route to it. Ordinary feature scratch, transcripts, +session handoffs, temporary checklists, and active progress belong outside the +worktree or in the owning GitHub work item. The merged pull request is the +implementation record. + +An ordinary bounded change should normally update zero to two primary owners. +More may be correct for privacy, architecture, retirement, upstream, or broad +program changes, but should trigger an ownership review rather than automatic +fan-out or omission. + ## Evidence Rules Durable factual claims should be grounded in one of: diff --git a/docs/operations/team-contribution-protocol.md b/docs/operations/team-contribution-protocol.md index bce5536..bb3a0ff 100644 --- a/docs/operations/team-contribution-protocol.md +++ b/docs/operations/team-contribution-protocol.md @@ -3,7 +3,7 @@ Status: Active Owner: Yaacov Created: 2026-07-22 -Last updated: 2026-07-27 +Last updated: 2026-08-28 Purpose: Defines the minimum shared workflow and verification evidence for contributions across maintained ScientFactory repositories. Doc type: Operational procedure @@ -71,6 +71,22 @@ Use separate pull requests for separate repositories. Cross-repository work must state its dependencies and landing order rather than relying on matching branch names. +Every implementation or documentation pull request must make its documentation +impact explicit in one concise declaration: + +```text +Documentation impact: None — +Documentation impact: Updated — +Documentation impact: Dependent PR — +``` + +Use one line, choosing the applicable form. `None` requires a real reason, not +silence. `Updated` points to the existing owners changed with the work. A +genuine cross-repository consequence uses `Dependent PR` and states the landing +order; do not copy the same prose into both repositories. This trial remains +deliberately smaller than a taxonomy checklist and should grow only if repeated +failures prove another field is needed. + ## Verification Standard Verification must match the behavior and risk being changed. Passing a broad @@ -222,7 +238,8 @@ should make these facts easy to find: - Quality Review findings and dispositions; - Integration Readiness Review verdict and remaining findings; - known limitations or deferrals; and -- cross-repository, deployment, migration, or release impact. +- cross-repository, deployment, migration, or release impact; and +- the concise documentation-impact declaration above. Small changes may answer briefly. Evidence should be proportional, not omitted or padded with irrelevant ceremony. diff --git a/docs/planning/scient-documentation-system-and-publishing.md b/docs/planning/scient-documentation-system-and-publishing.md index 3d7b88a..46a94b0 100644 --- a/docs/planning/scient-documentation-system-and-publishing.md +++ b/docs/planning/scient-documentation-system-and-publishing.md @@ -22,6 +22,15 @@ Until each rule is promoted into its durable owner, the current [Documentation Policy](../documentation-policy.md), repository AGENTS.md files, and area indexes remain operationally authoritative. +Phase 1 promotes recurring rules into the [Documentation +Policy](../documentation-policy.md), [Team Contribution +Protocol](../operations/team-contribution-protocol.md), and repository-local +agent, contributor, index, work-artifact, and pull-request surfaces. After those +dependent changes land, use those owners for recurring decisions. This accepted +planning note remains the implementation roadmap and decision record for the +inventory, pilots, publishing proof, migration, and automation phases; it does +not compete with the promoted policy. + Current product behavior belongs beside the implementation that provides it. Product direction and cross-product planning belong in this Scient repository. Website deployment remains owned by the website repository. From dcab07f391360f682def149882a551d5664be818 Mon Sep 17 00:00:00 2001 From: Yaacov Date: Fri, 28 Aug 2026 16:39:07 +0300 Subject: [PATCH 4/5] docs: add documentation inventory foundation --- docs/README.md | 4 + docs/planning/README.md | 3 + ...mentation-disposition-ledger-2026-08-28.md | 143 +++++++ docs/product/README.md | 3 + docs/product/scient-capability-map.md | 70 ++++ docs/research/README.md | 9 + scripts/generate-documentation-inventory.mjs | 353 ++++++++++++++++++ .../generate-documentation-inventory.test.mjs | 77 ++++ 8 files changed, 662 insertions(+) create mode 100644 docs/planning/documentation-disposition-ledger-2026-08-28.md create mode 100644 docs/product/scient-capability-map.md create mode 100644 scripts/generate-documentation-inventory.mjs create mode 100644 scripts/generate-documentation-inventory.test.mjs diff --git a/docs/README.md b/docs/README.md index c9abc51..11bffce 100644 --- a/docs/README.md +++ b/docs/README.md @@ -32,6 +32,9 @@ Start here: boundaries, candidate catalog, and validation order for reusable scientific skills; honor its Draft status, and use the accepted PRD to govern conflicts. - [Scient product identity](product/scient-product-identity.md) - accepted company, app, native-agent, external-agent, and naming vocabulary. +- [Scient capability map](product/scient-capability-map.md) - compact routing + from stable cross-product capability families to current implementation, + Help, architecture, roadmap, and dependency owners. - [Product philosophy](product/product-philosophy.md) - draft durable product principles; the accepted PRD governs conflicts. - [Technology stack](architecture/technology-stack.md) - current proposed stack direction. - [Idea inbox](planning/idea-inbox.md) - lightweight intake for unresolved ideas @@ -60,6 +63,7 @@ Start here: - [Design](design/README.md) - future home for product design principles and UI guidance. - [Quality](quality/README.md) - quality principles and testing philosophy. - [Planning](planning/README.md) - plans that guide upcoming work. +- [Documentation disposition ledger](planning/documentation-disposition-ledger-2026-08-28.md) - temporary reviewed migration dispositions and pilot/retirement gates for the generated Markdown inventory. - [Research](research/README.md) - external source evaluations, spikes, visual references, and raw or synthesized research. - [Development](development/README.md) - implemented contributor setup and future code, command, testing, and configuration documentation. diff --git a/docs/planning/README.md b/docs/planning/README.md index 0d4efa5..77b6925 100644 --- a/docs/planning/README.md +++ b/docs/planning/README.md @@ -15,6 +15,9 @@ Do not use planning docs as product truth, accepted architecture, or current imp Current planning docs: +- `documentation-disposition-ledger-2026-08-28.md` - temporary reviewed + migration disposition for every generated Markdown collection and named + exception, with preservation, pilot, deferment, and retirement gates. - `scient-documentation-system-and-publishing.md` - accepted cross-repository documentation authority; docs/user/-backed, release-qualified public Scient Docs publishing; internal capability and architecture structure; diff --git a/docs/planning/documentation-disposition-ledger-2026-08-28.md b/docs/planning/documentation-disposition-ledger-2026-08-28.md new file mode 100644 index 0000000..f4b89c3 --- /dev/null +++ b/docs/planning/documentation-disposition-ledger-2026-08-28.md @@ -0,0 +1,143 @@ +# Documentation Disposition Ledger — 2026-08-28 + +Status: Draft +Owner: Yaacov +Created: 2026-08-28 +Last updated: 2026-08-28 +Purpose: Records the reviewed migration disposition of existing Scient-family Markdown without turning the generated path inventory into a second documentation authority. +Doc type: Planning note + +## Document Rules + +This is a temporary migration authority. It reviews collections and named +exceptions against the exhaustive generated inventory. It does not authorize +bulk movement, deletion, public publication, or a claim that every document is +current. Preserve it until every in-scope collection has reached its durable +destination or an explicit retained state; then summarize any lasting +decisions in policy or the nearest owner and mark this ledger Historical. + +The generated companion +`docs/research/documentation-inventory-2026-08-28.generated.json` records every +tracked Markdown path, blob, title, exact repository revision, preliminary +logical role, and routing default. `scient-agent` is explicitly excluded and +was not inspected. + +## Disposition Vocabulary + +- **Retain** — the current path and role are durable. +- **Retain and maintain** — the path stays, but current truth must continue to + be reconciled as the product changes. +- **Qualify for publication** — canonical Help stays in `docs/user/`; a + reviewed, version-aware website view may publish it. +- **Route logically** — the current compatibility path stays while indexes + identify its logical role. +- **Historical or record** — preserve useful evidence but do not use it as + current guidance. +- **Structurally excluded** — keep the file for its source, fixture, or vendored + purpose; do not count it as authored product knowledge. +- **Generated view** — regenerate from owners; never hand-maintain a competing + prose copy. +- **Review exception** — a named file needs a specific correction, successor, + status, or later movement decision. + +No disposition silently deletes material. A later removal requires exact +target review, successor/history preservation where useful, link validation, +and ordinary PR authorization. + +## Reviewed Collections + +| Repository and collection | Logical owner and question answered | Primary dependency | Update trigger | Reviewed disposition | +| ----------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `Scient/docs/product/` | Product truth, philosophy, identity, and cross-product capability routing | Accepted PRD and explicit human acceptance | Product boundary, vocabulary, principle, or capability-family ownership changes | Retain and maintain. The capability map routes; it does not duplicate desktop implementation detail. | +| `Scient/docs/architecture/` | Cross-product architecture direction and accepted decisions | Product truth, implementation evidence, and decision status | Authority, invariant, hard-to-reverse boundary, or accepted decision changes | Retain. Do not promote proposals to accepted architecture implicitly. | +| `Scient/docs/planning/` | Roadmaps, implementation direction, intake, and historical migration plans | Product truth, capability map, research, and current implementation | Priority, sequencing, selected architecture, completion, supersession, or retirement changes | Retain with explicit status. Preserve historical and superseded plans with successors instead of flattening them into current truth. | +| `Scient/docs/research/`, `lab/external/` | Source evidence, evaluations, spikes, and raw external evidence | Inspected source and snapshot date | Source changes, adoption decision, invalidated evidence, or a new synthesis | Retain. Keep evidence separate from selected dependency or accepted architecture. Generated inventory lives here as audit evidence. | +| `Scient/docs/quality/`, `docs/development/`, `docs/operations/`, and `docs/design/` | Cross-product doctrine, contributor guidance, operations, and design principles | Real implementation, workflow, or accepted principle | Commands, gates, process, supported platform, or durable principle changes | Retain and maintain; placeholders must remain honest until the surface exists. | +| `Scient/lab/notes/` | Dated investigations and working records worth preserving | Snapshot evidence and a current successor when one exists | Record correction or promotion of a durable conclusion | Retain as records. Do not treat as policy or current implementation. | +| `Scient/skills/` and root orientation/protocol files | Repository-owned workflows and thin routing | Current repository paths and policy | Workflow, route, or contributor contract changes | Retain. Skills assist work but do not become product authority. | +| `Scient/docs/documentation-policy.md` and `docs/onboarding.md` | Family governance and collaborator development route | Accepted documentation system and current repository map | Documentation contract, authority, or onboarding route changes | Retain and maintain. Keep policy durable and onboarding navigational; neither replaces nearest owners. | +| `scient-desktop/docs/user/` | Canonical authored Help for released desktop behavior | Current supported release and implementation | User-visible behavior, limitation, setting, workflow, platform support, or correction changes | Retain and maintain; qualify each page for public Scient Docs through the temporary Help queue and later durable publication metadata. No copied website prose. | +| `scient-desktop/docs/internals/` | Mixed current capabilities, architecture, development, upstream context, and historical records | Current code, tests, `UPSTREAM.md`, and cross-product plans | Implementation, invariant, debugging workflow, T3 seam, or status changes | Route logically before moving. Keep compatibility paths through pilots; update existing owners before creating a new file. | +| `scient-desktop/docs/architecture/` | Desktop-specific architecture boundaries | Current desktop implementation and accepted architecture decisions | Renderer, authority, invariant, or hard-to-reverse implementation boundary changes | Retain and maintain. Keep this explicit architecture path; do not move it into mixed internals for symmetry. | +| `scient-desktop/docs/operations/` | Desktop runbooks and recovery procedures | Real commands, workflows, release paths, and service behavior | Operational process, command, platform, failure mode, or rollback changes | Retain and maintain. Historical rehearsals remain records with a clear label. | +| `scient-desktop/UPSTREAM.md` and dated upstream receipts in `docs/internals/` | T3 donor ancestry, protected divergences, conflicts, and reviewed integration evidence | Exact upstream and integration revisions | Upstream refresh, conflict resolution, protected-seam change, or divergence retirement | Retain. `UPSTREAM.md` is the current authority and routes to dated evidence; receipts remain records, not competing policy. | +| `scient-desktop/docs/reports/` | Dated forensic investigations and temporary migration records | Exact checkout/PR evidence and current durable successors | Factual correction, reconciliation, or completion of the migration purpose | Retain as records during this program. The three investigations become Historical evidence; temporary queues retire after their exit conditions. | +| `scient-desktop` package/source `README.md` files | Local development or component reference beside code | The owning package, source, command, or API | Local component behavior, setup, or contract changes | Retain beside source. Do not centralize merely for folder symmetry. | +| `scient-desktop/.agents/skills/` support Markdown and `.macroscope/` references | Repository-owned workflow and development-tooling guidance | The owning skill or check-run tool | Tool contract, fixture, convention, or validation behavior changes | Retain beside the workflow/tooling. Do not treat these files as product Help or architecture authority. | +| `scient-desktop/apps/marketing/tweets.md` | Dated product-communication material | Historical release/message context | Correction or explicit reuse | Retain as a record; it does not govern current product behavior. | +| Nested mobile-module `UPSTREAM.md` and `THIRD_PARTY_NOTICES.md` files | Local adaptation ancestry and third-party attribution | The owning adapted module, dependency, and license | Donor/dependency update, adaptation change, or attribution change | Retain beside source. Route nested upstream records as Upstream and notices as development references. | +| `scient-desktop/docs/fixtures/` | Markdown test inputs | Tests that consume them | Parser/rendering fixture requirement changes | Structurally excluded from authored documentation migration. | +| `scient-desktop/.repos/` Markdown | Vendored donor/reference material | Vendored source revision and license | Vendor refresh | Structurally excluded from Scient-authored totals and decisions; never rewrite as Scient documentation. | +| Website root governance and contributor Markdown | Website implementation, publishing, and deployment ownership | Website code and the selected docs source/version | Publishing architecture, build, deployment, or contribution contract changes | Retain and maintain in the website repository. | +| Website `docs/architecture/` | Website-specific architecture boundaries | Website implementation and accepted cross-repository publishing contract | Renderer, transport, source/version, deployment, or hard-to-reverse website boundary changes | Retain and maintain in the website repository; link to family policy without copying it. | +| Future website `/docs` content, indexes, and manifests | Public rendering, navigation, search, and exact source/version disclosure | Qualified `scient-desktop/docs/user/` source and independently deployable website | Help qualification, source revision, supported release, correction, or publishing failure | Generated or source-linked view only. Stable and preview truth must be explicit; rollback must not mutate canonical Help. | + +## Named Exceptions Already Reconciled + +- `scient-desktop/docs/internals/provider-lifecycle-unification-proposal.md` + is Historical delivery context. Current behavior belongs to + `provider-lifecycle.md`, `provider-lifecycle-capability-audit.md`, provider + Help, and current code. +- `scient-desktop/docs/internals/scient-fork-pr-descriptions.md` is Historical + PR wording for merged work. Current behavior belongs to + `scient-fork-divergence.md` and conversation-fork Help. +- `scient-desktop/docs/internals/scientific-artifact-studio.md` is a + superseded repository copy. The canonical proposed roadmap lives in + `Scient/docs/planning/scientific-artifact-studio.md`. +- `scient-desktop/docs/reports/scient-specific-capabilities.md`, + `scient-pr-and-evolution-ledger.md`, and + `scient-t3-divergence-integration-and-retirements.md` are dated forensic + evidence. They seed durable owners but must not become parallel living + manuals. +- `scient-desktop/docs/reports/scient-docs-help-qualification-queue-2026-08-28.md` + is temporary. It exits after every Help page has durable publication + metadata or a documented not-public disposition. +- The provider lifecycle plan in `Scient` remains Proposed product and + architecture direction; current desktop owners decide what is implemented. +- In-flight desktop PRs, including the draft `ComputeSession` foundation, are + not shipped truth. Plans may account for them explicitly without rebuilding + their accepted foundation or advertising them as current capability. + +## Migration Actions And Gates + +### Complete before broad normalization + +1. Generate and review the exact three-repository path inventory. +2. Complete the Help publication queue without rewriting all Help solely for + stylistic consistency. +3. Run three different pilots: Projects/Getting Started, Files/PDF/LaTeX, and + Providers. +4. In each pilot, prove nearest-owner updates, Help qualification, public + source/version metadata, cross-repository dependency handling, stale-page + correction, and rollback. +5. Record any repeated ambiguity. Promote only rules that proved necessary; + avoid role folders or metadata that do not solve a real maintenance problem. + +### Defer until the pilots prove value + +- broad movement out of inherited `docs/internals/` paths; +- final public information architecture for every Help page; +- a universal machine-readable document schema; +- additional mandatory feature templates or review bureaucracy; +- a documentation MCP; +- product architecture rebuilds or shared-infrastructure rewrites. + +The rest of the program does not wait: current truth repairs, governance, +inventory, capability routing, Help review, website publishing foundations, +and maintenance checks can proceed in this implementation goal. + +## Exit Review + +This ledger can retire only when: + +- the generated inventory has no unreviewed in-scope collection or named + exception; +- all Help pages have durable publication or not-public status; +- pilots have resolved the deferred structural choices; +- current indexes route every durable owner and useful historical record; +- links, metadata, and exact source/version publication checks pass; +- temporary queues have been removed or marked Historical with a successor; +- lasting rules have been promoted to policy, repository-local guidance, or + the nearest durable owner; and +- a final review confirms that no Scient-authored Markdown was lost, silently + reclassified as current, or confused with vendored T3 material. diff --git a/docs/product/README.md b/docs/product/README.md index 47c6fee..7b65f3b 100644 --- a/docs/product/README.md +++ b/docs/product/README.md @@ -12,6 +12,9 @@ Product truth belongs here. Current documents: - `PRD.md` - canonical product requirements and direction. +- `scient-capability-map.md` - compact cross-product map from stable Scient + capability families to current implementation, Help, architecture, roadmap, + and dependency owners; detailed behavior remains in the nearest repository. - `skills-system.md` - draft product model, trust boundaries, candidate catalog, and validation order for reusable scientific skills; the accepted PRD governs conflicts. diff --git a/docs/product/scient-capability-map.md b/docs/product/scient-capability-map.md new file mode 100644 index 0000000..14b0a64 --- /dev/null +++ b/docs/product/scient-capability-map.md @@ -0,0 +1,70 @@ +# Scient Capability Map + +Status: Draft +Owner: Yaacov +Created: 2026-08-28 +Last updated: 2026-08-28 +Purpose: Maps Scient's stable product-capability families to their nearest current implementation, documentation, architecture, roadmap, and dependency owners. +Doc type: Repo orientation + +## Document Rules + +This is the compact cross-product capability map. It owns stable family names +and routes collaborators to the nearest source of truth; it does not duplicate +feature behavior, claim that proposed work is shipped, or replace the detailed +desktop forensic record. Update it when a capability family is created, +retired, renamed, changes owning repository, or gains a different durable +documentation owner. Ordinary slices within an existing family update that +family's nearest owner instead. + +Current capability detail is implemented and maintained primarily in +`scient-desktop`. Product direction and future roadmaps live in `Scient`. +Public usage guidance is authored in `scient-desktop/docs/user/` and is +qualified separately for Scient Docs publication. `scient-agent` is outside +this map until native Scient-agent implementation begins. + +Evidence boundary: the family set is distilled from the 2026-08-28 +[desktop capability investigation](https://github.com/ScientFactory/scient-desktop/blob/main/docs/reports/scient-specific-capabilities.md), +including its reconciliation through desktop PR #190. Follow the linked +current owners for details and reverify against code when making architecture +or release decisions. + +## Capability Families + +| Stable capability family | Current implementation and detailed owner | Help | Product, architecture, or roadmap owner | Important dependency or boundary | +| ------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------- | +| Product identity, release, and isolated development | [`scient-desktop/UPSTREAM.md`](https://github.com/ScientFactory/scient-desktop/blob/main/UPSTREAM.md), release workflows, scripts, and [`docs/internals/scient-release-notes.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-release-notes.md) | [Install](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/install.md), [updating](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/updating.md) | [Product identity](scient-product-identity.md), [T3 migration record](../planning/t3-foundation-migration-plan.md) | T3 ancestry and protected seams remain explicit; stable and candidate state must stay isolated. | +| Project initialization and onboarding | [`scient-project-initialization.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-project-initialization.md), [`scient-onboarding.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-onboarding.md) | [Getting started](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/getting-started.md), [projects](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/projects.md) | [PRD](PRD.md) | Project creation must be safe, compact, and compatible with existing workspaces. | +| Conversations, forks, provider continuation, and projectless retirement | [`scient-fork-divergence.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-fork-divergence.md) | [Conversation forks](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/conversation-forks.md), [thread organization](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/thread-sidebar.md) | [PRD](PRD.md) | Fork continuity and projectless-thread retirement are separate behaviors; preserve provider/session semantics. | +| Provider lifecycle, authentication, managed runtime, awareness, and correction | [`providers.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/providers.md), [`provider-lifecycle.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/provider-lifecycle.md), [`scient-codex-runtime-auth.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-codex-runtime-auth.md) | [Providers](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/providers.md) and provider-specific pages | [Provider connection plan](../planning/provider-connection-and-lifecycle-experience.md), [model access evolution](../planning/model-access-and-routing-evolution.md) | Runtime, authentication, entitlement, enablement, readiness, advertised actions, and command acceptance are distinct states. | +| Local voice dictation | [`scient-voice.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-voice.md) | [Voice dictation](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/voice-dictation.md) | [PRD](PRD.md) | Local Whisper model lifecycle, privacy, and provider-specific correction are explicit boundaries. | +| Scient Skills | [`scient-skills.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-skills.md) | Capability guidance currently remains in the implementation owner pending a qualified Help page | [Skills system](skills-system.md) | Built-in, project-owned, and provider-delivered skills have different ownership, trust, digest, and invocation boundaries. | +| Sources, citations, and Zotero intake | [`scient-sources.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-sources.md) | [Sources](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/sources.md) | [PRD](PRD.md), [scientific document platform](../planning/scientific-document-platform-roadmap.md) | Local source authority, exact identifiers, metadata enrichment, citation formatting, and agent permissions must remain distinguishable. | +| Scientific chat rendering | [`scient-math.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-math.md), [`scient-chat-diagrams.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-chat-diagrams.md), [`scient-chat-visualizations.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-chat-visualizations.md), [`scient-chat-images.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-chat-images.md), and [`scient-content-direction.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-content-direction.md) | [Math](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/math-in-chat.md), [diagrams](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/diagrams-in-chat.md), [charts](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/charts-in-chat.md), [images](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/images-in-chat.md), [direction](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/content-direction.md) | [Scientific document platform](../planning/scientific-document-platform-roadmap.md), [Artifact Studio](../planning/scientific-artifact-studio.md) | Rich renderers need safe fallbacks, export/copy semantics, workspace-file authority, and BiDi correctness. | +| Universal file opening, presentation, freshness, and recovery | [`scient-universal-file-opening.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-universal-file-opening.md) | [File previews](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/file-previews.md) | [File/resource/presentation foundation](../planning/file-resource-and-presentation-foundation.md) | File identity, presentation selection, content freshness, relocation, and recovery are related but distinct layers. | +| PDF reading and browser PDF export | [`scient-pdf-reader.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-pdf-reader.md), [`scient-browser-pdf-export.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-browser-pdf-export.md) | [PDF reader](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/pdf-reader.md), [file previews](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/file-previews.md) | [Scientific document platform](../planning/scientific-document-platform-roadmap.md) | Local PDF reading and HTML-to-PDF export are separate surfaces sharing file and presentation infrastructure. | +| LaTeX, TinyTeX, builds, and SyncTeX | [`scient-latex.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-latex.md) | [LaTeX projects](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/latex.md) | [Scientific document platform](../planning/scientific-document-platform-roadmap.md) | Source editing, managed toolchain, build evidence, generated PDF freshness, and forward/inverse navigation must retain clear authorities. | +| Scientific compute, MATLAB, result promotion, and static artifacts | [`scient-analysis-runtime-foundation.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-analysis-runtime-foundation.md) | [Run a MATLAB file](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/matlab-run-file.md) | [Computing roadmap](../planning/scientific-computing-and-data-analysis-roadmap.md), [Python roadmap](../planning/scientific-python-environment-roadmap.md), [Artifact Studio](../planning/scientific-artifact-studio.md) | `ComputeSession`, `AnalysisRun`, and `DocumentBuild` are distinct; draft desktop work must not be described as shipped. | +| Durable thread queue and steer semantics | [`scient-thread-queue.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/scient-thread-queue.md) | [Composer](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/composer.md) | [PRD](PRD.md) | Client acceptance, capacity, provider adoption, steering, cancellation, persistence, and navigation are separate states. | +| Privacy-preserving product analytics | Implementation and tests in `scient-desktop`, with no active event collection by default | [Usage and privacy controls](https://github.com/ScientFactory/scient-desktop/blob/main/docs/user/usage.md) | [Measurement and analytics plan](../planning/product-measurement-and-analytics-plan.md) | Delivery remains disabled by default until privacy, governance, event-contract, and activation gates are satisfied. | +| Cross-cutting reliability, security, CI, and release preservation | [`ci.md`](https://github.com/ScientFactory/scient-desktop/blob/main/docs/internals/ci.md), operations runbooks, workflows, tests, and the detailed capability report | Relevant Help owner for the affected surface | [Quality](../quality/README.md), [development](../development/README.md) | These changes preserve capability boundaries across platforms and T3 refreshes; they are not a miscellaneous feature bucket. | + +## How To Maintain This Map + +For each feature change: + +1. Decide whether it extends an existing family or creates a genuinely new + stable family. +2. Update the nearest detailed owner when behavior, limits, architecture, + operations, Help, or upstream divergence changes. +3. Update this map only when its routing, family boundary, or durable + dependency changes. +4. Keep proposal and in-flight status in the owning plan or implementation + document; do not make a roadmap item appear shipped here. +5. Use the repository-family `Documentation impact` declaration to identify + the changed owners or an explicitly ordered dependent PR. + +The temporary +[documentation disposition ledger](../planning/documentation-disposition-ledger-2026-08-28.md) +governs the migration review. After that ledger retires, this map and the +nearest durable owners remain. diff --git a/docs/research/README.md b/docs/research/README.md index c1e74f0..3a43068 100644 --- a/docs/research/README.md +++ b/docs/research/README.md @@ -17,6 +17,15 @@ Current subfolders: - `spike-reports/` - reports from implementation or architecture spikes. - `visual-references/` - indexed screenshots and visual UI ideas kept as raw design research. +Generated audit evidence: + +- `documentation-inventory-2026-08-28.generated.json` - exhaustive tracked + Markdown inventory for exact clean `Scient`, `scient-desktop`, and website + candidate revisions, generated by + `scripts/generate-documentation-inventory.mjs`; `scient-agent` is explicitly + excluded and was not inspected. Review decisions live in the temporary + disposition ledger rather than this machine-generated file. + Current high-impact source synthesis includes the [Scient-agent foundation and capability strategy investigation](source-evaluations/scient-agent-foundation-and-capability-strategy-2026-08-06.md), which preserves the unselected Pi/OpenCode foundation comparison, other agent diff --git a/scripts/generate-documentation-inventory.mjs b/scripts/generate-documentation-inventory.mjs new file mode 100644 index 0000000..b55347d --- /dev/null +++ b/scripts/generate-documentation-inventory.mjs @@ -0,0 +1,353 @@ +#!/usr/bin/env node + +import { execFileSync } from "node:child_process"; +import { mkdirSync, readFileSync, realpathSync, writeFileSync } from "node:fs"; +import { dirname, resolve } from "node:path"; +import { pathToFileURL } from "node:url"; + +const REPOSITORY_NAMES = ["Scient", "scient-desktop", "website"]; + +function runGit(repositoryRoot, args) { + return execFileSync("git", ["-C", repositoryRoot, ...args], { + encoding: "utf8", + maxBuffer: 64 * 1024 * 1024, + }).trimEnd(); +} + +function rootRole(path) { + if (path === "AGENTS.md") return ["agent-protocol", "governance", "retain"]; + if (path === "CLAUDE.md") return ["tool-compatibility-router", "governance", "retain"]; + if (path === "CONTRIBUTING.md") return ["contribution", "governance", "retain"]; + if (path === "README.md") return ["orientation", "governance", "retain"]; + if (path === "UPSTREAM.md") return ["upstream", "upstream", "retain"]; + if (path.endsWith("SKILL.md")) return ["project-skill", "workflow", "retain"]; + return null; +} + +export function classifyPath(repository, path) { + if (repository === "scient-desktop" && path.startsWith(".repos/")) { + return { + documentKind: "vendored-source-documentation", + logicalRole: "donor-reference", + disposition: "retain-structurally-excluded", + sourceBoundary: "vendored-read-only", + }; + } + + const root = rootRole(path); + if (root) { + return { + documentKind: root[0], + logicalRole: root[1], + disposition: root[2], + sourceBoundary: "repository-owned-or-adapted", + }; + } + + if (path.endsWith("/SKILL.md")) { + return { + documentKind: "project-skill", + logicalRole: "workflow", + disposition: "retain", + sourceBoundary: "repository-owned-or-adapted", + }; + } + + if (path.endsWith("THIRD_PARTY_NOTICES.md")) { + return { + documentKind: "third-party-notice", + logicalRole: "development-reference", + disposition: "retain-beside-source", + sourceBoundary: "repository-owned-or-adapted", + }; + } + + if (repository === "Scient") { + if (path === "docs/documentation-policy.md") { + return { + documentKind: "documentation-policy", + logicalRole: "governance", + disposition: "retain", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path === "docs/onboarding.md") { + return { + documentKind: "collaborator-onboarding", + logicalRole: "development", + disposition: "retain", + sourceBoundary: "repository-owned-or-adapted", + }; + } + const routes = [ + ["docs/product/", "product"], + ["docs/architecture/", "architecture"], + ["docs/planning/", "planning"], + ["docs/research/", "research"], + ["docs/quality/", "quality"], + ["docs/development/", "development"], + ["docs/operations/", "operations"], + ["docs/design/", "design"], + ["lab/external/", "research"], + ["lab/notes/", "records"], + ["skills/", "workflow"], + ]; + const route = routes.find(([prefix]) => path.startsWith(prefix)); + if (route) { + return { + documentKind: path.endsWith("/README.md") ? "area-index" : "durable-documentation", + logicalRole: route[1], + disposition: route[1] === "records" ? "retain-record" : "retain", + sourceBoundary: "repository-owned-or-adapted", + }; + } + } + + if (repository === "scient-desktop") { + if (path.startsWith("docs/architecture/")) { + return { + documentKind: "architecture-documentation", + logicalRole: "architecture", + disposition: "retain", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.startsWith(".agents/skills/")) { + return { + documentKind: "project-skill-support", + logicalRole: "workflow", + disposition: "retain-beside-skill", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.startsWith(".macroscope/")) { + return { + documentKind: "development-tooling-reference", + logicalRole: "development", + disposition: "retain-beside-tooling", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path === "apps/marketing/tweets.md") { + return { + documentKind: "product-communication-record", + logicalRole: "records", + disposition: "retain-record", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.endsWith("/UPSTREAM.md")) { + return { + documentKind: "nested-upstream-record", + logicalRole: "upstream", + disposition: "retain-beside-adaptation", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.startsWith("docs/user/")) { + return { + documentKind: "public-help-source", + logicalRole: "help", + disposition: "retain-and-qualify-for-publication", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.startsWith("docs/operations/")) { + return { + documentKind: "durable-documentation", + logicalRole: "operations", + disposition: "retain", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.startsWith("docs/reports/")) { + return { + documentKind: "dated-record", + logicalRole: "records", + disposition: "retain-record", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.startsWith("docs/internals/")) { + return { + documentKind: "mixed-maintainer-documentation", + logicalRole: "capability-architecture-development-upstream-or-records", + disposition: "review-logically-before-any-move", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.startsWith("docs/fixtures/")) { + return { + documentKind: "test-fixture", + logicalRole: "fixture", + disposition: "retain-structurally-excluded", + sourceBoundary: "repository-owned-or-adapted", + }; + } + } + + if (repository === "website") { + if (path.startsWith("docs/architecture/")) { + return { + documentKind: "architecture-documentation", + logicalRole: "architecture", + disposition: "retain", + sourceBoundary: "repository-owned-or-adapted", + }; + } + if (path.startsWith("src/content/docs/")) { + return { + documentKind: "website-docs-view", + logicalRole: "help-rendering", + disposition: "generated-or-source-linked-only", + sourceBoundary: "website-owned-view", + }; + } + } + + if (path.endsWith("README.md")) { + return { + documentKind: "package-or-source-readme", + logicalRole: "development-reference", + disposition: "retain-beside-source", + sourceBoundary: "repository-owned-or-adapted", + }; + } + + if (path.startsWith(".github/")) { + return { + documentKind: "github-workflow-documentation", + logicalRole: "development", + disposition: "retain-beside-workflow", + sourceBoundary: "repository-owned-or-adapted", + }; + } + + return { + documentKind: "other-markdown", + logicalRole: "review", + disposition: "review-in-owning-context", + sourceBoundary: "repository-owned-or-adapted", + }; +} + +function firstHeading(repositoryRoot, path) { + const content = readFileSync(resolve(repositoryRoot, path), "utf8"); + const match = content.match(/^#\s+(.+)$/m); + return match?.[1]?.trim() ?? null; +} + +export function collectRepository(name, inputPath) { + if (!REPOSITORY_NAMES.includes(name)) throw new Error(`Unsupported repository name: ${name}`); + const repositoryRoot = realpathSync(inputPath); + const gitRoot = realpathSync(runGit(repositoryRoot, ["rev-parse", "--show-toplevel"])); + if (gitRoot !== repositoryRoot) { + throw new Error(`${name} path must be its Git root: ${repositoryRoot}`); + } + + const status = runGit(repositoryRoot, ["status", "--porcelain=v1", "--untracked-files=all"]); + if (status !== "") { + throw new Error(`${name} worktree must be clean before inventory generation:\n${status}`); + } + + const rawEntries = execFileSync( + "git", + ["-C", repositoryRoot, "ls-files", "-s", "-z", "--", "*.md"], + { encoding: "utf8", maxBuffer: 64 * 1024 * 1024 }, + ); + const entries = rawEntries + .split("\0") + .filter(Boolean) + .map((record) => { + const match = record.match(/^(\d+) ([0-9a-f]+) (\d+)\t(.+)$/); + if (!match) throw new Error(`Could not parse git ls-files record: ${record}`); + const [, mode, blob, stage, path] = match; + return { + path, + title: firstHeading(repositoryRoot, path), + mode, + blob, + stage: Number(stage), + ...classifyPath(name, path), + }; + }) + .sort((left, right) => left.path.localeCompare(right.path)); + + const byLogicalRole = Object.fromEntries( + [...new Set(entries.map((entry) => entry.logicalRole))] + .sort() + .map((role) => [role, entries.filter((entry) => entry.logicalRole === role).length]), + ); + + return { + name, + revision: runGit(repositoryRoot, ["rev-parse", "HEAD"]), + branch: runGit(repositoryRoot, ["branch", "--show-current"]), + remote: runGit(repositoryRoot, ["remote", "get-url", "origin"]), + worktreeClean: true, + markdownCount: entries.length, + byLogicalRole, + entries, + }; +} + +function parseArgs(argv) { + const values = new Map(); + for (let index = 0; index < argv.length; index += 2) { + const key = argv[index]; + const value = argv[index + 1]; + if (!key?.startsWith("--") || value === undefined) { + throw new Error("Arguments must be --name value pairs"); + } + values.set(key.slice(2), value); + } + for (const required of ["scient", "desktop", "website", "output", "generated-at"]) { + if (!values.has(required)) throw new Error(`Missing --${required}`); + } + return values; +} + +export function generateInventory(argv) { + const args = parseArgs(argv); + const repositories = [ + collectRepository("Scient", args.get("scient")), + collectRepository("scient-desktop", args.get("desktop")), + collectRepository("website", args.get("website")), + ]; + const output = resolve(args.get("output")); + const totalMarkdown = repositories.reduce((sum, repository) => sum + repository.markdownCount, 0); + const inventory = { + schemaVersion: 1, + generatedAt: args.get("generated-at"), + authority: + "Generated path inventory; dispositions are routing defaults, not migration authorization", + includedRepositories: REPOSITORY_NAMES, + excludedRepositories: [ + { + name: "scient-agent", + reason: + "Explicitly excluded until native Scient-agent implementation begins; inherited OpenCode Markdown was not inspected", + }, + ], + totalMarkdown, + repositories, + }; + mkdirSync(dirname(output), { recursive: true }); + writeFileSync(output, `${JSON.stringify(inventory, null, 2)}\n`, "utf8"); + return { output, totalMarkdown, repositories }; +} + +if (process.argv[1] && import.meta.url === pathToFileURL(resolve(process.argv[1])).href) { + try { + const result = generateInventory(process.argv.slice(2)); + const summary = result.repositories + .map((repository) => `${repository.name}=${repository.markdownCount}`) + .join(", "); + process.stdout.write( + `Wrote ${result.output} (${result.totalMarkdown} Markdown files; ${summary})\n`, + ); + } catch (error) { + process.stderr.write(`${error instanceof Error ? error.message : String(error)}\n`); + process.exitCode = 1; + } +} diff --git a/scripts/generate-documentation-inventory.test.mjs b/scripts/generate-documentation-inventory.test.mjs new file mode 100644 index 0000000..116b673 --- /dev/null +++ b/scripts/generate-documentation-inventory.test.mjs @@ -0,0 +1,77 @@ +import assert from "node:assert/strict"; +import { execFileSync } from "node:child_process"; +import { mkdtempSync, mkdirSync, rmSync, writeFileSync } from "node:fs"; +import { tmpdir } from "node:os"; +import { join } from "node:path"; +import test from "node:test"; + +import { classifyPath, collectRepository } from "./generate-documentation-inventory.mjs"; + +test("classifies desktop Help, records, internals, and vendored Markdown", () => { + assert.equal(classifyPath("scient-desktop", "docs/user/projects.md").logicalRole, "help"); + assert.equal(classifyPath("scient-desktop", "docs/reports/audit.md").logicalRole, "records"); + assert.equal( + classifyPath("scient-desktop", "docs/internals/provider.md").disposition, + "review-logically-before-any-move", + ); + assert.equal( + classifyPath("scient-desktop", ".repos/donor/README.md").sourceBoundary, + "vendored-read-only", + ); + assert.equal( + classifyPath("scient-desktop", ".repos/donor/skills/example/SKILL.md").logicalRole, + "donor-reference", + ); + assert.equal( + classifyPath("scient-desktop", "apps/mobile/modules/t3-markdown-text/UPSTREAM.md").logicalRole, + "upstream", + ); + assert.equal( + classifyPath("scient-desktop", "apps/web/THIRD_PARTY_NOTICES.md").logicalRole, + "development-reference", + ); + assert.equal( + classifyPath("website", "docs/architecture/terminal-renderers.md").logicalRole, + "architecture", + ); + assert.equal( + classifyPath("scient-desktop", "docs/architecture/terminal-renderers.md").logicalRole, + "architecture", + ); +}); + +test("collects only tracked Markdown from a clean exact Git root", () => { + const root = mkdtempSync(join(tmpdir(), "scient-doc-inventory-")); + try { + execFileSync("git", ["init", "-q", root]); + execFileSync("git", ["-C", root, "config", "user.email", "test@example.com"]); + execFileSync("git", ["-C", root, "config", "user.name", "Inventory Test"]); + execFileSync("git", [ + "-C", + root, + "remote", + "add", + "origin", + "https://example.com/ScientFactory/scient-desktop.git", + ]); + mkdirSync(join(root, "docs", "user"), { recursive: true }); + writeFileSync(join(root, "README.md"), "# Repository\n", "utf8"); + writeFileSync(join(root, "docs", "user", "projects.md"), "# Projects\n", "utf8"); + writeFileSync(join(root, "ignored.txt"), "not Markdown\n", "utf8"); + execFileSync("git", ["-C", root, "add", "."]); + execFileSync("git", ["-C", root, "commit", "-qm", "fixture"]); + + const result = collectRepository("scient-desktop", root); + assert.equal(result.worktreeClean, true); + assert.equal(result.markdownCount, 2); + assert.deepEqual( + result.entries.map((entry) => [entry.path, entry.title]), + [ + ["docs/user/projects.md", "Projects"], + ["README.md", "Repository"], + ], + ); + } finally { + rmSync(root, { recursive: true, force: true }); + } +}); From 965426e526b0821d97a4d4cef5301915ebef558b Mon Sep 17 00:00:00 2001 From: Yaacov Date: Fri, 28 Aug 2026 16:42:51 +0300 Subject: [PATCH 5/5] docs: record exhaustive Markdown inventory --- ...tation-inventory-2026-08-28.generated.json | 13326 ++++++++++++++++ 1 file changed, 13326 insertions(+) create mode 100644 docs/research/documentation-inventory-2026-08-28.generated.json diff --git a/docs/research/documentation-inventory-2026-08-28.generated.json b/docs/research/documentation-inventory-2026-08-28.generated.json new file mode 100644 index 0000000..d3742ac --- /dev/null +++ b/docs/research/documentation-inventory-2026-08-28.generated.json @@ -0,0 +1,13326 @@ +{ + "schemaVersion": 1, + "generatedAt": "2026-08-28", + "authority": "Generated path inventory; dispositions are routing defaults, not migration authorization", + "includedRepositories": [ + "Scient", + "scient-desktop", + "website" + ], + "excludedRepositories": [ + { + "name": "scient-agent", + "reason": "Explicitly excluded until native Scient-agent implementation begins; inherited OpenCode Markdown was not inspected" + } + ], + "totalMarkdown": 1204, + "repositories": [ + { + "name": "Scient", + "revision": "dcab07f391360f682def149882a551d5664be818", + "branch": "codex/documentation-inventory-20260828", + "remote": "https://github.com/ScientFactory/Scient.git", + "worktreeClean": true, + "markdownCount": 124, + "byLogicalRole": { + "architecture": 15, + "design": 4, + "development": 4, + "development-reference": 3, + "governance": 4, + "operations": 4, + "planning": 25, + "product": 6, + "quality": 3, + "records": 9, + "research": 44, + "workflow": 3 + }, + "entries": [ + { + "path": "AGENTS.md", + "title": "AGENTS.md", + "mode": "100644", + "blob": "e37900452a793ba8e45b4ff2f39589d76eb75533", + "stage": 0, + "documentKind": "agent-protocol", + "logicalRole": "governance", + "disposition": "retain", + "sourceBoundary": "repository-owned-or-adapted" + }, + { + "path": "CLAUDE.md", + "title": null, + "mode": "100644", + "blob": "c9209171818053a5e0284419c68dc4844e03ba16", + "stage": 0, + "documentKind": "tool-compatibility-router", + "logicalRole": "governance", + "disposition": "retain", + "sourceBoundary": "repository-owned-or-adapted" + }, + { + "path": "docs/architecture/agent-runtime.md", + "title": "Agent Runtime", + "mode": "100644", + "blob": "a973d41f69795df04317a5707ad4fa73ab3f171d", + "stage": 0, + "documentKind": "durable-documentation", + "logicalRole": "architecture", + "disposition": "retain", + "sourceBoundary": "repository-owned-or-adapted" + }, + { + "path": "docs/architecture/collaboration-model.md", + "title": "Collaboration Model", + "mode": "100644", + "blob": "e2fbe418720748e1a3ffaa21c8cef8b6900e6de5", + "stage": 0, + "documentKind": "durable-documentation", + "logicalRole": "architecture", + "disposition": "retain", + "sourceBoundary": "repository-owned-or-adapted" + }, + { + "path": "docs/architecture/decisions/ADR-0001-synara-opencode-foundation-and-scient-ownership-boundary.md", + "title": "ADR-0001: Synara And OpenCode Foundations With A Scient Ownership Boundary", + "mode": "100644", + "blob": "dd6727e61c6eb1819c12c53f605f7f1e08d6c09c", + "stage": 0, + "documentKind": "durable-documentation", + "logicalRole": "architecture", + "disposition": "retain", + "sourceBoundary": "repository-owned-or-adapted" + }, + { + "path": "docs/architecture/decisions/ADR-0002-standalone-source-ownership-and-upstream-authority.md", + "title": "ADR-0002: Standalone Source Ownership And Upstream Authority", + "mode": "100644", + "blob": "bf8bba9cc379451c9989aa508f4a8c093a24ccd1", + "stage": 0, + "documentKind": "durable-documentation", + "logicalRole": "architecture", + "disposition": "retain", + "sourceBoundary": "repository-owned-or-adapted" + }, + { + "path": "docs/architecture/decisions/ADR-0003-built-in-skills-portfolio-and-project-activation.md", + "title": "ADR-0003: Built-In Skills Portfolio And Project Activation", + "mode": "100644", + "blob": "216c47fe2306fd94e509759e6817df7034e117e3", + "stage": 0, + "documentKind": "durable-documentation", + "logicalRole": "architecture", + "disposition": "retain", + "sourceBoundary": "repository-owned-or-adapted" + }, + { + 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