docs: complete documentation inventory and normalization

docs/README.md

@@ -26,12 +26,15 @@ 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.
+- [Scient documentation system and publishing](planning/scient-documentation-system-and-publishing.md) - accepted repository-family authority, public Docs direction, implementation sequence, completed corpus decisions, remaining review 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
   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.

docs/planning/README.md

@@ -15,13 +15,16 @@ Do not use planning docs as product truth, accepted architecture, or current imp
 
 Current planning docs:
 
+- `documentation-disposition-ledger-2026-08-28.md` - historical record of the
+  completed one-time Markdown migration review, lasting dispositions, and
+  temporary-ledger retirement evidence.
 - `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.
+  real-change maintenance evidence; generated inventory and retired migration
+  ledgers; first-principles architecture gates; acceptance package;
+  implementation progress; 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.

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.

docs/research/README.md

@@ -3,7 +3,7 @@
 Status: Active
 Owner: Yaacov
 Created: 2026-06-27
-Last updated: 2026-08-06
+Last updated: 2026-08-29
 Purpose: Maps where Scient external research, source evaluations, and spike reports live.
 Doc type: Repo orientation
 
@@ -17,6 +17,16 @@ 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`, merged `scient-desktop`, and
+  merged website revisions, generated by
+  `scripts/generate-documentation-inventory.mjs`; `scient-agent` is explicitly
+  excluded and was not inspected. Review decisions are preserved in the
+  completed historical 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