docs: complete documentation inventory and normalization

[yaacovcorcos]

Summary

• adds the generated cross-repository Markdown inventory and its tested generator
• adds the active capability-family map and final nearest-owner routing
• closes the one-time disposition ledger as Historical after every durable decision moved to policy, repository guidance, indexes, canonical Help, the capability map, or website publishing architecture
• records the completed 31-page Help and public Docs review, the six-category publishing model, and the decision to keep useful inherited paths instead of performing broad cosmetic moves
• preserves the explicit scient-agent exclusion without inspecting its inherited OpenCode corpus

The exact generated inventory contains 1,203 tracked Markdown files: Scient 124, scient-desktop 1,072, and website 7. It includes 31 canonical Help pages and structurally excludes 928 vendored donor-reference files.

Documentation impact: Updated — documentation-system program, completed disposition record, active capability map, area indexes, exact inventory, and generator tests.

Exact source evidence

• Scient Markdown: e875fd2be1084798e198cf127630816092529ecc
• scient-desktop merged main: 7d2187eb383505956e95c8ebcfcfe8006d6edba2
• website merged main: 36b92247ead94cb5d4e38f54e3fc48ca3eaf74ec
• final PR head: b178f2c319f78d75937b58f7d98b699ac54c8e5d

The final PR commit changes only generated JSON, so the recorded Scient revision exactly inventories every Markdown file in this PR.

Consolidated dependencies

This PR consolidates the net result of historical Scient candidates #104–#106 after the dependent product documentation landed:

• scient-desktop #188, #194, and #199
• ScientFactory-website docs: add memory architecture discovery #28, docs: align memory discovery references #29, and Document LitRev memory reference #31

Stable-release publication, a documentation MCP, and product-architecture rebuilding remain separately gated and are not claimed by this PR.

Validation

• Oxfmt 0.57.0 passed on all changed authored Markdown
• metadata and local-link validation passed on all changed authored Markdown
• workspace bootstrap shell syntax and safety/idempotency passed
• Gate 1.5 evidence manifest passed
• 20 owned-source evidence tests passed
• owned-source consistency passed
• 2 generated-inventory tests passed
• exact clean-head inventory regeneration passed at all three revisions above
• JSON parse, expected totals, and git diff --check passed
• hosted evidence-manifest rerun attempt 2 passed on the final PR head after the repository was explicitly made public on 2026-08-29
• hosted evidence-manifest rerun attempt 2 also passed on merged main 3689423e411cdf66b48a2ef86235319aa27dc060

The original hosted attempts were blocked before execution by the account billing/spending-limit condition. Per docs/operations/github-operating-model.md, the exact workflow was also run locally before integration. The successful hosted reruns now supply the previously missing GitHub Actions evidence.

[yaacovcorcos]

Final exact-head evidence for b178f2c319f78d75937b58f7d98b699ac54c8e5d:

• GitHub job 99077329945 created zero steps and no runner. Its annotation says the job was not started because recent account payments failed or the spending limit must be increased.
• Per docs/operations/github-operating-model.md, I ran the exact evidence-manifest workflow locally with Node 24: bootstrap script syntax passed; workspace bootstrap safety/idempotency passed; Gate 1.5 manifest passed; all 20 owned-source evidence tests passed; owned-source consistency passed.
• The PR-specific inventory suite also passed: 2 generator tests, exact clean-head regeneration at Scient e875fd2be1084798e198cf127630816092529ecc, desktop 7d2187eb383505956e95c8ebcfcfe8006d6edba2, and website 36b92247ead94cb5d4e38f54e3fc48ca3eaf74ec; 1,203 total Markdown, 31 Help pages, and 928 excluded donor-reference files; authored Markdown formatting, metadata, local links, JSON parse, expected totals, and diff checks all passed.

The hosted failure is therefore billing infrastructure evidence, not a source failure.

[yaacovcorcos]

Hosted CI follow-up: after the explicitly authorized temporary public visibility change, evidence-manifest rerun attempt 2 passed on both this exact PR head and merged main. PR run: https://github.com/ScientFactory/Scient/actions/runs/33243701641 — main run: https://github.com/ScientFactory/Scient/actions/runs/33243748062.