docs: GA polish — site publishing scope, HLD v1.2, ragctl reference, port + link fixes

[officialCodeWork]

Summary

The seven highest-impact fixes from the GA documentation review, in one pass:

1. Public site publishing scope — the Docusaurus site published every docs/ subdir, including internal process docs. website/docusaurus.config.ts now carries an explicit, commented exclude list: ga/ (GA-readiness process tracking) and pilots/ (partner-program templates/kits) stay GitHub-only. Links into them from published pages (release notes, ADR-0046/0052, pilot guide + reference, docs index) now point at GitHub so nothing 404s on the site. runbooks/, spikes/, research/, and adr/ remain deliberately public (operator value / evidence chain / marketing content) — flipping any of these is now a one-line change.
2. HLD → v1.2 (GA) — was headed v1.1 / 24 May / Draft for review. Now: Released status, GA status lines in the header + exec summary, §5 gains a Shipped as column mapping all 25 problems to the ADR / architecture doc where the capability landed (buyer-FAQ index), §8.1 reflects the real OpenAI-compat surface, §10 records the ACL egress verifier shipping as defense-in-depth (ADR-0036), §12 marked complete.
3. ragctl reference rewritten — the doc described the Step 0.10 scaffold (4 working groups); the CLI has 37 commands + 13 groups. Full catalog by lifecycle area, worked examples, only the 3 real scaffolds (plugin/logs/secret) listed as such. The stale module-docstring table in main.py (it listed query as a scaffold) is replaced with a pointer to the doc.
4. Port standardized to 8000 — curl-quickstart, operator-console-live, reference/gateway.md, and reference/status-api.md used 8080 while six other quickstarts used 8000. (backends.md's 8080 is Weaviate's real default and stays.)
5. Root README rewritten — GA positioning, a "run a query in 5 minutes" path into the quickstarts, corrected repo tree; removes the duplicate "Quick start" section and a stray copy-pasted tree fragment with a dangling code fence.
6. Generated REST reference cross-links — gen_api_reference.py stripped Markdown links and left reST doc refs as plain text. It now emits real links resolved from docs/reference/ and verifies anchors against the target file's headings (stale anchor → file-level link), so rest-api.md's five cross-references are clickable and lychee-safe. Plus 3 broken links fixed (ADR files renamed since: ADR-0003, ADR-0005, ADR-0009).
7. CLAUDE.md de-staled — the "Current build status" block still said Phase 5 (62/84) while the repo shipped GA; replaced with the GA status + a hard rule that TRACKER.md is the single source of truth. Stale package versions dropped from the table; repo tree + docs-pipeline note brought current.

Documentation

• Updated: docs/architecture/RAG-Platform-HLD.md, docs/reference/ragctl.md, docs/reference/rest-api.md (regenerated), docs/reference/gateway.md, docs/reference/status-api.md, docs/reference/pilot.md, docs/guides/curl-quickstart.md, docs/guides/operator-console-live.md, docs/guides/design-partner-pilots.md, docs/release-notes/v1.0.0.md, docs/adr/ADR-0041/0046/0052, docs/architecture/agent-loop-v0.md, docs/README.md, root README.md, CLAUDE.md
• Tooling: scripts/gen_api_reference.py, website/docusaurus.config.ts, website/sidebars.ts, packages/ragctl/src/ragctl/main.py (docstring only)

Verification

• pytest tests/docs packages/ragctl — 191 passed
• ruff check + ruff format --check + mypy on touched Python — clean
• Relative-link sweep over docs/ + root README + CLAUDE.md: 1207 links, 0 broken
• npm run build (Docusaurus): green; built output contains adr/, runbooks/, spikes/, research/ and does not contain ga/ or pilots/
• gen_api_reference.py output is committed in the same change, so the API-reference drift gate stays green

🤖 Generated with Claude Code

[officialCodeWork]

Second commit (e26f637): rewrote the root README as a proper "how to run the product" document — demo mode, real backends via rag.yaml + a tested serve.py (rag_config.load → build_app_from_config, builds 58 routes), admin console, and the four production install channels.

While verifying the production section, found a real v1.0.0 gap (not fixed here — it's product code, tracked separately for v1.0.1): the published gateway image's default CMD prints the version instead of serving, the Helm chart sets RAG_CONFIG_PATH that nothing in the codebase reads, and its readiness probe targets a /readyz route that doesn't exist. The README documents the working workaround (pass the uvicorn command explicitly) under an explicit "Known gap at v1.0.0" callout.