fix(review): refresh capped RAG files on full reindex

[JSONbored]

Motivation

• A full-RAG reindex could treat a repository already at MAX_CHUNKS_PER_REPO as fully done before inspecting per-path metadata, which prevented changed files from being deleted/replaced and left stale chunks in capped repos.

Description

• Change src/review/rag-index.ts so the per-repo cap is checked only after consulting the stored per-path metadata and the unchanged-blob (blobSha) shortcut; the loop now allows processing a path if it has known stored chunks to delete and replace while still stopping for unknown/new paths once the cap is reached.
• The new logic checks if (stored >= MAX_CHUNKS_PER_REPO && (!known || known.count <= 0)) to preserve the cap for genuinely new content but permit refreshes of existing paths.
• Add a regression unit test in test/unit/rag-index.test.ts that seeds a repo already at the cap, marks one path as changed (new blob_sha) and asserts that the changed file is re-embedded and the repo remains capped overall.

Testing

• Ran the targeted test: npx vitest run test/unit/rag-index.test.ts -t "refreshes changed files", and it passed (regression reproduced and fixed).
• Ran the full test/unit/rag-index.test.ts; the targeted regression and related index tests passed, but three existing cron fan-out tests in that file timed out (15s timeout) and are unrelated to the cap change.
• Verified repository-style checks locally (format/linters for the edited files) and no changed-line/style errors were produced.

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Codex Task

[superagent-security]

Superagent didn't find any vulnerabilities or security issues in this PR.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.96%. Comparing base (64fb1a3) to head (90fc490).
⚠️ Report is 3 commits behind head on main.
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4405   +/-   ##
=======================================
  Coverage   93.96%   93.96%           
=======================================
  Files         401      401           
  Lines       36892    36892           
  Branches    13490    13490           
=======================================
  Hits        34667    34667           
  Misses       1569     1569           
  Partials      656      656           

Files with missing lines	Coverage Δ
src/review/rag-index.ts	93.90% <100.00%> (ø)

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