Record the two refspec traps #109 only found in review

[BigSimmo]

Summary

One row of docs/outstanding-issues.md. No code change — the guards themselves shipped in #1392 and #1398; this is the durable memory they left behind.

#109 recorded the shallow clone and the single-branch refspec, but not the two failure modes found after those fixes landed. Both reach the same wrong answer — an empty branch inventory reported as complete — and both came from checking only half of the refspec:

1. The destination matters as much as the source, because the sweep enumerates refs/remotes/origin and nothing else. With +refs/heads/*:refs/remotes/upstream/*, every branch is fetched, refs/remotes/origin stays empty, and the sweep exits 0 with "branches": [].
2. Git substitutes the matched suffix into <dst>, so a refs/* source nests one level deeper. +refs/*:refs/remotes/origin/* writes refs/remotes/origin/heads/main; origin/main then does not resolve at all, every comparison fails into 0/0, and the sweep exits 0 naming both heads/feature and heads/main as deletion candidates:

2 deletion candidate(s) (no unique patch content — squash-merged or empty):
  - heads/feature
  - heads/main
EXIT=0

A green run recommending the deletion of main. That is the strongest available argument for why the guard exists, and it was not written down anywhere durable — the code comments and test bodies carry the mechanism, but the ledger is what survives a session.

Both measured on git 2.43.0.

Verification

• npm run docs:check-links — docs link check passed: 1375 repo path references resolve.
• npx vitest run tests/repo-hygiene.test.ts — Tests 40 passed (40), confirming the shipped guards still hold at this base.
• Ledger integrity after the edit: 115 rows, 115 unique ids, no row added or dropped.
• npx prettier --write docs/outstanding-issues.md — clean.
• Full verify:cheap not re-run for this commit: the diff is one markdown row, and the code it describes was gated at verify:cheap on both Refuse to report a branch inventory from a shallow clone #1392 and Refuse a branch inventory that cannot be shown to cover every branch #1398 (Test Files 432 passed (432)).
• UI verification not run: no UI, routing, styling or browser behaviour changed.
• Retrieval/answer evals not run: no retrieval, ranking, selection or answer-generation change.
• npm run check:production-readiness not run: no clinical workflow, privacy, environment, Supabase, source-governance or deployment change.

Risk and rollout

• Risk: none to runtime. One documentation row; no code, schema, API, or gate behaviour is touched.
• Rollback: revert this PR. The ledger loses the two measurements.
• Provider or production effects: None.

Clinical Governance Preflight

Not applicable to this diff. The only changed path is docs/outstanding-issues.md; classifyPullRequestFiles reports clinicalRisk: false for it. No ingestion, answer generation, search/ranking, source rendering, document access, privacy or clinical output behaviour changed.

Notes

RAG impact: no retrieval behaviour change — no file under src/lib/rag/**, clinical-search, retrieval-selection, released-search-order, ranking-config, answer-ranking, the eval harness, the golden fixture, or the retrieval RPCs is touched.

Worth recording for the next reader of this sequence: the second trap was reported by Codex and fixed by cursoragent while #1398 was open, and I verified that claim against a real fixture rather than taking it. The fixture is what produced the heads/main line above — a stronger consequence than either the report or the fix had stated. The branch was restarted from the post-#1398 main, so this is a new branch and a new PR rather than a reopen.

🤖 Generated with Claude Code

https://claude.ai/code/session_012YRCXgX4AWZ579bKN6sk6b

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