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fix(repo): transcripts::reindex scans outside the index lock and merges concurrent ingest (#274) - #277

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fix/274-transcripts-reindex-lock
Oct 21, 2026
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tonibergholm-codento merged 3 commits into
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fix/274-transcripts-reindex-lock

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@tonibergholm-codento tonibergholm-codento commented Oct 21, 2026 •

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Closes #274

transcripts::reindex (run after signatures::reindex on clone) did its scan and rewrite of .sc/transcripts / .sc/transcript-drops with no catch-up for objects a serve-path ingest stored meanwhile, so that ingest's index lines and drop lines could be overwritten.

Change

Same pattern as #273:

  • The scan and tombstone signature checks run outside the index lock.
  • Up to four unlocked catch-up passes pick up objects ingested meanwhile.
  • A final pass under the lock judges only what is new, then rewrites both files: transcripts whose snapshot landed after they were listed, tombstones not yet honored (signature or trust landed since), tombstones whose dropped body is new.
  • Each pass re-reads the trusted set and the signature index. A changed trusted set discards earlier verdicts, so only trusted signers are honored (trust gate unchanged).
  • Pending ring, O_APPEND drop appends, --no-transcripts and lock reentrancy are untouched. The ingest holds the lock only around its own index updates, so there is no new lock nesting.
  • Listing decision: the locked pass calls Store::reload_packs() first, so packs another handle wrote since the store opened are seen (one .idx read under the lock). signatures::reindex still relists loose objects only; noted in the ADR.

ADR-0038 addendum extended with a #274 bullet.

Tests

New in transcripts.rs (all use a reindex_with hook to interleave at two points: right after the first scan and just before the lock):

  • reindex_keeps_an_ingest_that_lands_during_its_scan: a concurrent ingest of a body, a tombstone and its trusted signature loses no index line and no drop line.
  • reindex_judges_again_what_lands_after_the_first_scan: a transcript whose snapshot lands late, a tombstone whose signature lands late; a late signature by an untrusted key honors nothing.
  • reindex_sees_a_pack_another_handle_wrote_since_the_store_opened.

Mutation checks: dropping the locked pass, the pack reload, the waiting-transcript retry, or the re-judging of unhonored tombstones each makes at least one of these fail.

Verification

cargo fmt --all, cargo clippy --workspace --all-targets -- -D warnings, cargo test -p scl-repo -p scl-cli: all pass.

Summary by CodeRabbit

  • Bug Fixes
    • Improved transcript reindexing when new data is added during the process.
    • Ensured late-arriving snapshots, signatures, and packed objects are included.
    • Preserved concurrent ingests so newly added transcripts are not lost.
    • Re-evaluated tombstones when relevant trust or signature information changes.
    • Improved handling of transcript and snapshot mismatches during reindexing.
    • Ensured index updates remain consistent when changes occur during scanning.
  • Documentation
    • Added guidance describing safe transcript reindexing during concurrent activity.

…es concurrent ingest (#274)

The clone's post-clone transcript reindex scanned and rewrote
.sc/transcripts and .sc/transcript-drops without holding the index lock
across the scan, so a serve-path ingest into the same destination during
the scan lost its appended lines.

Same pattern as the signature rebuild (#273): scan and tombstone
signature checks run unlocked, up to four unlocked catch-up passes, then
a final pass under the lock judges only what is new (transcripts whose
snapshot landed late, tombstones not honored yet, tombstones whose dropped
body is new) before the rewrite. Trusted set and signature index are
re-read each pass; a changed trusted set discards earlier verdicts. The
locked listing also reloads the pack index so packs another handle wrote
since open count. ADR-0038 addendum updated.
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📝 Code Review ✅ Completed 2026-10-21T05:02:01.908013Z 8eecc8a New commits
🔒 Security Review ✅ Completed 2026-10-21T05:04:34.837709Z 8eecc8a New commits
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Reviewing files that changed from the base of the PR and between 58c61c3 and a09993a.

📒 Files selected for processing: 2
  • crates/repo/src/transcripts.rs
  • docs/adr/0038-agent-session-transcripts.md
🚧 Files skipped from review as they are similar to previous changes: 1
  • docs/adr/0038-agent-session-transcripts.md

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📝 Walkthrough

transcripts::reindex now performs unlocked scans and catch-up passes, reloads pack indexes, and completes a final scan under the index lock before rewriting transcript and drop indexes. Tests cover concurrent ingests, late-arriving objects, trust changes, and external pack writes.

Changes: Concurrent transcript reindexing

Layer / File(s) Summary
Scan, catch up, and commit indexes
crates/repo/src/transcripts.rs
reindex tracks scan state across unlocked passes, reloads packs under the lock, performs a final scan, and rewrites transcript and drop indexes.
Re-evaluate tombstones and trust state
crates/repo/src/transcripts.rs
Scan::judge re-evaluates tombstones when signatures, snapshots, or trusted keys change. It removes verdicts that no longer pass trusted-signature and snapshot checks.
Validate concurrent and late-arriving objects
crates/repo/src/transcripts.rs, docs/adr/0038-agent-session-transcripts.md
Tests cover concurrent ingest, late snapshots and signatures, external pack writes, trust withdrawal, and snapshot or body mismatches. The ADR documents the updated reindex flow and pending-state behavior.

Priority: ➖ Normal

Estimated code review effort: 4 (Complex) | ~60 minutes

Change: Bug fix · Severity of issue fixed: Medium

Merge Risk: ⚪ Minimal · up to a0999

No merge-blocking issue remains identified; the final reindex pass can see late loose objects from another store handle.

Security architecture risk: 🔵 Low · up to a0999

The rebuild now catches concurrent arrivals before replacing the indexes and preserves trusted-signature checks. No introduced authorization bypass was established. Residual uncertainty concerns interrupted recovery and concurrency behavior assessed from source rather than executed tests.

Retained concerns
No architecture-level concerns identified.

Security review details

Security Blast Radius

  • inferred — The demonstrated sensitive outcome is transcript suppression or retention in the repository addressed by the supplied layout. The inspected lifecycle operates on that repository's object store, trusted keys, signature index, transcript index, and drop index; the evidence does not establish broader service or tenant exposure.

Security Findings and Attack Paths

  • observed — For the inspected candidate-tombstone path, arrival in the store does not by itself authorize a drop. The changed caller requires a trusted-signer mapping and invokes the existing cryptographic and snapshot/body checks before creating an honored drop entry. No introduced bypass was established for this path.

Trust Boundaries and Controls

  • observed — Tombstone authorization still requires a local Snapshot, a matching non-tombstone body when that body is held, and a trusted signature over the domain-separated drop digest. The new lifecycle refreshes trust between passes and invalidates cached authorization decisions when that trust changes.

Resilience and Maintainability Implications

  • inferred — The final locked refresh addresses the previous overwrite window for concurrent ingest, including loss of drop lines. Bounded catch-up prevents endless unlocked retry, although final work remains proportional to newly discovered objects and tombstones requiring reevaluation; it is not a fixed lock-duration guarantee.
Pre-merge checks: Passed 5
Check name Status Explanation
Description Check Passed Check skipped - CodeRabbit’s high-level summary is enabled.
Title check Passed The title clearly and concisely describes the main change: moving transcript reindex scanning outside the index lock and merging concurrent ingest. It is directly related to the pull request objective…
Linked Issues check Passed Issue [#274] requires verification outside the lock, catch-up passes, and a final pass under the lock. crates/repo/src/transcripts.rs implements the multi-pass scan and locked rewrite. The implement…
Out of Scope Changes check Passed The changes stay within issue [#274]. The source changes fix the transcripts::reindex race. The tests verify the required concurrent-ingest behavior. The ADR addendum documents the changed reindex b…
Docstring Coverage Passed Docstring coverage is 82.35% which is sufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 17 functions across 1 files. (1 skipped: 1 …
Full details: Title check

Explanation

The title clearly and concisely describes the main change: moving transcript reindex scanning outside the index lock and merging concurrent ingest. It is directly related to the pull request objectives.

Full details: Linked Issues check

Explanation

Issue [#274] requires verification outside the lock, catch-up passes, and a final pass under the lock. crates/repo/src/transcripts.rs implements the multi-pass scan and locked rewrite. The implementation reloads packs in the locked pass, re-reads trust and signature state, and rejudges late snapshots and tombstones. The reported tests cover concurrent ingest, late signatures, trust rejection, and external pack writes. The ADR addendum records the loose-object listing behavior.

Full details: Out of Scope Changes check

Explanation

The changes stay within issue [#274]. The source changes fix the transcripts::reindex race. The tests verify the required concurrent-ingest behavior. The ADR addendum documents the changed reindex behavior. No unrelated product behavior is identified.

Full details: Docstring Coverage

Explanation

Docstring coverage is 82.35% which is sufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 17 functions across 1 files. (1 skipped: 1 unsupported.)

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Actionable comments posted: 1


  • 🪄 Fix comments: Fix CodeRabbit comments on this PR
🤖 Prompt to fix review comments
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Inline comments:
Review comments at @crates/repo/src/transcripts.rs:
- Around line 769-778: In the tombstone loop of judge, before calling
tombstone_honored, use only trusted and sigs to detect whether any trusted
signer has an indexed signature for the tombstone ID. If none exists, remove the
ID from self.honored and continue without reading t.snapshot or dropped;
preserve the existing tombstone_honored path when a trusted signature is
present.

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  • crates/repo/src/transcripts.rs
  • docs/adr/0038-agent-session-transcripts.md

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Comment thread crates/repo/src/transcripts.rs Resolved

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Reviewed commit: 58c61c35c7

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self.fp = fp;
}
let wanted: BTreeSet<ObjectId> = self.tombs.keys().copied().collect();
let sigs = crate::signatures::load_sig_index(layout, Some(&wanted), &trusted)?;

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P2 Badge Keep signature scans out of the index lock

When the store contains any tombstone, the final Scan::pass runs under with_index_lock and reaches this call, where load_sig_index parses the entire signatures.v2 file before the subsequent tombstone checks. With a large signature index or many unhonored tombstones, this makes the supposedly short-lived critical section unbounded; a concurrent put_pack can exceed the 30-second lock wait after its objects have already been stored, leaving that ingest's derived indexes unupdated. Snapshot or otherwise narrow the signature data before acquiring the lock so the locked pass only merges newly arrived state and performs the rewrites.

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Not changing this. The locked pass must read the current signature index: a signature stored by an ingest that finished before the lock was taken is exactly what it has to see, so it cannot be snapshotted earlier. It is one read of signatures.v2 (the same read every serve-path ingest does in index_incoming), and as of a09993a it is skipped when no trusted signer exists or no tombstone needs a verdict, and unsigned tombstones no longer cost object reads. The scan and per-object work stay outside the lock.

…rust-change tests (#274)

Skip the signature index read when no trusted signer exists or no
tombstone needs a verdict, refuse an unsigned tombstone before reading
objects, and pin the trust-withdrawn and mismatched-body cases with tests.
ADR addendum notes the pack reload is defensive.

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Approved: two independent Opus passes (no blockers), Codex clean on head, CI green.

@tonibergholm-codento
tonibergholm-codento merged commit 5422489 into main Oct 21, 2026
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Approved: two independent code-reviewer passes (no blockers), Codex security clean, CI green; rejected Codex P2 reasoned (locked pass must read the current signature index).

@tonibergholm-codento
tonibergholm-codento deleted the fix/274-transcripts-reindex-lock branch October 21, 2026 08:58
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transcripts::reindex has the same unlocked-scan race as signatures::reindex (follow-up to #273)

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