fix(store): make cleanupOrphanedVectors atomic across both vector tables (#766)

[tobi]

Summary

• Rebases / lands the fix(store): make cleanupOrphanedVectors atomic across both vector tables #766 fix on current main after fix(cli): report orphaned embedding vectors and add cleanup --dry-run #851 extracted countOrphanedVectors. cleanupOrphanedVectors now runs the orphan count and both DELETEs (vectors_vec then content_vectors) in one BEGIN IMMEDIATE transaction.
• An interruption between the two DELETEs could leave stale content_vectors rows for a hash that no longer has vec rows. A later reactivation then looked already-embedded, so qmd embed skipped it and the document was silently unsearchable by vector.
• Adds unit tests for the happy path, injected mid-delete failure (rollback), outer-transaction savepoint rollback, and inner-savepoint isolation.

Supersedes #766 (same fix, rebased onto post-#851 main).

Test plan

• Local Bun store tests: 264 pass, 13 skip
• Local Node store tests: 264 pass, 13 skip
• Local Node test/: 976 pass, 73 skip
• Local Bun test/: 976 pass, 80 skip
• CI Bun + Node 22/23 green

[PowderAddicts]

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On Thu, Aug 13 2026, at 02:15 AM, tobi/qmd ***@***.***> wrote: Summary * Rebases / lands the #766 fix on current (#766) main after #851 extracted (#851) countOrphanedVectors. cleanupOrphanedVectors now runs the orphan count and both DELETEs ( vectors_vec then content_vectors) in one BEGIN IMMEDIATE transaction. * An interruption between the two DELETEs could leave stale content_vectors rows for a hash that no longer has vec rows. A later reactivation then looked already-embedded, so qmd embed skipped it and the document was silently unsearchable by vector. * Adds unit tests for the happy path, injected mid-delete failure (rollback), outer-transaction savepoint rollback, and inner-savepoint isolation. Supersedes #766 (same fix, rebased onto post- (#766) #851 (#851) main). Test plan Local Bun store tests: 264 pass, 13 skip Local Node store tests: 264 pass, 13 skip Local Node test/: 976 pass, 73 skip Local Bun test/: 976 pass, 80 skip CI Bun + Node 22/23 green You can view, comment on, or merge this pull request online at: #856 (#856) Commit Summary 1bf23f2 fix(store): make cleanupOrphanedVectors atomic across both vector tables (#766) (1bf23f2) File Changes ( 4 files) (https://github.com/tobi/qmd/pull/856/files) M CHANGELOG.md (8) (https://github.com/tobi/qmd/pull/856/files#diff-06572a96a58dc510037d5efa622f9bec8519bc1beab13c9f251e97e657a9d4ed) M src/db.ts (4) (https://github.com/tobi/qmd/pull/856/files#diff-1d214e57ddda9095d296e5700ebce701333bfefcf417e234c584d14091b2f50d) M src/store.ts (59) (https://github.com/tobi/qmd/pull/856/files#diff-2717c7fb31c2070dd96f07394997809bc9be7f3fff03ab638db696cc480f39b6) M test/store.test.ts (133) (https://github.com/tobi/qmd/pull/856/files#diff-ecc9e7b9a74de1ebac3cd3038ffc91cd42684ca2890738d3b93139c723c36407) Patch Links: https://github.com/tobi/qmd/pull/856.patch (https://github.com/tobi/qmd/pull/856.patch) https://github.com/tobi/qmd/pull/856.diff (https://github.com/tobi/qmd/pull/856.diff) — Reply to this email directly, view it on GitHub, or (#856?email_source=notifications&email_token=BRF3HG45HEAXJQ3KKITZWQ35JUQEXA5CNFSNUABEM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UF42DENRXGUYDIMJVGSTHEZLBONXW5KTTOVRHGY3SNFRGKZFFMV3GK3TUVRTG633UMVZF6Y3MNFRWW) unsubscribe. (https://github.com/notifications/unsubscribe-auth/BRF3HG6367WVD7EOBWX5IDT5JUQEXAVCNFSNUABGKJSXA33TNF2G64TZHMYTCMJSGM3DKMZQGE5US43TOVSTWNJRGM3TAOJTGA2DJILWAI) Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS and (https://github.com/notifications/mobile/ios/BRF3HG3O2VIYD27KYHNHDHT5JUQEXA5CNFSNUABEM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UF42DENRXGUYDIMJVGSTHEZLBONXW5KTTOVRHGY3SNFRGKZFFMV3GK3TUVJTG633UMVZF62LPOM) Android. Download it today! (https://github.com/notifications/mobile/android/BRF3HG7NFRRZV5ZS2MWWGO35JUQEXA5CNFSNUABEM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UF42DENRXGUYDIMJVGSTHEZLBONXW5KTTOVRHGY3SNFRGKZFFMV3GK3TUVZTG633UMVZF6YLOMRZG62LE) You are receiving this because you are subscribed to this thread. Message ID: <tobi/qmd/pull/856 @ github . com> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#856?email_source=notifications\u0026email_token=BRF3HG7WU5DVZ2OWSJZ6VP35JUQEXA5CNFSNUABEM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UF42DENRXGUYDIMJVGSTHEZLBONXW5KTTOVRHGY3SNFRGKZFFMV3GK3TUVNTW2YLJNRPWG3DJMNVQ", "url": "#856?email_source=notifications\u0026email_token=BRF3HG7WU5DVZ2OWSJZ6VP35JUQEXA5CNFSNUABEM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UF42DENRXGUYDIMJVGSTHEZLBONXW5KTTOVRHGY3SNFRGKZFFMV3GK3TUVNTW2YLJNRPWG3DJMNVQ", "name": "View Pull Request" }, "description": "View this Pull Request on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]