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beads/internal/storage/sqlite
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Steve Yegge 240a4e2dbc feat: add bd doctor check for orphaned issues (bd-5hrq) 
- Add CheckOrphanedIssues to detect issues referenced in commits but still open
- Pattern matches (prefix-xxx) in git log against open issues in database
- Reports warning with issue IDs and commit hashes
- Add 8 comprehensive tests for the new check

Also:
- Add tests for mol spawn --attach functionality (bd-f7p1)
- Document commit message convention in AGENT_INSTRUCTIONS.md
- Fix CheckpointWAL to use wrapDBError for consistency

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
2025-12-21 22:05:14 -08:00
..
migrations
feat(types): add template molecules infrastructure for beads-1ra
2025-12-19 22:03:22 -08:00
adaptive_e2e_test.go
test: Tag 16 slow integration tests with build tags
2025-11-21 14:40:22 -05:00
adaptive_length_test.go
fix: resolve test failures from speedup changes
2025-11-04 01:08:21 -08:00
adaptive_length.go
Switch from hex to Base36 encoding for issue IDs (GH #213)
2025-11-03 12:02:15 -08:00
batch_ops_test.go
fix(import): defensive handling for closed issues missing closed_at timestamp
2025-12-14 17:21:44 -08:00
batch_ops.go
fix(storage): add batch ID conflict detection and fix schema indexes
2025-12-18 19:11:50 -08:00
batch_test.go
Fix N+1 query pattern in export operations (bd-rcmg)
2025-11-23 19:53:44 -08:00
bench_helpers_test.go
fix: Remove duplicate context variable declarations in benchmark tests
2025-11-23 19:35:52 -08:00
blocked_cache_test.go
fix: replace string(rune()) with strconv.Itoa in tests (bd-fmc)
2025-12-02 22:41:07 -08:00
blocked_cache.go
feat(status): add deferred status for icebox issues (bd-4jr)
2025-12-20 14:24:48 -08:00
child_counters_migration_test.go
Extract SQLite migrations into separate files (bd-fb95094c.7)
2025-11-06 20:06:45 -08:00
child_counters_test.go
Implement 6-char progressive hash IDs (bd-166, bd-167)
2025-10-30 14:04:03 -07:00
child_id_test.go
Complete bd-ar2 P2 tasks: metadata, resurrection, and testing improvements
2025-11-21 11:40:37 -05:00
collision_test.go
Document external_ref in content hash behavior (bd-9f4a)
2025-11-08 02:22:15 -08:00
collision.go
Document external_ref in content hash behavior (bd-9f4a)
2025-11-08 02:22:15 -08:00
comments_test.go
fix: replace string(rune()) with strconv.Itoa in tests (bd-fmc)
2025-12-02 22:41:07 -08:00
comments.go
Fix N+1 query pattern in export operations (bd-rcmg)
2025-11-23 19:53:44 -08:00
compact_bench_test.go
fix: replace string(rune()) with strconv.Itoa in tests (bd-fmc)
2025-12-02 22:41:07 -08:00
compact_test.go
Fix FK constraint failures in AddComment and ApplyCompaction (bd-5arw)
2025-11-20 18:55:10 -05:00
compact.go
feat(status): add deferred status for icebox issues (bd-4jr)
2025-12-20 14:24:48 -08:00
config.go
feat(bd-1pj6): Add custom status states via config
2025-11-28 23:19:21 -08:00
cycle_bench_test.go
Performance Improvements (#319)
2025-11-15 12:46:13 -08:00
cycle_detection_test.go
fix(deps): exclude relates-to from cycle detection (fixes #661)
2025-12-20 13:33:15 -08:00
delete_test.go
feat(mol): filter ephemeral issues from JSONL export (bd-687g)
2025-12-21 14:37:22 -08:00
dependencies_test.go
fix(deps): exclude relates-to from cycle detection (fixes #661)
2025-12-20 13:33:15 -08:00
dependencies.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
dirty_helpers.go
Refactor: consolidate ID generation and shared helpers (bd-0702, bd-1445)
2025-11-02 14:49:27 -08:00
dirty_test.go
fix: Remove unsafe ClearDirtyIssues() method (bd-b6xo)
2025-12-17 19:10:13 -08:00
dirty.go
fix: Remove unsafe ClearDirtyIssues() method (bd-b6xo)
2025-12-17 19:10:13 -08:00
epics_test.go
…
epics.go
…
errors_test.go
Centralize error handling patterns in storage layer (bd-bwk2)
2025-11-24 00:59:49 -08:00
errors.go
Centralize error handling patterns in storage layer (bd-bwk2)
2025-11-20 19:17:57 -05:00
events_helpers.go
Refactor: consolidate ID generation and shared helpers (bd-0702, bd-1445)
2025-11-02 14:49:27 -08:00
events_test.go
fix: Remove unsafe ClearDirtyIssues() method (bd-b6xo)
2025-12-17 19:10:13 -08:00
events.go
fix(pin): add 'pinned' field to allowed update fields (gt-zr0a)
2025-12-20 19:57:16 -08:00
external_ref_test.go
Add external_ref UNIQUE constraint and validation
2025-11-02 16:27:42 -08:00
freshness_test.go
fix(storage): race condition when reconnect closes db mid-query (GH#607)
2025-12-18 11:28:13 -08:00
freshness_unix.go
fix: Windows build + gosec lint errors (#585)
2025-12-16 13:26:51 -08:00
freshness_windows.go
fix: Windows build + gosec lint errors (#585)
2025-12-16 13:26:51 -08:00
freshness.go
fix: Windows build + gosec lint errors (#585)
2025-12-16 13:26:51 -08:00
graph_links_test.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
hash_id_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
hash_ids.go
Complete bd-ar2 P2 tasks: metadata, resurrection, and testing improvements
2025-11-21 11:40:37 -05:00
hash.go
Fix bd-160: Implement JSONL integrity validation and prevent export deduplication data loss
2025-10-29 21:57:15 -07:00
ids_test.go
fix(orphan): handle prefixes with dots in orphan detection (GH#508)
2025-12-14 17:23:46 -08:00
ids.go
feat: Linear Integration (#655)
2025-12-19 17:58:24 -08:00
issues.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
labels_test.go
fix: Remove unsafe ClearDirtyIssues() method (bd-b6xo)
2025-12-17 19:10:13 -08:00
labels.go
feat(types): add template molecules infrastructure for beads-1ra
2025-12-19 22:03:22 -08:00
migration_invariants_test.go
Add migration inspection tools for AI agents (bd-627d Phase 2)
2025-11-02 14:03:14 -08:00
migration_invariants.go
Add migration inspection tools for AI agents (bd-627d Phase 2)
2025-11-02 14:03:14 -08:00
migrations_test.go
feat(types): add template molecules infrastructure for beads-1ra
2025-12-19 22:03:22 -08:00
migrations.go
feat(types): add template molecules infrastructure for beads-1ra
2025-12-19 22:03:22 -08:00
multirepo_export.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
multirepo_test.go
fix(multirepo): handle out-of-order dependencies during JSONL import (#414)
2025-11-29 22:07:52 -08:00
multirepo.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
orphan_handling_test.go
fix: orphan detection false positive with dots in directory name
2025-12-16 01:06:14 -08:00
prefix_validation_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
queries.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
ready_test.go
feat: add --unassigned flag to bd ready command
2025-11-30 00:37:12 -08:00
ready.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
rename_dependency_prefix_test.go
fix(storage): implement RenameDependencyPrefix to preserve dependencies (#642)
2025-12-19 17:52:44 -08:00
resurrection_test.go
Fix P0 bug: JSONL lookup now returns LAST match (bd-58c0)
2025-11-04 22:25:33 -08:00
resurrection.go
Complete bd-ar2 P2 tasks: metadata, resurrection, and testing improvements
2025-11-21 11:40:37 -05:00
schema_probe_test.go
Add schema compatibility probe to prevent silent migration failures (bd-ckvw)
2025-11-08 15:40:19 -08:00
schema_probe.go
fix(schema): add pinned column to schema compatibility checks
2025-12-19 19:57:14 -08:00
schema.go
feat(status): add deferred status for icebox issues (bd-4jr)
2025-12-20 14:24:48 -08:00
sqlite_bench_test.go
feat(cli): add 'bd thanks' command to thank contributors
2025-12-14 12:40:32 -08:00
sqlite_test.go
fix(test): remove incorrect duplicate ID rollback test
2025-12-18 18:24:28 -08:00
sqlite.go
refactor: Split monolithic sqlite.go into focused files (bd-0a43)
2025-11-23 19:04:34 -08:00
store.go
feat: add bd doctor check for orphaned issues (bd-5hrq)
2025-12-21 22:05:14 -08:00
test_helpers.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
tombstone_test.go
fix(cleanup): resolve CHECK constraint failure and add tombstone pruning
2025-12-14 00:37:54 -08:00
transaction_test.go
Add tests for Decision 004 Phase 4 edge schema consolidation
2025-12-18 11:25:17 -08:00
transaction.go
refactor: rename Ephemeral → Wisp (Steam Engine metaphor)
2025-12-21 15:22:45 -08:00
underlying_db_test.go
Context propagation with graceful cancellation (bd-rtp, bd-yb8, bd-2o2)
2025-11-20 21:57:23 -05:00
util_test.go
Implement transaction retry logic for SQLITE_BUSY (bd-ola6)
2025-11-24 01:10:16 -08:00
util.go
fix: resolve golangci-lint errors
2025-11-24 22:21:55 -08:00
validators_test.go
feat(bd-1pj6): Add custom status states via config
2025-11-28 23:19:21 -08:00
validators.go
fix(types): add tombstone validation and block direct status update (bd-md2, bd-y68)
2025-12-05 15:41:35 -08:00