bd sync: 2025-11-23 18:15:28

.beads/beads.jsonl

@@ -12,7 +12,7 @@
 {"id":"bd-08e556f2","content_hash":"28b2065e9b7db7e38076149d06be8bfbe8dbebc93454ee170c567c1c106e9cc7","title":"Remove Cache Configuration Docs","description":"Remove documentation of deprecated cache env vars","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-28T10:50:15.125488-07:00","updated_at":"2025-10-30T17:12:58.216329-07:00","closed_at":"2025-10-28T10:48:20.606979-07:00","source_repo":"."}
 {"id":"bd-08fd","content_hash":"1fc998c05fb1ccb8725bc0fe9b930b201c0c291353b9f9d578c44865eef5dde9","title":"Test child issue","description":"","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-02T11:50:40.640901-08:00","updated_at":"2025-11-02T11:50:47.309652-08:00","closed_at":"2025-11-02T11:50:47.309652-08:00","source_repo":".","dependencies":[{"issue_id":"bd-08fd","depends_on_id":"bd-ce75","type":"blocks","created_at":"2025-11-02T11:50:40.642073-08:00","created_by":"stevey"}]}
 {"id":"bd-09b5f2f5","content_hash":"e729e70867f4f0c7310e8098b226172374ad145450da0f050c868f5df22a8585","title":"Daemon fails to auto-import after git pull updates JSONL","description":"After git pull updates .beads/issues.jsonl, daemon doesn't automatically re-import changes, causing stale data to be shown until next sync cycle (up to 5 minutes).\n\nReproduction:\n1. Repo A: Close issues, export, commit, push\n2. Repo B: git pull (successfully updates .beads/issues.jsonl)\n3. bd show \u003cissue\u003e shows OLD status from daemon's SQLite db\n4. JSONL on disk has correct new status\n\nRoot cause: Daemon sync cycle runs on timer (5min). When user manually runs git pull, daemon doesn't detect JSONL was updated externally and continues serving stale data from SQLite.\n\nImpact:\n- High for AI agents using beads in git workflows\n- Breaks fundamental git-as-source-of-truth model\n- Confusing UX: git log shows commit, bd shows old state\n- Data consistency issues between JSONL and daemon\n\nSee WYVERN_SYNC_ISSUE.md for full analysis.","notes":"**Fixed in v0.21.2!**\n\nThe daemon auto-import is fully implemented:\n- internal/autoimport package handles staleness detection\n- internal/importer package provides shared import logic (used by both CLI and daemon)\n- daemon's checkAndAutoImportIfStale() calls autoimport.AutoImportIfNewer()\n- importFunc uses importer.ImportIssues() with auto-rename enabled\n- All tests passing\n\nThe critical data corruption bug is FIXED:\n✅ After git pull, daemon detects JSONL is newer (mtime check)\n✅ Daemon auto-imports before serving requests\n✅ No stale data served\n✅ No data loss in multi-agent workflows\n\nVerification needed: Run two-repo test to confirm end-to-end behavior.","status":"closed","priority":0,"issue_type":"epic","created_at":"2025-10-25T23:13:12.270766-07:00","updated_at":"2025-11-01T16:52:50.931197-07:00","closed_at":"2025-11-01T16:52:50.931197-07:00","source_repo":"."}
-{"id":"bd-0a43","content_hash":"36ff43c769f6b0d227c892b20c3af9b1092b38e06cc0f31c0d7c313528be716e","title":"Split monolithic sqlite.go into focused files","description":"internal/storage/sqlite/sqlite.go is 1050 lines containing initialization, 20+ CRUD methods, query building, and schema management.\n\nSplit into:\n- store.go: Store struct \u0026 initialization (150 lines)\n- bead_queries.go: Bead CRUD (300 lines)\n- work_queries.go: Work queries (200 lines)  \n- stats_queries.go: Statistics (150 lines)\n- schema.go: Schema \u0026 migrations (150 lines)\n- helpers.go: Common utilities (100 lines)\n\nImpact: Impossible to understand at a glance; hard to find specific functionality; high cognitive load\n\nEffort: 6-8 hours","status":"open","priority":0,"issue_type":"task","created_at":"2025-11-16T14:51:16.520465-08:00","updated_at":"2025-11-16T14:51:16.520465-08:00","source_repo":"."}
+{"id":"bd-0a43","content_hash":"6aa4836cc78d49f96881bcdd240f0f1af5eea9f3cf7f3819ae80bcaecde37c53","title":"Split monolithic sqlite.go into focused files","description":"internal/storage/sqlite/sqlite.go is 1050 lines containing initialization, 20+ CRUD methods, query building, and schema management.\n\nSplit into:\n- store.go: Store struct \u0026 initialization (150 lines)\n- bead_queries.go: Bead CRUD (300 lines)\n- work_queries.go: Work queries (200 lines)  \n- stats_queries.go: Statistics (150 lines)\n- schema.go: Schema \u0026 migrations (150 lines)\n- helpers.go: Common utilities (100 lines)\n\nImpact: Impossible to understand at a glance; hard to find specific functionality; high cognitive load\n\nEffort: 6-8 hours","status":"closed","priority":0,"issue_type":"task","created_at":"2025-11-16T14:51:16.520465-08:00","updated_at":"2025-11-23T18:15:24.333304-08:00","closed_at":"2025-11-23T18:15:24.333304-08:00","source_repo":"."}
 {"id":"bd-0a90","content_hash":"be65e469d77c475570c8592d4897ca51dccc3f32b45f00f2dee2d8a938eb02f3","title":"bd show --json doesn't include dependency type field","description":"Fix GitHub issue #202. The JSON output from bd show and bd list commands should include the dependency type field (and optionally created_at, created_by) to match internal storage format and enable better tooling integration.","notes":"PR #203 updated with cleaner implementation: https://github.com/steveyegge/beads/pull/203\n\n## Final Implementation\n\nCleanest possible approach - no internal helper methods needed:\n\n**Design:**\n- `GetDependenciesWithMetadata()` / `GetDependentsWithMetadata()` - canonical implementations with full SQL query\n- `GetDependencies()` / `GetDependents()` - thin wrappers that strip metadata for backward compat\n- `scanIssuesWithDependencyType()` - shared helper for scanning rows with dependency type\n\n**Benefits:**\n- Single source of truth - the `...WithMetadata()` methods ARE the implementation\n- Eliminated ~139 lines of duplicated SQL and scanning code\n- All tests passing (14 dependency-related tests)\n- Backward compatible\n- dependency_type field appears correctly in JSON output\n\n**Note on scan helpers:**\nThe duplication between `scanIssues()` and `scanIssuesWithDependencyType()` is necessary because they handle different SQL result shapes (16 vs 17 columns). This is justified as they serve fundamentally different purposes based on query structure.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-02T09:42:08.712725096Z","updated_at":"2025-11-02T11:50:54.292546-08:00","closed_at":"2025-11-02T11:50:54.292546-08:00","source_repo":"."}
 {"id":"bd-0d9c","content_hash":"a61ba371d6c50f21a92e4debeaaa00a4c3eb77ef96fbcdfa89f80e9b13ffff7a","title":"YABB: Spurious issue updates during normal operations","description":"Issue bd-627d was updated during config refactoring session without any actual changes to it. Only timestamps and content_hash changed.\n\nObserved: Running various bd commands (list, create, etc.) caused bd-627d updated_at to change from 14:14 to 14:31.\n\nExpected: Issues should only be updated when explicitly modified.\n\nThis causes:\n- Dirty JSONL after every session\n- False conflicts in git\n- Confusing git history\n\nLikely culprit: Daemon auto-import/export cycle or database migration touching all issues.","notes":"Investigated thoroughly - unable to reproduce. The import logic has IssueDataChanged() checks before calling UpdateIssue (importer/importer.go:458). All tests pass. May have been fixed by recent refactorings. Closing as cannot reproduce - please reopen with specific repro steps if it occurs again.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-02T14:36:31.023552-08:00","updated_at":"2025-11-02T16:27:39.023535-08:00","closed_at":"2025-11-02T16:27:39.023539-08:00","source_repo":"."}
 {"id":"bd-0dcea000","content_hash":"5f3eccf8635195729691e83818486c31c81e608d939e03a2241f944f645ce90d","title":"Add tests for internal/importer package","description":"Currently 0.0% coverage. Need tests for JSONL import logic including collision detection and resolution.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-29T14:06:21.071024-07:00","updated_at":"2025-11-08T22:42:08.859374-08:00","closed_at":"2025-11-08T18:06:20.150657-08:00","source_repo":".","dependencies":[{"issue_id":"bd-0dcea000","depends_on_id":"bd-cbed9619.5","type":"blocks","created_at":"2025-10-29T19:52:05.531279-07:00","created_by":"import-remap"},{"issue_id":"bd-0dcea000","depends_on_id":"bd-cbed9619.4","type":"blocks","created_at":"2025-10-29T19:52:05.53166-07:00","created_by":"import-remap"}]}
@@ -273,6 +273,7 @@
 {"id":"bd-9b13","content_hash":"9a17da93fb23cdcfcc294d2e7e00239973530ab8c5cc08f110112c9924ca94e1","title":"Backend task","description":"","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-03T19:11:59.359262-08:00","updated_at":"2025-11-05T00:25:06.484312-08:00","closed_at":"2025-11-05T00:25:06.484312-08:00","source_repo":"."}
 {"id":"bd-9bsx","content_hash":"f84ca8560b9f09a14af959b4f567647aec050faaa9348775aa08955d913fe9e1","title":"Recurring dirty state after merge conflicts - bd sync keeps failing","description":"## Problem\n\n`bd sync` consistently fails with merge conflicts in `.beads/beads.jsonl`, creating a loop:\n1. User runs `bd sync`\n2. Git merge conflict occurs\n3. User resolves with `git checkout --theirs` (takes remote)\n4. Daemon auto-exports database state (which has local changes)\n5. JSONL becomes dirty again immediately\n6. Repeat\n\nThis has been happening for **weeks** and is extremely frustrating.\n\n## Root Cause\n\nThe recommended conflict resolution (`git checkout --theirs`) throws away local database state (comments, dependencies, closed issues). The daemon then immediately re-exports, creating a dirty state.\n\n## Current Workaround\n\nManual `bd export -o .beads/beads.jsonl \u0026\u0026 git add \u0026\u0026 git commit \u0026\u0026 git push` after every failed sync.\n\n## Example Session\n\n```bash\n$ bd sync\nCONFLICT (content): Merge conflict in .beads/beads.jsonl\n\n$ git checkout --theirs .beads/beads.jsonl \u0026\u0026 bd import \u0026\u0026 git add \u0026\u0026 git commit \u0026\u0026 git push\n# Pushed successfully\n\n$ git status\nmodified: .beads/beads.jsonl  # DIRTY AGAIN!\n```\n\n## Lost Data in Recent Session\n\n- bd-ry1u closure (lost in merge)\n- Comments on bd-08fd, bd-23a8, bd-6049, bd-87a0 (lost)\n- Dependencies that existed only in local DB\n\n## Potential Solutions\n\n1. **Use beads-merge tool** - Implement proper 3-way JSONL merge (bd-bzfy)\n2. **Smarter conflict resolution** - Detect when `--theirs` will lose data, warn user\n3. **Sync validation** - Check if JSONL == DB after merge, re-export if needed\n4. **Daemon awareness** - Pause auto-export during merge resolution\n5. **Transaction log** - Replay local changes after merge instead of losing them\n\n## Related Issues\n\n- bd-bzfy (beads-merge integration)\n- Possibly related to daemon auto-export behavior","notes":"## Solution Implemented\n\nFixed the recurring dirty state after merge conflicts by adding **sync validation** before re-exporting.\n\n### Root Cause\nLines 217-237 in `sync.go` unconditionally re-exported DB to JSONL after every import, even when they were already in sync. This created an infinite loop:\n1. User runs `bd sync` which pulls and imports remote JSONL\n2. Sync unconditionally re-exports DB (which has local changes)\n3. JSONL becomes dirty immediately\n4. Repeat\n\n### Fix\nAdded `dbNeedsExport()` function in `integrity.go` that checks:\n- If JSONL exists\n- If DB modification time is newer than JSONL\n- If DB and JSONL issue counts match\n\nNow `bd sync` only re-exports if DB actually has changes that differ from JSONL.\n\n### Changes\n- Added `dbNeedsExport()` in `cmd/bd/integrity.go` (lines 228-271)\n- Updated `sync.go` lines 217-251 to check before re-exporting\n- Added comprehensive tests in `cmd/bd/sync_merge_test.go`\n\n### Testing\nAll tests pass including 4 new tests:\n- `TestDBNeedsExport_InSync` - Verifies no export when synced\n- `TestDBNeedsExport_DBNewer` - Detects DB modifications\n- `TestDBNeedsExport_CountMismatch` - Catches divergence\n- `TestDBNeedsExport_NoJSONL` - Handles missing JSONL\n\nThis prevents the weeks-long frustration of merge conflicts causing infinite dirty loops.","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-05T17:52:14.776063-08:00","updated_at":"2025-11-05T17:58:35.611942-08:00","closed_at":"2025-11-05T17:58:35.611942-08:00","source_repo":"."}
 {"id":"bd-9cdc","content_hash":"8fcd4366fd76c0db14c73d0c2623abae40ad4c31a2ca663c15f8d3d52ee572d0","title":"Update docs for import bug fix","description":"Update AGENTS.md, README.md, TROUBLESHOOTING.md with import.orphan_handling config documentation. Document resurrection behavior, tombstones, config modes. Add troubleshooting section for import failures with deleted parents.","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-04T12:32:30.770415-08:00","updated_at":"2025-11-04T12:32:30.770415-08:00","source_repo":"."}
+{"id":"bd-9csf","content_hash":"eb8d0bcf406579b2ec37bc462506718fd75fd01c45ea36aab47c4e716dd3e815","title":"Create store.go with Store struct and initialization logic","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-23T18:08:12.295554-08:00","updated_at":"2025-11-23T18:09:47.893126-08:00","closed_at":"2025-11-23T18:09:47.893126-08:00","source_repo":"."}
 {"id":"bd-9e23","content_hash":"fa94af8126d5d8c816a6f83d5ad191ebdb954687abb87ce30e4f67eee4f1a9ce","title":"Optimize Memory backend GetIssueByExternalRef with index","description":"Currently GetIssueByExternalRef in Memory storage uses O(n) linear search through all issues.\n\nCurrent code (memory.go:282-308):\nfor _, issue := range m.issues {\n    if issue.ExternalRef != nil \u0026\u0026 *issue.ExternalRef == externalRef {\n        return \u0026issueCopy, nil\n    }\n}\n\nProposed optimization:\n- Add externalRefToID map[string]string to MemoryStorage\n- Maintain it in CreateIssue, UpdateIssue, DeleteIssue\n- Achieve O(1) lookup like SQLite's index\n\nImpact: Low (--no-db mode typically has smaller datasets)\nRelated: bd-1022","status":"open","priority":4,"issue_type":"chore","created_at":"2025-11-02T15:32:30.242357-08:00","updated_at":"2025-11-02T15:32:30.242357-08:00","source_repo":"."}
 {"id":"bd-9e8d","content_hash":"bde8f3625189415e8f00b06acf530454bec619cabee1332132836d45b26771ed","title":"Test Issue","description":"","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-10-31T21:41:11.107393-07:00","updated_at":"2025-11-01T20:02:28.292279-07:00","closed_at":"2025-11-01T20:02:28.292279-07:00","source_repo":"."}
 {"id":"bd-9f1fce5d","content_hash":"06b6c591090df9e565a67086b354875c5029fce5b60245bce97af7bd63d26166","title":"Add internal/ai package for LLM integration","description":"Shared AI client for repair commands.\n\nProviders:\n- Anthropic (Claude)\n- OpenAI (GPT)\n- Ollama (local)\n\nEnv vars:\n- BEADS_AI_PROVIDER\n- BEADS_AI_API_KEY\n- BEADS_AI_MODEL\n\nFiles: internal/ai/client.go (new)","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-28T14:48:29.072473-07:00","updated_at":"2025-11-06T19:36:13.972045-08:00","closed_at":"2025-11-06T19:27:19.128093-08:00","source_repo":"."}
@@ -603,6 +604,7 @@
 {"id":"bd-srwk","content_hash":"31323f14c508597f94ddfa4a7581728e27433b37615b6bda749778405e9c26ad","title":"bd export should detect and prevent stale database exports","description":"## Problem\n\nWhen `bd export` is run with a stale database (older than issues.jsonl), it silently overwrites the JSONL file with stale data, causing data loss.\n\n## What Happened (vc project)\n\n1. Agent A created 4 new issues and exported to issues.jsonl (commit 99a9d58)\n2. Agent A closed an issue and exported again (commit 58b4613) - JSONL now has 4 epics\n3. Agent B had stale database (from before step 1)\n4. Agent B worked on unrelated issue and exported (commit 0609233)\n5. Agent B's export **overwrote issues.jsonl**, removing the 4 epics created by Agent A\n6. Required manual recovery by re-exporting from Agent A's correct database\n\n## Expected Behavior\n\n`bd export` should detect that the database is stale and either:\n- **Refuse to export** with error message explaining the issue\n- **Warn prominently** and require explicit --force flag to override\n- **Auto-import first** to sync database before exporting\n\n## How to Detect Staleness\n\nCompare modification times (similar to VC's ValidateDatabaseFreshness):\n1. Check .db, .db-wal, .db-shm timestamps (use newest for WAL mode)\n2. Check issues.jsonl timestamp\n3. If JSONL is newer by \u003e1 second: database is stale\n\n## Suggested Fix\n\nAdd staleness check in `bd export`:\n\n```go\nfunc Export(dbPath, jsonlPath string, force bool) error {\n    // Check if database is stale\n    if !force {\n        if err := checkDatabaseFreshness(dbPath, jsonlPath); err != nil {\n            return fmt.Errorf(\"database is stale: %w\\n\" +\n                \"Run 'bd import %s' first to sync, or use --force to override\",\n                err, jsonlPath)\n        }\n    }\n    \n    // Proceed with export...\n}\n```\n\n## Impact\n\n- **Severity**: High (silent data loss)\n- **Frequency**: Happens in multi-agent workflows when agents don't sync\n- **Workaround**: Manual recovery (re-export from correct database)\n\n## References\n\n- VC issue tracker: commits 58b4613 -\u003e 0609233 -\u003e c41c638\n- VC has similar check: `storage.ValidateDatabaseFreshness()`\n- Tolerance: 1 second (handles filesystem timestamp precision)","notes":"Fixed with ID-based comparison instead of just count. Now detects:\n1. DB has fewer issues than JSONL (count check)\n2. DB has different issues than JSONL (ID comparison)\n\nBoth scenarios now properly refuse export unless --force is used.\n\nImplementation uses getIssueIDsFromJSONL() to build a set of IDs from JSONL, then checks if any JSONL IDs are missing from DB. Shows specific missing issue IDs in error message.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-07T19:39:24.172154-08:00","updated_at":"2025-11-07T20:05:13.649736-08:00","closed_at":"2025-11-07T19:58:43.300177-08:00","source_repo":"."}
 {"id":"bd-t3b","content_hash":"c32a3a0f2f836148033fb330e209ac22e06dbecf18894153c15e2036f5afae1c","title":"Add test coverage for internal/config package","description":"","design":"Config package has 1 test file. Need comprehensive tests. Target: 70% coverage","acceptance_criteria":"- At least 3 test files\n- Package coverage \u003e= 70%","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:22.91657-05:00","updated_at":"2025-11-20T21:21:22.91657-05:00","source_repo":".","dependencies":[{"issue_id":"bd-t3b","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.201036-05:00","created_by":"daemon"}]}
 {"id":"bd-t4u1","content_hash":"5558c6e25c6aae4be03fd9f112d892f6e69dc020dee2292a24ec185fb7b6a054","title":"False positive detection by Kaspersky Antivirus (Trojan)","description":"Kaspersky Antivirus falsely detects beads (bd.exe v0.23.1) as a Trojan (PDM:Trojan.Win32.Generic) and removes it.\nEvent: Malicious object detected\nComponent: System Watcher\nObject name: bd.exe\n","status":"open","priority":1,"issue_type":"task","created_at":"2025-11-20T18:56:12.498187-05:00","updated_at":"2025-11-20T18:56:12.498187-05:00","source_repo":"."}
+{"id":"bd-t596","content_hash":"c8c1f1fa6e39e85124c5bdf3072c39d4315f0cd8a09747cb9fc80554e9b106af","title":"Create comments.go with comment methods","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-23T18:08:15.987782-08:00","updated_at":"2025-11-23T18:13:57.446443-08:00","closed_at":"2025-11-23T18:13:57.446443-08:00","source_repo":"."}
 {"id":"bd-t5o","content_hash":"0685a34b3db702956f3ae1478eb6f746db3023ed9cf6a84d94deea9c43bba61d","title":"Document error handling strategy for metadata update failures","description":"Multiple places silently ignore metadata update failures (sync.go:614-617, import.go:320-322) with non-fatal warnings. This is intentional (degrades gracefully to mtime-based approach) but not well documented.\n\nAdd comments explaining:\n- Why these failures are non-fatal\n- How system degrades gracefully\n- What the fallback behavior is (mtime-based detection)","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-20T21:31:12.366861-05:00","updated_at":"2025-11-20T21:36:16.972395-05:00","closed_at":"2025-11-20T21:36:16.972395-05:00","source_repo":".","dependencies":[{"issue_id":"bd-t5o","depends_on_id":"bd-khnb","type":"blocks","created_at":"2025-11-20T21:31:12.367744-05:00","created_by":"daemon"}]}
 {"id":"bd-tbz3","content_hash":"ac416dd2c873a4abb653dfbb689464834000b0c11410c09adf0efb2396a33c48","title":"bd init UX Improvements","description":"bd init leaves users with incomplete setup, requiring manual bd doctor --fix. Issues found: (1) git hooks not installed if user declines prompt, (2) no auto-migration when CLI is upgraded, (3) stale merge driver configs from old versions. Fix by making bd init more robust with better defaults and auto-migration.","status":"open","priority":1,"issue_type":"epic","created_at":"2025-11-21T23:16:00.333543-08:00","updated_at":"2025-11-21T23:16:37.811233-08:00","source_repo":"."}
 {"id":"bd-tmdx","content_hash":"0976d6529458902f06108d5d316fda3bf6ed299eaa684501aada481d9e4b10a5","title":"Investigate database pollution - unexpected issue count increases","description":"Two repositories showing unexpected issue counts:\n- ~/src/beads: 280 issues (expected ~209-220)\n- ~/src/dave/beads: 895 issues (675 open, 149 closed)\n\nThis suggests database pollution - issues from one repository leaking into another. Need to investigate:\n1. Run bd detect-pollution on both repos\n2. Check for cross-repo contamination\n3. Identify source of pollution (daemon? multi-repo config? import issues?)\n4. Clean up polluted databases\n5. Prevent future pollution","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-06T22:50:16.957689-08:00","updated_at":"2025-11-07T00:05:38.994405-08:00","closed_at":"2025-11-07T00:05:38.994405-08:00","source_repo":"."}
@@ -627,9 +629,12 @@
 {"id":"bd-wfmw","content_hash":"21706f1701be9fb51fa9e17d1dded6343bc2585e4bdb608239a20c5853d00220","title":"Integration Layer Implementation","description":"Build the adapter layer that makes Agent Mail optional and non-intrusive.","notes":"Progress: bd-m9th (Python adapter library) completed with full test coverage. Next: bd-fzbg (update python-agent example with Agent Mail integration).","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-11-07T22:42:09.356429-08:00","updated_at":"2025-11-08T00:20:30.888756-08:00","closed_at":"2025-11-08T00:20:30.888756-08:00","source_repo":".","dependencies":[{"issue_id":"bd-wfmw","depends_on_id":"bd-spmx","type":"blocks","created_at":"2025-11-07T22:42:09.357488-08:00","created_by":"daemon"}]}
 {"id":"bd-wgu4","content_hash":"31cf5cc105fee5de26f4c2756b8368c90b18eb5f65c656eb0d90f96b23daf21d","title":"Standardize daemon detection: use tryDaemonLock probe before RPC","description":"Before attempting RPC connection, call tryDaemonLock() to check if lock is held:\n- If lock NOT held: skip RPC attempt (no daemon running)\n- If lock IS held: proceed with RPC + short timeout\n\nThis is extremely cheap and eliminates unnecessary connection attempts.\n\nApply across all client entry points that probe for daemon.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-07T16:42:12.709802-08:00","updated_at":"2025-11-07T20:15:23.282181-08:00","closed_at":"2025-11-07T20:15:23.282181-08:00","source_repo":".","dependencies":[{"issue_id":"bd-wgu4","depends_on_id":"bd-ndyz","type":"discovered-from","created_at":"2025-11-07T16:42:12.710564-08:00","created_by":"daemon"}]}
 {"id":"bd-woro","content_hash":"c638f71927d96ea8e8f8aeeb9f8bcd236241124fbaf1589d2b62977b64db3ebb","title":"Separate canonical BD_GUIDE.md from AGENTS.md","description":"Create architectural separation between bd-specific instructions and project-specific instructions.\n\n## Problem\nCurrently AGENTS.md mixes:\n- bd tool documentation (changes with bd upgrades)\n- Project-specific workflow (stable, manually maintained)\n\nThis makes it hard to update bd instructions without touching project docs.\n\n## Solution\n1. Generate .beads/BD_GUIDE.md from 'bd onboard' output\n2. Mark it as auto-generated (never manually edit)\n3. Version-stamp header with bd version\n4. AGENTS.md references it instead of duplicating content\n5. Auto-update BD_GUIDE.md when bd version changes\n\n## Implementation\n- Add 'bd onboard --output .beads/BD_GUIDE.md' option\n- Detect version changes and offer to regenerate\n- Add header: '\u003c!-- Auto-generated by bd v0.24.2 - DO NOT EDIT --\u003e'\n- Update AGENTS.md to reference BD_GUIDE.md\n\n## Benefits\n- Clear separation of concerns\n- Deterministic updates (no agent LLM involved)\n- Git-trackable diffs show exactly what changed\n- Progressive disclosure (agents read when needed)\n\n## Acceptance Criteria\n- BD_GUIDE.md auto-generated and version-stamped\n- AGENTS.md references it appropriately\n- Upgrade workflow auto-updates BD_GUIDE.md\n- Git diffs clearly show bd instruction changes\n","status":"open","priority":3,"issue_type":"feature","created_at":"2025-11-23T16:21:55.451925-08:00","updated_at":"2025-11-23T16:21:55.451925-08:00","source_repo":".","dependencies":[{"issue_id":"bd-woro","depends_on_id":"bd-nxgk","type":"parent-child","created_at":"2025-11-23T16:21:55.453758-08:00","created_by":"daemon"}]}
+{"id":"bd-wpkz","content_hash":"b969a61c088b0ef8381a01b47299d33a8fd363673cc4f350276bb077611bc6b2","title":"Run tests to ensure refactoring didn't break anything","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-23T18:08:17.264759-08:00","updated_at":"2025-11-23T18:15:22.990153-08:00","closed_at":"2025-11-23T18:15:22.990153-08:00","source_repo":".","dependencies":[{"issue_id":"bd-wpkz","depends_on_id":"bd-9csf","type":"blocks","created_at":"2025-11-23T18:08:30.928086-08:00","created_by":"daemon"},{"issue_id":"bd-wpkz","depends_on_id":"bd-wrfz","type":"blocks","created_at":"2025-11-23T18:08:31.009873-08:00","created_by":"daemon"},{"issue_id":"bd-wpkz","depends_on_id":"bd-x2ba","type":"blocks","created_at":"2025-11-23T18:08:31.080663-08:00","created_by":"daemon"},{"issue_id":"bd-wpkz","depends_on_id":"bd-t596","type":"blocks","created_at":"2025-11-23T18:08:31.153866-08:00","created_by":"daemon"}]}
+{"id":"bd-wrfz","content_hash":"eba509a0eb4d64d4287c412fe3bc805954eeb29b48c86af179cbd5d08ae236ec","title":"Create queries.go with core issue CRUD methods","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-23T18:08:13.46714-08:00","updated_at":"2025-11-23T18:12:55.233765-08:00","closed_at":"2025-11-23T18:12:55.233765-08:00","source_repo":"."}
 {"id":"bd-wta","content_hash":"3ddfd95f7568b1de017abeea869dfead922ee11e656edd2ece5f9544e6995976","title":"Add performance benchmarks for multi-repo hydration","description":"The contributor-workflow-analysis.md asserts sub-second queries (line 702) and describes smart caching via file mtime tracking (Decision #4, lines 584-618), but doesn't provide concrete performance benchmarks.\n\nVC's requirement (from VC feedback section):\n- Executor polls GetReadyWork() every 5-10 seconds\n- Queries must be sub-second (ideally \u003c100ms)\n- Smart caching must avoid re-parsing JSONLs on every query\n\nSuggested performance targets to validate:\n- File stat overhead: \u003c1ms per repo\n- Hydration (when needed): \u003c500ms for typical JSONL (\u003c25k)\n- Query (from cache): \u003c10ms\n- Total GetReadyWork(): \u003c100ms (VC's requirement)\n\nAlso test at scale:\n- N=1 repo (baseline)\n- N=3 repos (typical)\n- N=10 repos (edge case)\n\nThese benchmarks are critical for library consumers like VC that run automated polling loops.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-03T20:24:39.331528-08:00","updated_at":"2025-11-05T14:17:15.079226-08:00","closed_at":"2025-11-05T14:17:15.079226-08:00","source_repo":"."}
 {"id":"bd-wv9l","content_hash":"8d3b659a15de39980c6e9e643b909e9f60ceb2e1515a6474a9232eb53bd70d59","title":"Code Review Sweep: thorough","description":"Perform thorough code review sweep based on accumulated activity.\n\n**AI Reasoning:**\nSignificant code activity with 7608 lines added and 120 files changed indicates substantial modifications. Multiple high-churn areas (cmd/bd, internal/rpc) suggest potential for subtle issues and emerging patterns that warrant review.\n\n**Scope:** thorough\n**Target Areas:** cmd/bd, internal/rpc, .beads\n**Estimated Files:** 12\n**Estimated Cost:** $5\n\n**Task:**\nReview files for non-obvious issues that agents miss during focused work:\n- Inefficiencies (algorithmic, resource usage)\n- Subtle bugs (race conditions, off-by-one, copy-paste)\n- Poor patterns (coupling, complexity, duplication)\n- Missing best practices (error handling, docs, tests)\n- Unnamed anti-patterns\n\nFile discovered issues with detailed reasoning and suggestions.","status":"open","priority":1,"issue_type":"task","created_at":"2025-11-21T23:23:16.056392-08:00","updated_at":"2025-11-21T23:23:16.056392-08:00","source_repo":"."}
 {"id":"bd-ww0g","content_hash":"973e5e6eb58975fcbe80f804b69a900cde824af4b51243737ef5fca404d0b1c1","title":"MCP server: \"No workspace set\" and \"chunk longer than limit\" errors","description":"Two related errors reported in beads-mcp v0.21:\n\n**Error 1: \"No workspace set\" after successful set_context**\n```\n✓ Set beads context\n✗ list\n  Error calling tool 'list': No workspace set. Either provide workspace_root\n  parameter or call set_context() first.\n```\n\nHypothesis: Environment variable persistence issue between MCP tool calls, or ContextVar not being set correctly by @with_workspace decorator.\n\n**Error 2: \"Separator is found, but chunk is longer than limit\"**\n```\n✗ list\n  Error calling tool 'list': Separator is found, but chunk is longer than limit\n```\n\nHypothesis: MCP protocol output size limit exceeded. Large issue databases may produce JSON output that exceeds MCP stdio buffer limits.\n\nPlatform: Fedora 43, using copilot-cli with Sonnet 4.5\n\nWorkaround: CLI works fine (`bd list --status open --json`)","notes":"## Fixes Implemented\n\n**Issue 1: \"No workspace set\" after successful set_context** ✅ FIXED\n\nRoot cause: os.environ doesn't persist across MCP tool calls. When set_context() set BEADS_WORKING_DIR in os.environ, that change was lost on the next tool call.\n\nSolution:\n- Added module-level _workspace_context dict for persistent storage (server.py:51)\n- Modified set_context() to store in both persistent dict and os.environ (server.py:265-287)\n- Modified with_workspace() decorator to check persistent context first (server.py:129-133)\n- Updated where_am_i() to check persistent context (server.py:302-330)\n\n**Issue 2: \"chunk longer than limit\"** ✅ FIXED\n\nRoot cause: MCP stdio protocol has buffer limits. Large issue lists with full dependencies/dependents exceed this.\n\nSolution:\n- Reduced default list limit from 50 to 20 (server.py:356, models.py:122)\n- Reduced max list limit from 1000 to 100 (models.py:122)\n- Strip dependencies/dependents from list() and ready() responses (server.py:343-350, 368-373)\n- Full dependency details still available via show() command\n\n## Testing\n\n✅ Python syntax validated with py_compile\n✅ Changes are backward compatible\n✅ Persistent context falls back to os.environ for compatibility\n\nUsers should now be able to call set_context() once and have it persist across all subsequent tool calls. Large databases will no longer cause buffer overflow errors.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-07T14:32:18.315155-08:00","updated_at":"2025-11-07T21:02:55.470937-08:00","closed_at":"2025-11-07T16:53:46.929942-08:00","source_repo":"."}
+{"id":"bd-x2ba","content_hash":"ed3979ae9f312546d4fcd06ba3f47818bb1c06d684e8ef2c8817147d979743b9","title":"Create config.go with config and metadata methods","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-23T18:08:14.746163-08:00","updated_at":"2025-11-23T18:13:11.540896-08:00","closed_at":"2025-11-23T18:13:11.540896-08:00","source_repo":"."}
 {"id":"bd-x47","content_hash":"154fbcc3e83f9acb57f9bf9def045444d58ff06f8c8a444c5ce2eba6059f7abf","title":"Add guidance for self-hosting projects","description":"The contributor-workflow-analysis.md is optimized for OSS contributors making PRs to upstream projects. However, it doesn't address projects like VC that use beads for their own development (self-hosting).\n\nSelf-hosting projects differ from OSS contributors:\n- No upstream/downstream distinction (they ARE the project)\n- May run automated executors (not just humans)\n- In bootstrap/early phase (stability matters)\n- Single team/owner (not multiple contributors with permissions)\n\nGuidance needed on:\n- When self-hosting projects should stay single-repo (default, recommended)\n- When they should adopt multi-repo (team planning, multi-phase dev)\n- How automated executors should handle multi-repo (if at all)\n- Special considerations for projects in bootstrap phase\n\nExamples of self-hosting projects: VC (building itself with beads), internal tools, pet projects","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-03T20:24:27.805341-08:00","updated_at":"2025-11-05T14:16:34.69662-08:00","closed_at":"2025-11-05T14:16:34.69662-08:00","source_repo":"."}
 {"id":"bd-xo6b","content_hash":"a8f6100ae8d6569c75565d5a1aacbc0e55806fab917399ab473fb212fa694b80","title":"Review multi-repo deletion tracking implementation","description":"Thoroughly review the multi-repo deletion tracking fix (bd-4oob):\n\nFiles changed:\n- cmd/bd/deletion_tracking.go: Added getMultiRepoJSONLPaths() helper\n- cmd/bd/daemon_sync.go: Updated snapshot capture/update logic for multi-repo\n- cmd/bd/deletion_tracking_test.go: Added 2 new tests (287 lines)\n\nReview focus areas:\n1. Correctness: Does getMultiRepoJSONLPaths() handle all edge cases?\n2. Performance: Calling getMultiRepoJSONLPaths() 3x per sync (snapshot capture, merge, base update) - should we cache?\n3. Error handling: What if some repos fail snapshot operations but others succeed?\n4. Race conditions: Multiple daemons in different repos?\n5. Test coverage: Are TestMultiRepoDeletionTracking and TestMultiRepoSnapshotIsolation sufficient?\n6. Path handling: Absolute vs relative paths, tilde expansion\n\nThis is fresh code - needs careful review before considering deletion tracking production-ready.","notes":"Code review completed. Overall assessment: Core deletion tracking logic is sound, but error handling and path handling issues make this not yet production-ready for multi-repo scenarios.\n\nKey findings:\n\nCRITICAL ISSUES (Priority 1):\n1. Inconsistent error handling in daemon_sync.go - snapshot/merge fail hard but base update warns. Can leave DB in inconsistent state with no rollback. See bd-sjmr.\n2. No path normalization in getMultiRepoJSONLPaths() - tilde expansion, relative paths, duplicates not handled. See bd-iye7.\n\nSHOULD FIX (Priority 2):\n3. Missing test coverage for edge cases - empty paths, duplicates, partial failures. See bd-kdoh.\n4. Performance - getMultiRepoJSONLPaths() called 3x per sync (minor issue). See bd-we4p.\n\nWHAT WORKS WELL:\n- Atomic file operations with PID-based temp files\n- Good snapshot isolation between repos\n- Race condition protection via exclusive locks\n- Solid test coverage for happy path scenarios\n\nVERDICT: Address bd-iye7 and bd-sjmr before considering deletion tracking production-ready for multi-repo mode.\n\nDetailed review notes available in conversation history.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-06T19:23:52.402949-08:00","updated_at":"2025-11-06T19:32:34.160341-08:00","closed_at":"2025-11-06T19:32:34.160341-08:00","source_repo":".","dependencies":[{"issue_id":"bd-xo6b","depends_on_id":"bd-rbxi","type":"parent-child","created_at":"2025-11-06T19:23:52.403723-08:00","created_by":"daemon"}]}
 {"id":"bd-xwo","content_hash":"48264aedbfd8cd9ea8ab6ca37882497be431f2827004554058645b610adc3009","title":"Fix validatePreExport to use content hash instead of mtime","description":"validatePreExport() in integrity.go:70 still uses isJSONLNewer() (mtime-based), creating inconsistent behavior. Auto-import correctly uses hasJSONLChanged() (hash-based) but export validation still uses the old mtime approach. This can cause false positive blocks after git operations.\n\nFix: Replace isJSONLNewer() call with hasJSONLChanged() in validatePreExport().\n\nImpact: Without this fix, the bd-khnb solution is incomplete - we prevent resurrection but still have export blocking issues.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-20T21:31:03.183164-05:00","updated_at":"2025-11-20T21:34:00.200803-05:00","closed_at":"2025-11-20T21:34:00.200803-05:00","source_repo":".","dependencies":[{"issue_id":"bd-xwo","depends_on_id":"bd-khnb","type":"blocks","created_at":"2025-11-20T21:31:03.184049-05:00","created_by":"daemon"}]}