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bd sync: 2025-11-28 19:50:16

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Steve Yegge
2025-11-28 19:50:16 -08:00
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@@ -11,7 +11,7 @@
{"id":"bd-4ew","title":"bd doctor should detect fresh clone and recommend 'bd init'","description":"When running `bd doctor` on a fresh clone (JSONL exists, no .db file), it should:\n\n1. Detect this is a fresh clone situation\n2. Recommend `bd init --prefix \u003cdetected-prefix\u003e` as the fix\n3. Show the prefix detected from the JSONL file\n\nCurrently it shows various warnings (git hooks, merge driver, etc.) but doesn't address the fundamental issue: the database needs to be hydrated.","status":"open","priority":2,"issue_type":"feature","created_at":"2025-11-27T20:21:15.691764-08:00","updated_at":"2025-11-27T20:21:15.691764-08:00"}
{"id":"bd-4h3","title":"Add test coverage for internal/git package","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:23.497486-05:00","updated_at":"2025-11-20T21:21:23.497486-05:00","dependencies":[{"issue_id":"bd-4h3","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.277639-05:00","created_by":"daemon"}]}
{"id":"bd-4l5","title":"bd prime: Detect ephemeral branches and adjust workflow output","description":"When 'bd prime' runs on a branch with no upstream (ephemeral branch), it should output a different SESSION CLOSE PROTOCOL.\n\n**Current output (wrong for ephemeral branches):**\n```\n[ ] 1. git status\n[ ] 2. git add \u003cfiles\u003e\n[ ] 3. bd sync\n[ ] 4. git commit -m \"...\"\n[ ] 5. bd sync\n[ ] 6. git push\n```\n\n**Needed output for ephemeral branches:**\n```\n[ ] 1. git status\n[ ] 2. git add \u003cfiles\u003e\n[ ] 3. bd sync --from-main (pull updates from main)\n[ ] 4. git commit -m \"...\"\n[ ] 5. (no push - branch is ephemeral)\n```\n\n**Detection:** `git rev-parse --abbrev-ref --symbolic-full-name @{u}` returns error code 128 if no upstream.\n\nAlso update Sync \u0026 Collaboration section to mention `bd sync --from-main` for ephemeral branches.\n\n**Use case:** Gastown polecats work on ephemeral local branches that are never pushed. Their code gets merged to main via local merge, and beads changes stay local (communicated via gm mail to Overseer).","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-11-25T16:55:24.984104-08:00","updated_at":"2025-11-25T17:12:46.604978-08:00","closed_at":"2025-11-25T17:12:46.604978-08:00"}
{"id":"bd-4pv","title":"bd export only outputs 1 issue after auto-import corrupts database","description":"When auto-import runs and purges issues (due to git history backfill bug), subsequent 'bd export' only exports 1 issue even though the database should have many.\n\nReproduction:\n1. Have issues.jsonl with 55 issues\n2. Auto-import triggers and purges all issues via git history backfill\n3. Run 'bd export' - only exports 1 issue (the last one created before corruption)\n\nThe database gets into an inconsistent state where most issues are purged but export doesn't realize this.\n\nWorkaround: Rebuild database from scratch with 'rm .beads/beads.db \u0026\u0026 bd init --prefix bd'","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:40.828866-08:00","updated_at":"2025-11-28T18:52:00.34687-08:00","closed_at":"2025-11-27T22:50:35.036227-08:00"}
{"id":"bd-4pv","title":"bd export only outputs 1 issue after auto-import corrupts database","description":"When auto-import runs and purges issues (due to git history backfill bug), subsequent 'bd export' only exports 1 issue even though the database should have many.\n\nReproduction:\n1. Have issues.jsonl with 55 issues\n2. Auto-import triggers and purges all issues via git history backfill\n3. Run 'bd export' - only exports 1 issue (the last one created before corruption)\n\nThe database gets into an inconsistent state where most issues are purged but export doesn't realize this.\n\nWorkaround: Rebuild database from scratch with 'rm .beads/beads.db \u0026\u0026 bd init --prefix bd'","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:40.828866-08:00","updated_at":"2025-11-28T17:28:55.545056-08:00","closed_at":"2025-11-27T22:50:35.036227-08:00"}
{"id":"bd-4t7","title":"Auto-import runs during --no-auto-import operations via stats/ready commands","description":"Even when using --no-auto-import flag, certain commands like 'bd stats' and 'bd ready' still trigger auto-import internally, which can cause the git history backfill bug to corrupt data.\n\nExample:\n bd stats --no-auto-import\n # Still prints 'Purged bd-xxx (recovered from git history...)'\n\nThe flag should completely disable auto-import for the command, but it appears some code paths still trigger it.\n\nWorkaround: Use --allow-stale instead, or --sandbox mode.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:59.305898-08:00","updated_at":"2025-11-27T00:54:20.335013-08:00","closed_at":"2025-11-27T00:54:12.561872-08:00"}
{"id":"bd-5bj","title":"Registry has cross-process race condition","description":"The global daemon registry (~/.beads/registry.json) can be corrupted when multiple daemons from different workspaces write simultaneously.\n\n**Root cause:**\n- Registry uses an in-process mutex but no file-level locking\n- Register() and Unregister() release the mutex between read and write\n- Multiple daemon processes can interleave their read-modify-write cycles\n\n**Evidence:**\nFound registry.json with double closing bracket: `]]` instead of `]`\n\n**Fix options:**\n1. Use file locking (flock/fcntl) around the entire read-modify-write cycle\n2. Use atomic write pattern (write to temp file, rename)\n3. Both (belt and suspenders)\n\n**Files:**\n- internal/daemon/registry.go:46-64 (readEntries)\n- internal/daemon/registry.go:67-87 (writeEntries)\n- internal/daemon/registry.go:90-108 (Register - the race window)","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-27T13:55:50.426188-08:00","updated_at":"2025-11-27T14:07:06.22622-08:00","closed_at":"2025-11-27T14:07:06.22622-08:00"}
{"id":"bd-736d","title":"Refactor path canonicalization into helper function","description":"The path canonicalization logic (filepath.Abs + EvalSymlinks) is duplicated in 3 places:\n- beads.go:131-137 (BEADS_DIR handling)\n- cmd/bd/main.go:446-451 (--no-db cleanup)\n- cmd/bd/nodb.go:26-31 (--no-db initialization)\n\nRefactoring suggestion:\nExtract to a helper function like:\n func canonicalizePath(path string) string\n\nThis would:\n- Reduce code duplication\n- Make the logic easier to maintain\n- Ensure consistent behavior across all path handling\n\nRelated to bd-e16b implementation.","status":"closed","priority":3,"issue_type":"chore","created_at":"2025-11-02T18:33:47.727443-08:00","updated_at":"2025-11-25T22:27:33.738672-08:00","closed_at":"2025-11-25T22:27:33.738672-08:00"}
@@ -30,7 +30,7 @@
{"id":"bd-c4rq","title":"Refactor: Move staleness check inside daemon branch","description":"## Problem\n\nCurrently ensureDatabaseFresh() is called before the daemon mode check, but it checks daemonClient != nil internally and returns early. This is redundant.\n\n**Location:** All read commands (list.go:196, show.go:27, ready.go:102, status.go:80, etc.)\n\n## Current Pattern\n\nCall happens before daemon check, function checks daemonClient internally.\n\n## Better Pattern\n\nMove staleness check to direct mode branch only, after daemon check.\n\n## Impact\nLow - minor performance improvement (avoids one function call per command in daemon mode)\n\n## Effort\nMedium - requires refactoring 8 command files\n\n## Priority\nLow - can defer to future cleanup PR","status":"open","priority":3,"issue_type":"chore","created_at":"2025-11-20T20:17:45.119583-05:00","updated_at":"2025-11-20T20:17:45.119583-05:00"}
{"id":"bd-c8x","title":"Don't search parent directories for .beads databases","description":"bd currently walks up the directory tree looking for .beads directories, which can find unrelated databases (e.g., ~/.beads). This causes confusing warnings and potential data pollution.\n\nShould either:\n1. Stop at git root (don't search above it)\n2. Only use explicit BEADS_DB env var or local .beads\n3. At minimum, don't search in home directory","status":"open","priority":2,"issue_type":"bug","created_at":"2025-11-27T22:10:41.992686-08:00","updated_at":"2025-11-27T22:10:41.992686-08:00"}
{"id":"bd-d4i","title":"Create tip system infrastructure for contextual hints","description":"Implement a tip/hint system that shows helpful contextual messages after successful commands. This is different from the existing error-path \"Hint:\" messages - tips appear on success paths to educate users about features they might not know about.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-11T23:29:15.693956-08:00","updated_at":"2025-11-25T17:47:30.747566-08:00","closed_at":"2025-11-25T17:47:30.747566-08:00"}
{"id":"bd-dmb","title":"Fresh clone: bd should suggest 'bd init' when no database exists","description":"On a fresh clone of a repo using beads, running `bd stats` or `bd list` gives a cryptic error:\n\n```\nError: failed to open database: post-migration validation failed: migration invariants failed:\n - required_config_present: required config key missing: issue_prefix (database has 2 issues)\n```\n\n**Expected**: A helpful message like:\n```\nNo database found. This appears to be a fresh clone.\nRun 'bd init --prefix \u003cprefix\u003e' to hydrate from the committed JSONL file.\nFound: .beads/beads.jsonl (38 issues)\n```\n\n**Why this matters**: The current UX is confusing for new contributors or fresh clones. The happy path should be obvious.","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-11-27T20:21:04.947959-08:00","updated_at":"2025-11-28T18:52:00.347638-08:00","closed_at":"2025-11-27T22:40:11.654051-08:00"}
{"id":"bd-dmb","title":"Fresh clone: bd should suggest 'bd init' when no database exists","description":"On a fresh clone of a repo using beads, running `bd stats` or `bd list` gives a cryptic error:\n\n```\nError: failed to open database: post-migration validation failed: migration invariants failed:\n - required_config_present: required config key missing: issue_prefix (database has 2 issues)\n```\n\n**Expected**: A helpful message like:\n```\nNo database found. This appears to be a fresh clone.\nRun 'bd init --prefix \u003cprefix\u003e' to hydrate from the committed JSONL file.\nFound: .beads/beads.jsonl (38 issues)\n```\n\n**Why this matters**: The current UX is confusing for new contributors or fresh clones. The happy path should be obvious.","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-11-27T20:21:04.947959-08:00","updated_at":"2025-11-27T22:40:11.654051-08:00","closed_at":"2025-11-27T22:40:11.654051-08:00"}
{"id":"bd-e166","title":"Improve timestamp comparison readability in import","description":"The timestamp comparison logic uses double-negative which can be confusing:\n\nCurrent code:\nif !incoming.UpdatedAt.After(existing.UpdatedAt) {\n // skip update\n}\n\nMore readable:\nif incoming.UpdatedAt.After(existing.UpdatedAt) {\n // perform update\n} else {\n // skip (local is newer)\n}\n\nThis is a minor refactor for code clarity.\n\nRelated: bd-1022\nFiles: internal/importer/importer.go:411, 488","status":"closed","priority":4,"issue_type":"chore","created_at":"2025-11-02T15:32:12.27108-08:00","updated_at":"2025-11-26T22:25:27.124071-08:00","closed_at":"2025-11-26T22:25:27.124071-08:00"}
{"id":"bd-e6x","title":"bd sync --squash: batch multiple syncs into single commit","description":"For solo developers who don't need real-time multi-agent coordination, add a --squash option to bd sync that accumulates changes and commits them in a single commit rather than one commit per sync.\n\nThis addresses the git history pollution concern (many 'bd sync: timestamp' commits) while preserving the default behavior needed for orchestration.\n\n**Proposed behavior:**\n- `bd sync --squash` accumulates pending exports without committing\n- Commits accumulated changes on session end or explicit `bd sync` (without --squash)\n- Default behavior unchanged (immediate commits for orchestration)\n\n**Use case:** Solo developers who want cleaner git history but don't need real-time coordination between agents.\n\n**Related:** PR #411 (docs: reduce bd sync commit pollution)\n**See also:** Multi-repo support as alternative solution (docs/MULTI_REPO_AGENTS.md)","status":"open","priority":3,"issue_type":"feature","created_at":"2025-11-28T18:21:47.789887-08:00","updated_at":"2025-11-28T18:21:47.789887-08:00"}
{"id":"bd-e92","title":"Add test coverage for internal/autoimport package","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:22.338577-05:00","updated_at":"2025-11-20T21:21:22.338577-05:00","dependencies":[{"issue_id":"bd-e92","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.128625-05:00","created_by":"daemon"}]}
@@ -39,8 +39,8 @@
{"id":"bd-ge7","title":"Improve Beads test coverage from 46% to 80%","description":"","status":"open","priority":1,"issue_type":"epic","created_at":"2025-11-20T21:21:03.700271-05:00","updated_at":"2025-11-20T21:21:03.700271-05:00"}
{"id":"bd-ghb","title":"Add --yes flag to bd doctor --fix for non-interactive mode","description":"## Feature Request\n\nAdd a `--yes` or `-y` flag to `bd doctor --fix` that automatically confirms all prompts, enabling non-interactive usage in scripts and CI/CD pipelines.\n\n## Current Behavior\n`bd doctor --fix` prompts for confirmation before applying fixes, which blocks automated workflows.\n\n## Desired Behavior\n`bd doctor --fix --yes` should apply all fixes without prompting.\n\n## Use Cases\n- CI/CD pipelines that need to auto-fix issues\n- Scripts that automate repository setup\n- Pre-commit hooks that want to silently fix issues","status":"open","priority":3,"issue_type":"feature","created_at":"2025-11-26T23:22:45.486584-08:00","updated_at":"2025-11-26T23:22:45.486584-08:00"}
{"id":"bd-gqo","title":"Implement health checks in daemon event loop","description":"Add health checks to checkDaemonHealth() function in daemon_event_loop.go:170:\n- Database integrity check\n- Disk space check\n- Memory usage check\n\nCurrently it's just a no-op placeholder.","status":"open","priority":3,"issue_type":"feature","created_at":"2025-11-21T18:55:07.534304-05:00","updated_at":"2025-11-21T18:55:07.534304-05:00"}
{"id":"bd-guc","title":"bd sync should not stage gitignored snapshot files","description":"## Problem\n\n`gitCommitBeadsDir` in `cmd/bd/sync.go` runs `git add .beads/` which stages all files in the directory, including snapshot files that are listed in `.beads/.gitignore`.\n\nIf a snapshot file (e.g., `beads.left.meta.json`) was ever committed before being added to `.gitignore`, git continues to track it. This causes merge conflicts when multiple polecats run `bd sync` concurrently, since each one modifies and commits these temporary files.\n\n## Root Cause\n\nLine ~568 in sync.go:\n```go\naddCmd := exec.CommandContext(ctx, \"git\", \"add\", beadsDir)\n```\n\nThis stages everything in `.beads/`, but `.gitignore` only prevents *untracked* files from being added - it doesn't affect already-tracked files.\n\n## Suggested Fix\n\nOption A: After `git add .beads/`, run `git reset` on snapshot files:\n```go\nexec.Command(\"git\", \"reset\", \"HEAD\", \".beads/beads.*.jsonl\", \".beads/*.meta.json\")\n```\n\nOption B: Stage only specific files instead of the whole directory:\n```go\nexec.Command(\"git\", \"add\", \".beads/issues.jsonl\", \".beads/deletions.jsonl\", \".beads/metadata.json\")\n```\n\nOption C: Detect and untrack snapshot files if they're tracked:\n```go\n// Check if file is tracked: git ls-files --error-unmatch \u003cfile\u003e\n// If tracked, run: git rm --cached \u003cfile\u003e\n```\n\nOption B is probably cleanest - explicitly add only the files that should be committed.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-27T20:47:14.603799-08:00","updated_at":"2025-11-28T18:52:00.347919-08:00","closed_at":"2025-11-27T22:34:23.336713-08:00"}
{"id":"bd-hdt","title":"Implement auto-merge functionality in duplicates command","description":"The duplicates.go file has a TODO at line 95 to implement the performMerge function for automatic duplicate merging. Currently it just prints a warning message. This would automate the merge process instead of just suggesting commands.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-21T18:55:02.828619-05:00","updated_at":"2025-11-27T22:36:11.517878-08:00","closed_at":"2025-11-27T22:36:11.517878-08:00"}
{"id":"bd-guc","title":"bd sync should not stage gitignored snapshot files","description":"## Problem\n\n`gitCommitBeadsDir` in `cmd/bd/sync.go` runs `git add .beads/` which stages all files in the directory, including snapshot files that are listed in `.beads/.gitignore`.\n\nIf a snapshot file (e.g., `beads.left.meta.json`) was ever committed before being added to `.gitignore`, git continues to track it. This causes merge conflicts when multiple polecats run `bd sync` concurrently, since each one modifies and commits these temporary files.\n\n## Root Cause\n\nLine ~568 in sync.go:\n```go\naddCmd := exec.CommandContext(ctx, \"git\", \"add\", beadsDir)\n```\n\nThis stages everything in `.beads/`, but `.gitignore` only prevents *untracked* files from being added - it doesn't affect already-tracked files.\n\n## Suggested Fix\n\nOption A: After `git add .beads/`, run `git reset` on snapshot files:\n```go\nexec.Command(\"git\", \"reset\", \"HEAD\", \".beads/beads.*.jsonl\", \".beads/*.meta.json\")\n```\n\nOption B: Stage only specific files instead of the whole directory:\n```go\nexec.Command(\"git\", \"add\", \".beads/issues.jsonl\", \".beads/deletions.jsonl\", \".beads/metadata.json\")\n```\n\nOption C: Detect and untrack snapshot files if they're tracked:\n```go\n// Check if file is tracked: git ls-files --error-unmatch \u003cfile\u003e\n// If tracked, run: git rm --cached \u003cfile\u003e\n```\n\nOption B is probably cleanest - explicitly add only the files that should be committed.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-27T20:47:14.603799-08:00","updated_at":"2025-11-28T17:28:55.54563-08:00","closed_at":"2025-11-27T22:34:23.336713-08:00"}
{"id":"bd-hdt","title":"Implement auto-merge functionality in duplicates command","description":"The duplicates.go file has a TODO at line 95 to implement the performMerge function for automatic duplicate merging. Currently it just prints a warning message. This would automate the merge process instead of just suggesting commands.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-21T18:55:02.828619-05:00","updated_at":"2025-11-28T19:50:01.115881-08:00","closed_at":"2025-11-27T22:36:11.517878-08:00"}
{"id":"bd-ho5","title":"Add 'town report' command for aggregated swarm status","description":"## Problem\nGetting a full swarm status requires running 6+ commands:\n- `town list \u003crig\u003e` for each rig\n- `town mail inbox` as Boss\n- `bd list --status=open/in_progress` per rig\n\nThis is slow and error-prone for both humans and agents.\n\n## Proposed Solution\nAdd `town report [RIG]` command that aggregates:\n- All rigs with polecat states (running/stopped, awake/asleep)\n- Boss inbox summary (unread count, recent senders)\n- Aggregate issue counts per rig (open/in_progress/blocked)\n\nExample output:\n```\n=== beads ===\nPolecats: 5 (5 running, 0 stopped)\nIssues: 20 open, 0 in_progress, 0 blocked\n\n=== gastown ===\nPolecats: 6 (4 running, 2 stopped)\nIssues: 0 open, 0 in_progress, 0 blocked\n\n=== Boss Mail ===\nUnread: 10 | Total: 22\nRecent: rictus (21:19), scrotus (21:14), immortanjoe (21:14)\n```\n\n## Acceptance Criteria\n- [ ] `town report` shows all rigs\n- [ ] `town report \u003crig\u003e` shows single rig detail\n- [ ] Output is concise and scannable\n- [ ] Completes in \u003c2 seconds","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-27T22:55:36.8919-08:00","updated_at":"2025-11-27T22:56:08.071838-08:00","closed_at":"2025-11-27T22:56:08.071838-08:00"}
{"id":"bd-imj","title":"Deletion propagation via deletions manifest","description":"## Problem\n\nWhen `bd cleanup -f` or `bd delete` removes issues in one clone, those deletions don't propagate to other clones. The import logic only creates/updates, never deletes. This causes \"resurrection\" where deleted issues reappear.\n\n## Root Cause\n\nImport sees DB issues not in JSONL and assumes they're \"local unpushed work\" rather than \"intentionally deleted upstream.\"\n\n## Solution: Deletions Manifest\n\nAdd `.beads/deletions.jsonl` - an append-only log of deleted issue IDs with metadata.\n\n### Format\n```jsonl\n{\"id\":\"bd-xxx\",\"ts\":\"2025-11-25T10:00:00Z\",\"by\":\"stevey\"}\n{\"id\":\"bd-yyy\",\"ts\":\"2025-11-25T10:05:00Z\",\"by\":\"claude\",\"reason\":\"duplicate of bd-zzz\"}\n```\n\n### Fields\n- `id`: Issue ID (required)\n- `ts`: ISO 8601 UTC timestamp (required)\n- `by`: Actor who deleted (required)\n- `reason`: Optional context (\"cleanup\", \"duplicate of X\", etc.)\n\n### Import Logic\n```\nFor each DB issue not in JSONL:\n 1. Check deletions manifest → if found, delete from DB\n 2. Fallback: check git history → if found, delete + backfill manifest\n 3. Neither → keep (local unpushed work)\n```\n\n### Conflict Resolution\nSimultaneous deletions from multiple clones are handled naturally:\n- Append-only design means both clones append their deletion records\n- On merge, file contains duplicate entries (same ID, different timestamps)\n- `LoadDeletions` deduplicates by ID (keeps any/first entry)\n- Result: deletion propagates correctly, duplicates are harmless\n\n### Pruning Policy\n- Default retention: 7 days (configurable via `deletions.retention_days`)\n- Auto-compact during `bd sync` is **opt-in** (disabled by default)\n- Hard cap: `deletions.max_entries` (default 50000)\n- Git fallback handles pruned entries (self-healing)\n\n### Self-Healing\nWhen git fallback catches a resurrection (pruned entry), it backfills the manifest. One-time git scan cost, then fast again.\n\n### Size Estimates\n- ~80 bytes/entry\n- 7-day retention with 100 deletions/day = ~56KB\n- Git compressed: ~10KB\n\n## Benefits\n- ✅ Deletions propagate across clones\n- ✅ O(1) lookup (no git scan in normal case)\n- ✅ Works in shallow clones\n- ✅ Survives history rewrite\n- ✅ Audit trail (who deleted what when)\n- ✅ Self-healing via git fallback\n- ✅ Bounded size via time-based pruning\n\n## References\n- Investigation session: 2025-11-25\n- Related: bd-2q6d (stale database warnings)","status":"closed","priority":0,"issue_type":"epic","created_at":"2025-11-25T09:56:01.98027-08:00","updated_at":"2025-11-25T16:36:27.965168-08:00","closed_at":"2025-11-25T16:36:27.965168-08:00","dependencies":[{"issue_id":"bd-imj","depends_on_id":"bd-qsm","type":"blocks","created_at":"2025-11-25T09:57:42.821911-08:00","created_by":"daemon"},{"issue_id":"bd-imj","depends_on_id":"bd-x2i","type":"blocks","created_at":"2025-11-25T09:57:42.851712-08:00","created_by":"daemon"},{"issue_id":"bd-imj","depends_on_id":"bd-44e","type":"blocks","created_at":"2025-11-25T09:57:42.88154-08:00","created_by":"daemon"},{"issue_id":"bd-imj","depends_on_id":"bd-bhd","type":"blocks","created_at":"2025-11-25T14:56:23.675787-08:00","created_by":"daemon"},{"issue_id":"bd-imj","depends_on_id":"bd-bgs","type":"blocks","created_at":"2025-11-25T14:56:23.744648-08:00","created_by":"daemon"},{"issue_id":"bd-imj","depends_on_id":"bd-f0n","type":"blocks","created_at":"2025-11-25T14:56:23.80649-08:00","created_by":"daemon"},{"issue_id":"bd-imj","depends_on_id":"bd-v29","type":"blocks","created_at":"2025-11-25T14:56:23.864569-08:00","created_by":"daemon"},{"issue_id":"bd-imj","depends_on_id":"bd-mdw","type":"blocks","created_at":"2025-11-25T14:56:48.592492-08:00","created_by":"daemon"},{"issue_id":"bd-imj","depends_on_id":"bd-03r","type":"blocks","created_at":"2025-11-25T14:56:54.295851-08:00","created_by":"daemon"}]}
{"id":"bd-j3zt","title":"Fix mypy errors in beads-mcp","description":"Running `mypy .` in `integrations/beads-mcp` reports 287 errors. These should be addressed to improve type safety and code quality.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-20T18:53:28.557708-05:00","updated_at":"2025-11-27T00:54:20.336256-08:00","closed_at":"2025-11-27T00:37:17.188443-08:00"}
@@ -52,20 +52,20 @@
{"id":"bd-mdw","title":"Add integration test for cross-clone deletion propagation","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T14:56:38.997009-08:00","updated_at":"2025-11-25T16:35:59.052914-08:00","closed_at":"2025-11-25T16:35:59.052914-08:00"}
{"id":"bd-mnap","title":"Investigate performance issues in VS Code Copilot (Windows)","description":"Beads unusable in Windows 11 VS Code Copilot chat with Sonnet 4.5.\nSummary event happens every 3-4 turns, taking 3 minutes.\nCopilot summarizes after ~125k tokens despite model supporting 1M.\nLarge context size of beads might be triggering aggressive summarization.\nNeed workaround or optimization for context size.\n","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T18:56:30.124918-05:00","updated_at":"2025-11-20T18:56:30.124918-05:00"}
{"id":"bd-nq41","title":"Fix Homebrew warning about Ruby file location","description":"Homebrew warning: Found Ruby file outside steveyegge/beads tap formula directory.\nWarning points to: /opt/homebrew/Library/Taps/steveyegge/homebrew-beads/bd.rb\nIt should likely be inside a Formula/ directory or similar structure expected by Homebrew taps.\n","status":"closed","priority":2,"issue_type":"chore","created_at":"2025-11-20T18:56:21.226579-05:00","updated_at":"2025-11-26T22:25:37.362928-08:00","closed_at":"2025-11-26T22:25:37.362928-08:00"}
{"id":"bd-nsb","title":"Doctor should exclude merge artifacts from 'multiple JSONL' warning","description":"Doctor command warns about 'multiple JSONL files' when .base.jsonl and .left.jsonl merge artifacts exist. These are expected during/after merge operations and should be excluded from the warning.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-28T17:27:36.988178-08:00","updated_at":"2025-11-28T18:22:16.903917-08:00","closed_at":"2025-11-28T17:41:50.700658-08:00"}
{"id":"bd-nsb","title":"Doctor should exclude merge artifacts from 'multiple JSONL' warning","description":"Doctor command warns about 'multiple JSONL files' when .base.jsonl and .left.jsonl merge artifacts exist. These are expected during/after merge operations and should be excluded from the warning.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-28T17:27:36.988178-08:00","updated_at":"2025-11-28T18:36:52.087768-08:00","closed_at":"2025-11-28T17:41:50.700658-08:00"}
{"id":"bd-o2e","title":"bd sync --squash: batch multiple syncs into single commit","description":"For solo developers who don't need real-time multi-agent coordination, add a --squash option to bd sync that accumulates changes and commits them in a single commit rather than one commit per sync.\n\nThis addresses the git history pollution concern (many 'bd sync: timestamp' commits) while preserving the default behavior needed for orchestration.\n\n**Proposed behavior:**\n- `bd sync --squash` accumulates pending exports\n- Only commits when explicitly requested or on session end\n- Default behavior unchanged (immediate commits for orchestration)\n\n**Use case:** Solo developers who want cleaner git history but don't need real-time coordination between agents.\n\n**Related:** PR #411 (docs: reduce bd sync commit pollution)\n**See also:** Multi-repo support as alternative solution (docs/MULTI_REPO_AGENTS.md)","status":"open","priority":3,"issue_type":"feature","created_at":"2025-11-28T17:59:37.918686-08:00","updated_at":"2025-11-28T17:59:37.918686-08:00"}
{"id":"bd-ov1","title":"Doctor: exclude merge artifacts from 'multiple JSONL' warning","description":"## Problem\n`bd doctor` warns about 'Multiple JSONL files found' when merge artifact files exist:\n```\nJSONL Files: Multiple JSONL files found: beads.base.jsonl, beads.left.jsonl, issues.jsonl ⚠\n```\n\nThis is confusing because these aren't real issue JSONL files - they're temporary snapshots for deletion tracking.\n\n## Fix\nExclude known merge artifact patterns from the multiple-JSONL warning:\n\n```go\n// In doctor JSONL check\nskipPatterns := map[string]bool{\n \"beads.base.jsonl\": true,\n \"beads.left.jsonl\": true, \n \"beads.right.jsonl\": true,\n}\n```\n\n## Files\n- cmd/bd/doctor/ (JSONL check logic)","status":"open","priority":1,"issue_type":"bug","created_at":"2025-11-28T17:06:26.266097-08:00","updated_at":"2025-11-28T17:06:26.266097-08:00"}
{"id":"bd-p6vp","title":"Clarify .beads/.gitattributes handling in Protected Branches docs","description":"Protected Branches docs quick start leaves untracked `.beads` directory and `.gitattributes`.\nQuestion: Are these changes meant to be checked into the protected branch?\nNeed to clarify if these should be ignored or committed, or if the instructions are missing a step.\n","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T18:56:25.79407-05:00","updated_at":"2025-11-26T22:25:47.574326-08:00","closed_at":"2025-11-26T22:25:47.574326-08:00"}
{"id":"bd-pg1","title":"[CRITICAL] Sync validation false positive - legitimate deletions trigger 'data loss detected'","description":"Sync preflight validation incorrectly detects 'data loss' when legitimate deletions occur. This blocks all syncs and is the highest priority fix.","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-28T17:27:42.179281-08:00","updated_at":"2025-11-28T18:22:16.903409-08:00","closed_at":"2025-11-28T17:42:49.92251-08:00"}
{"id":"bd-pg1","title":"[CRITICAL] Sync validation false positive - legitimate deletions trigger 'data loss detected'","description":"Sync preflight validation incorrectly detects 'data loss' when legitimate deletions occur. This blocks all syncs and is the highest priority fix.","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-28T17:27:42.179281-08:00","updated_at":"2025-11-28T18:36:52.088427-08:00","closed_at":"2025-11-28T17:42:49.92251-08:00"}
{"id":"bd-qsm","title":"Auto-compact deletions during bd sync","description":"Parent: bd-imj\n\n## Task\nOptionally prune deletions manifest during sync when threshold exceeded.\n\n**Note: Opt-in feature** - disabled by default to avoid sync latency.\n\n## Implementation\n\nIn `bd sync`:\n```go\nfunc (s *Syncer) Sync() error {\n // ... existing sync logic ...\n \n // Auto-compact only if enabled\n if s.config.GetBool(\"deletions.auto_compact\", false) {\n deletionCount := deletions.Count(\".beads/deletions.jsonl\")\n threshold := s.config.GetInt(\"deletions.auto_compact_threshold\", 1000)\n \n if deletionCount \u003e threshold {\n retentionDays := s.config.GetInt(\"deletions.retention_days\", 7)\n if err := s.compactor.PruneDeletions(retentionDays); err != nil {\n log.Warnf(\"Failed to auto-compact deletions: %v\", err)\n // Non-fatal, continue sync\n }\n }\n }\n \n // ... rest of sync ...\n}\n```\n\n## Configuration\n```yaml\ndeletions:\n retention_days: 7\n auto_compact: false # Opt-in, disabled by default\n auto_compact_threshold: 1000 # Trigger when \u003e N entries (if enabled)\n```\n\n## Acceptance Criteria\n- [ ] Auto-compact disabled by default\n- [ ] Enabled via config `deletions.auto_compact: true`\n- [ ] Sync checks deletion count only when enabled\n- [ ] Auto-prunes when threshold exceeded\n- [ ] Failure is non-fatal (logged warning)\n- [ ] Test: no compaction when disabled\n- [ ] Test: compaction triggers when enabled and threshold exceeded","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-25T09:57:04.522795-08:00","updated_at":"2025-11-25T15:03:01.469629-08:00","closed_at":"2025-11-25T15:03:01.469629-08:00"}
{"id":"bd-s0z","title":"Consider extracting error handling helpers","description":"Evaluate creating FatalError() and WarnError() helpers as suggested in ERROR_HANDLING.md to reduce boilerplate and enforce consistency. Prototype in a few files first to validate the approach.","status":"open","priority":4,"issue_type":"task","created_at":"2025-11-24T00:28:57.248959-08:00","updated_at":"2025-11-24T00:28:57.248959-08:00"}
{"id":"bd-t3b","title":"Add test coverage for internal/config package","description":"","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","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-tne","title":"Add Claude setup tip with dynamic priority","description":"Add a predefined tip that suggests running `bd setup claude` when Claude Code is detected but not configured. This tip should have higher priority (shown more frequently) until the setup is complete.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-11T23:29:29.871324-08:00","updated_at":"2025-11-25T17:52:35.044989-08:00","closed_at":"2025-11-25T17:52:35.044989-08:00","dependencies":[{"issue_id":"bd-tne","depends_on_id":"bd-d4i","type":"blocks","created_at":"2025-11-11T23:29:29.872081-08:00","created_by":"daemon"}]}
{"id":"bd-tqo","title":"deletions.jsonl gets corrupted with full issue objects instead of deletion records","description":"## Bug Description\n\nThe deletions.jsonl file was found to contain full issue objects (like issues.jsonl) instead of deletion records.\n\n### Expected Format (DeletionRecord)\n```json\n{\"id\":\"bd-xxx\",\"timestamp\":\"2025-...\",\"actor\":\"user\",\"reason\":\"deleted\"}\n```\n\n### Actual Content Found\n```json\n{\"id\":\"bd-03r\",\"title\":\"Document deletions manifest...\",\"description\":\"...\",\"status\":\"closed\",...}\n```\n\n## Impact\n- bd sync sanitization step reads deletions.jsonl and removes any matching IDs from issues.jsonl\n- With 60 full issue objects in deletions.jsonl, ALL 60 issues were incorrectly removed during sync\n- This caused complete data loss of the issue database\n\n## Root Cause (suspected)\nSomething wrote issues.jsonl content to deletions.jsonl. Possible causes:\n- Export writing to wrong file\n- File path confusion during sync\n- Race condition between export and deletion tracking\n\n## Related Issues\n- bd-0b2: --no-git-history flag (just fixed)\n- bd-4pv: export outputs only 1 issue after corruption \n- bd-4t7: auto-import runs during --no-auto-import\n\n## Reproduction\nUnknown - discovered during bd sync session on 2025-11-26\n\n## Fix\nNeed to investigate what code path could write issue objects to deletions.jsonl","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-26T23:17:01.938931-08:00","updated_at":"2025-11-26T23:25:21.445143-08:00","closed_at":"2025-11-26T23:25:02.209911-08:00"}
{"id":"bd-tru","title":"Update documentation for bd prime and Claude integration","description":"Update AGENTS.md, README.md, and QUICKSTART.md to document the new `bd prime` command, `bd setup claude` command, and tip system.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-11T23:30:22.77349-08:00","updated_at":"2025-11-25T17:47:30.807069-08:00","closed_at":"2025-11-25T17:47:30.807069-08:00"}
{"id":"bd-tt0","title":"Sync validation false positive: legitimate deletions trigger 'data loss detected'","description":"## Problem\n`bd sync` fails with false positive data loss detection when legitimate deletions occur:\n```\nPost-import validation failed: import reduced issue count: 26 → 25 (data loss detected!)\n```\n\n## Root Cause\nThe validation in `sync.go:329-340` counts DB issues BEFORE import, but `purgeDeletedIssues()` in `importer.go:159` legitimately removes issues DURING import. The validation doesn't account for expected deletions.\n\n**The Flow:**\n```\nsync.go:293 → beforeCount = countDBIssues() = 26\nsync.go:310-319 → sanitizeJSONL removes deleted issues from JSONL (RemovedCount=N)\nsync.go:323 → importFromJSONL() runs subprocess\n └→ importer.go:159 purgeDeletedIssues() removes issues from DB\nsync.go:331 → afterCount = countDBIssues() = 25\nsync.go:335 → validatePostImport(26, 25) → ERROR\n```\n\n## Fix\nPass `sanitizeResult.RemovedCount` to validation and account for expected deletions:\n\n```go\n// sync.go around line 335\nexpectedDecrease := 0\nif sanitizeResult != nil {\n expectedDecrease = sanitizeResult.RemovedCount\n}\nif err := validatePostImportWithDeletions(beforeCount, afterCount, expectedDecrease); err != nil {\n // ...\n}\n```\n\n```go\n// integrity.go - new or modified function\nfunc validatePostImportWithDeletions(before, after, expectedDeletions int) error {\n if after \u003c before - expectedDeletions {\n return fmt.Errorf(\"unexpected data loss: %d → %d (expected max decrease: %d)\", \n before, after, expectedDeletions)\n }\n // ...\n}\n```\n\n## Files\n- cmd/bd/sync.go:329-340\n- cmd/bd/integrity.go:289-301","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-28T17:06:15.515768-08:00","updated_at":"2025-11-28T18:46:19.722924-08:00","closed_at":"2025-11-28T18:46:19.722924-08:00"}
{"id":"bd-tt0","title":"Sync validation false positive: legitimate deletions trigger 'data loss detected'","description":"## Problem\n`bd sync` fails with false positive data loss detection when legitimate deletions occur:\n```\nPost-import validation failed: import reduced issue count: 26 → 25 (data loss detected!)\n```\n\n## Root Cause\nThe validation in `sync.go:329-340` counts DB issues BEFORE import, but `purgeDeletedIssues()` in `importer.go:159` legitimately removes issues DURING import. The validation doesn't account for expected deletions.\n\n**The Flow:**\n```\nsync.go:293 → beforeCount = countDBIssues() = 26\nsync.go:310-319 → sanitizeJSONL removes deleted issues from JSONL (RemovedCount=N)\nsync.go:323 → importFromJSONL() runs subprocess\n └→ importer.go:159 purgeDeletedIssues() removes issues from DB\nsync.go:331 → afterCount = countDBIssues() = 25\nsync.go:335 → validatePostImport(26, 25) → ERROR\n```\n\n## Fix\nPass `sanitizeResult.RemovedCount` to validation and account for expected deletions:\n\n```go\n// sync.go around line 335\nexpectedDecrease := 0\nif sanitizeResult != nil {\n expectedDecrease = sanitizeResult.RemovedCount\n}\nif err := validatePostImportWithDeletions(beforeCount, afterCount, expectedDecrease); err != nil {\n // ...\n}\n```\n\n```go\n// integrity.go - new or modified function\nfunc validatePostImportWithDeletions(before, after, expectedDeletions int) error {\n if after \u003c before - expectedDeletions {\n return fmt.Errorf(\"unexpected data loss: %d → %d (expected max decrease: %d)\", \n before, after, expectedDeletions)\n }\n // ...\n}\n```\n\n## Files\n- cmd/bd/sync.go:329-340\n- cmd/bd/integrity.go:289-301","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-28T17:06:15.515768-08:00","updated_at":"2025-11-28T19:50:01.116426-08:00","closed_at":"2025-11-28T18:46:19.722924-08:00"}
{"id":"bd-tys","title":"Git history fallback has incorrect logic for detecting deletions","description":"## Problem\n\nThe `wasInGitHistory` function in `internal/importer/importer.go:891` returns true if the ID is found **anywhere** in git history. But finding an ID in history doesn't necessarily mean it was deleted - it could mean:\n\n1. The issue was added (appears in a commit adding it)\n2. The issue was modified (appears in commits updating it)\n3. The issue was deleted (appears in a commit removing it)\n\nThe current logic incorrectly treats all three cases as 'deleted'.\n\n## Correct Logic\n\n`git log -S` with `--oneline` shows commits where the string was added OR removed. To detect deletion specifically:\n\n1. ID appears in git history (was once in JSONL)\n2. ID is NOT currently in JSONL\n\nThe second condition is already checked by the caller (`purgeDeletedIssues`), so technically the logic is correct in context. But the function name and doc comment are misleading.\n\n## Fix Options\n\n1. **Rename function** to `wasEverInJSONL` and update doc comment to clarify\n2. **Add explicit check** for current JSONL state in the function itself\n\nOption 1 is simpler and correct since caller already filters.","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-11-25T12:46:16.073661-08:00","updated_at":"2025-11-25T15:11:54.426093-08:00","closed_at":"2025-11-25T15:11:54.426093-08:00"}
{"id":"bd-upd","title":"Sync should cleanup snapshot files after completion","description":"After sync completion, orphan .base.jsonl and .left.jsonl snapshot files remain in .beads/ directory. These should be cleaned up on successful sync.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-28T17:27:36.727246-08:00","updated_at":"2025-11-28T18:22:16.904307-08:00","closed_at":"2025-11-28T17:42:14.57165-08:00"}
{"id":"bd-upd","title":"Sync should cleanup snapshot files after completion","description":"After sync completion, orphan .base.jsonl and .left.jsonl snapshot files remain in .beads/ directory. These should be cleaned up on successful sync.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-28T17:27:36.727246-08:00","updated_at":"2025-11-28T18:36:52.088915-08:00","closed_at":"2025-11-28T17:42:14.57165-08:00"}
{"id":"bd-v0x","title":"Auto-detect issue prefix from existing JSONL in 'bd init'","description":"When running `bd init` in a fresh clone with existing JSONL, it should auto-detect the issue prefix from the JSONL file instead of requiring `--prefix`.\n\nCurrently you must specify `--prefix ef` manually. But the JSONL file already contains issues like `ef-1it`, `ef-1jp` etc., so the prefix is known.\n\n**Ideal UX**:\n```\n$ bd init\nDetected issue prefix 'ef' from existing JSONL (38 issues).\n✓ Database initialized...\n```\n\nThis would make fresh clone hydration a single command: `bd init` with no flags.","status":"open","priority":2,"issue_type":"feature","created_at":"2025-11-27T20:21:21.049215-08:00","updated_at":"2025-11-27T20:21:21.049215-08:00"}
{"id":"bd-v29","title":"Deletions pruning doesn't include results in JSON output","description":"## Problem\n\nWhen `bd compact --json` runs with deletions pruning, the prune results are silently discarded:\n\n```go\n// Only report if there were deletions to prune\nif result.PrunedCount \u003e 0 {\n if jsonOutput {\n // JSON output will be included in the main response\n return // \u003c-- BUG: results are NOT included anywhere\n }\n ...\n}\n```\n\n## Location\n`cmd/bd/compact.go:925-929`\n\n## Impact\n- JSON consumers don't know deletions were pruned\n- No way to audit pruning via automation\n\n## Fix\nReturn prune results and include in JSON output structure:\n\n```json\n{\n \"success\": true,\n \"compacted\": {...},\n \"deletions_pruned\": {\n \"count\": 5,\n \"retention_days\": 7\n }\n}\n```","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-25T12:48:59.730979-08:00","updated_at":"2025-11-25T15:11:54.363653-08:00","closed_at":"2025-11-25T15:11:54.363653-08:00"}
{"id":"bd-wcl","title":"Document CLI + hooks as recommended approach over MCP","description":"Update documentation to position CLI + bd prime hooks as the primary recommended approach over MCP server, explaining why minimizing context matters even with large context windows (compute cost, energy, environment, latency).","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-12T00:15:25.923025-08:00","updated_at":"2025-11-26T20:13:52.891053-08:00","closed_at":"2025-11-26T18:06:51.020351-08:00"}