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8fa680a88025fa0d6e085e4d588968394667aca4
beads/.beads/issues.jsonl
Steve Yegge 8fa680a880 docs: update beads refinery CLAUDE.md with new terminology 
Replace Imperator→Refinery, polecat→roughneck terminology.

Closes: gt-supz.5

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

Co-Authored-By: Claude <noreply@anthropic.com>
2025-12-05 14:22:38 -08:00

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{"id":"bd-03r","title":"Document deletions manifest in AGENTS.md and README","description":"Parent: bd-imj\n\n## Task\nAdd documentation about the deletions manifest feature.\n\n## Locations to Update\n\n### AGENTS.md\n- Explain that deletions.jsonl is tracked in git\n- Document that `bd delete` records to the manifest\n- Explain cross-clone propagation mechanism\n\n### README.md \n- Brief mention in .beads directory structure section\n- Link to detailed docs if needed\n\n### docs/deletions.md (new file)\n- Full technical documentation\n- Format specification\n- Pruning policy\n- Git history fallback\n- Troubleshooting\n\n## Acceptance Criteria\n- AGENTS.md updated with deletion workflow\n- README.md mentions deletions.jsonl purpose\n- New docs/deletions.md with complete reference","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T14:56:49.13027-08:00","updated_at":"2025-11-25T15:17:23.145944-08:00","closed_at":"2025-11-25T15:17:23.145944-08:00"}
{"id":"bd-0b2","title":"Need --no-git-history flag to disable git history backfill during import","description":"During JSONL migration (beads.jsonl → issues.jsonl), the git history backfill mechanism causes data loss by finding issues in the old beads.jsonl git history and incorrectly treating them as deleted.\n\nA --no-git-history flag for 'bd import' and 'bd sync' would allow users to disable the git history fallback when it's causing problems.\n\nUse cases:\n- JSONL filename migrations\n- Repos with complex git history\n- Debugging import issues\n- Performance (skip slow git scans)\n\nRelated: bd-0gh (migration causes spurious deletions)","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-26T22:28:22.5286-08:00","updated_at":"2025-11-26T23:10:49.354436-08:00","closed_at":"2025-11-26T23:10:49.354436-08:00"}
{"id":"bd-0e3","title":"Remove duplicate countIssuesInJSONLFile function","description":"init.go and doctor.go both defined countIssuesInJSONLFile. Removed the init.go version which is now unused. The doctor.go version (which calls countJSONLIssues) is the canonical implementation.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-29T00:35:52.359237464-07:00","updated_at":"2025-11-29T00:36:18.03477857-07:00","closed_at":"2025-11-29T00:36:18.034782016-07:00","dependencies":[{"issue_id":"bd-0e3","depends_on_id":"bd-63l","type":"discovered-from","created_at":"2025-11-29T00:35:52.366221162-07:00","created_by":"matt"}]}
{"id":"bd-0io","title":"Sync should cleanup snapshot files after completion","description":"## Problem\n`bd sync` leaves orphaned merge artifact files (beads.base.jsonl, beads.left.jsonl) after completion, causing:\n1. Doctor warnings about 'Multiple JSONL files found'\n2. Confusion during debugging\n3. Potential stale data issues on next sync\n\n## Root Cause\n`SnapshotManager` creates these files for 3-way merge deletion tracking but `Cleanup()` is never called after sync completes (success or failure).\n\n## Fix\nCall `SnapshotManager.Cleanup()` at end of successful sync:\n\n```go\n// sync.go after successful validation\nsm := NewSnapshotManager(jsonlPath)\nsm.Cleanup()\n```\n\n## Files\n- cmd/bd/sync.go (add cleanup call)\n- cmd/bd/snapshot_manager.go (Cleanup method exists at line 188)","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-28T17:06:20.881183-08:00","updated_at":"2025-11-28T21:53:44.37689-08:00","closed_at":"2025-11-28T21:53:44.37689-08:00"}
{"id":"bd-0v4","title":"Short tests taking 13+ minutes (performance regression)","description":"","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-27T00:54:03.350344-08:00","updated_at":"2025-11-27T13:23:19.376658-08:00","closed_at":"2025-11-27T01:36:06.684059-08:00"}
{"id":"bd-1kf","title":"mergePriority: negative priorities not handled consistently","description":"","status":"closed","priority":4,"issue_type":"bug","created_at":"2025-12-02T21:56:17.99534-08:00","updated_at":"2025-12-02T22:12:28.396719-08:00","closed_at":"2025-12-02T22:12:28.396719-08:00"}
{"id":"bd-1pj6","title":"Proposal: Custom status states via config","description":"Proposal to add 'custom status states' via `bd config`.\nUsers could define an optional issue status enum (e.g., awaiting_review, review_in_progress) in the config.\nThis would enable multi-step pipelines to process issues where each step correlates to a specific status.\n\nExamples:\n- awaiting_verification\n- awaiting_docs\n- awaiting_testing\n","status":"closed","priority":3,"issue_type":"feature","created_at":"2025-11-20T18:55:48.670499-05:00","updated_at":"2025-11-29T22:06:06.329058-08:00","closed_at":"2025-11-28T23:18:45.862553-08:00"}
{"id":"bd-1u4","title":"Fix gosec lint warnings in doctor.go, main.go, and fix subdirectory","description":"CI lint job failing with 4 gosec warnings:\n- cmd/bd/doctor.go:664 (G304: file inclusion via variable)\n- cmd/bd/doctor/fix/database_config.go:166 (G304: file inclusion via variable) \n- cmd/bd/doctor/fix/untracked.go:61 (G204: subprocess launched with variable)\n- cmd/bd/main.go:645 (G304: file inclusion via variable)\n\nEither suppress with `// #nosec` if false positives, or refactor to validate paths properly.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-29T00:43:07.393406783-07:00","updated_at":"2025-11-29T23:31:20.977129-08:00","closed_at":"2025-11-29T23:31:16.4478-08:00"}
{"id":"bd-2au","title":"bd doctor: add SQLite integrity check (PRAGMA integrity_check)","description":"Add a database integrity check using SQLite's PRAGMA integrity_check to detect corruption. Currently bd doctor checks schema compatibility but not data integrity. This would help diagnose corrupted databases that pass schema checks but have internal inconsistencies.","status":"open","priority":3,"issue_type":"feature","created_at":"2025-12-02T12:52:17.5244-08:00","updated_at":"2025-12-02T12:52:17.5244-08:00"}
{"id":"bd-2e0","title":"Add TTL to deletions manifest entries","description":"Deletions manifest entries should have a TTL (time-to-live) to automatically expire after a certain period. Stale deletion entries can poison beads installations when an agent gets out of sync, causing issues to remain deleted even when they shouldn't be. Adding expiration would limit the blast radius of stale deletions.","status":"open","priority":3,"issue_type":"feature","created_at":"2025-12-03T17:40:59.994296-08:00","updated_at":"2025-12-03T17:40:59.994296-08:00"}
{"id":"bd-2em","title":"Expand checkHooksQuick to verify all hook versions","description":"Currently checkHooksQuick only checks post-merge hook version. Should also check pre-commit, pre-push, and post-checkout for completeness. Keep it lightweight but catch more outdated hooks.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T19:27:47.432243-08:00","updated_at":"2025-11-25T19:50:21.378464-08:00","closed_at":"2025-11-25T19:50:21.378464-08:00"}
{"id":"bd-35o","title":"Add --yes flag to bd doctor --fix","description":"bd doctor --fix prompts for confirmation, which blocks automation (CI/CD, scripts, hooks).\n\nRequirements:\n1. Add --yes or -y flag to bd doctor command\n2. When --yes is passed, skip confirmation prompts\n3. Still log what's being fixed (don't go completely silent)","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-30T21:14:08.696905-08:00","updated_at":"2025-11-30T21:14:49.867041-08:00","closed_at":"2025-11-30T21:14:49.867041-08:00"}
{"id":"bd-39o","title":"Rename last_import_hash metadata key to jsonl_content_hash","description":"The metadata key 'last_import_hash' is misleading because it's updated on both import AND export (sync.go:614, import.go:320).\n\nBetter names:\n- jsonl_content_hash (more accurate)\n- last_sync_hash (clearer intent)\n\nThis is a breaking change requiring migration of existing metadata values.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T21:31:07.568739-05:00","updated_at":"2025-11-29T22:06:06.329653-08:00","closed_at":"2025-11-28T23:13:46.885978-08:00"}
{"id":"bd-3gc","title":"Audit remaining cmd/bd files for error handling consistency","description":"Extend ERROR_HANDLING_AUDIT.md to cover: daemon_sync.go, update.go, list.go, show.go, close.go, reopen.go, dep.go, label.go, comments.go, delete.go, compact.go, config.go, validate.go and other high-usage command files","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-24T00:28:55.890991-08:00","updated_at":"2025-11-29T22:06:06.32994-08:00","closed_at":"2025-11-28T23:37:52.251887-08:00"}
{"id":"bd-3s8","title":"Imperator clone on beads-sync branch causes bd sync failures","description":"","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-30T22:53:51.056763-08:00","updated_at":"2025-12-02T23:28:48.751447-08:00","closed_at":"2025-12-02T18:05:16.968092-08:00"}
{"id":"bd-3xl","title":"bd doctor: per-fix confirmation mode","description":"Add an interactive mode where users can approve/reject each fix individually rather than all-or-nothing. Currently --fix prompts once for all fixes. This would give users more control over which repairs to apply, especially useful when some fixes may have side effects.","status":"open","priority":4,"issue_type":"feature","created_at":"2025-12-02T12:52:38.137201-08:00","updated_at":"2025-12-02T12:52:38.137201-08:00"}
{"id":"bd-44e","title":"Ensure deletions.jsonl is tracked in git","description":"Parent: bd-imj\n\nEnsure deletions.jsonl is tracked in git (not ignored).\n\nUpdate bd init and gitignore upgrade logic to:\n1. NOT add deletions.jsonl to .gitignore\n2. Ensure it is committed alongside beads.jsonl\n\nThe file must be in git for cross-clone propagation to work.\n\nAcceptance criteria:\n- bd init does not ignore deletions.jsonl\n- Existing .gitignore files are not broken\n- File appears in git status when modified","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T09:57:21.663196-08:00","updated_at":"2025-11-25T14:55:43.225883-08:00","closed_at":"2025-11-25T14:55:43.225883-08:00"}
{"id":"bd-4aao","title":"Fix failing integration tests in beads-mcp","description":"The `beads-mcp` test suite has failures in `tests/test_bd_client_integration.py` (assertion error in `test_init_creates_beads_directory`) and errors in `tests/test_worktree_separate_dbs.py` (setup failures finding database). These need to be investigated and fixed to ensure a reliable CI baseline.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T18:53:28.4803-05:00","updated_at":"2025-11-25T21:39:20.967106-08:00","closed_at":"2025-11-25T21:39:20.967106-08:00"}
{"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":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-27T20:21:15.691764-08:00","updated_at":"2025-11-28T22:14:49.092112-08:00","closed_at":"2025-11-28T22:14:49.092112-08:00"}
{"id":"bd-4h3","title":"Add test coverage for internal/git package","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:23.497486-05:00","updated_at":"2025-11-28T22:17:12.606732-08:00","closed_at":"2025-11-28T21:55:45.2527-08:00","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-4pd","title":"Imperator lacks mail hooks for automatic notification","description":"","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-30T22:53:52.007971-08:00","updated_at":"2025-12-02T23:28:48.751957-08:00","closed_at":"2025-12-01T22:01:27.835516-08:00"}
{"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-4u8","title":"Config option sync.require_confirmation_on_mass_delete","description":"Add config option for paranoid users who want confirmation before pushing after mass deletion.\n\nOption: sync.require_confirmation_on_mass_delete\nDefault: false\n\nWhen enabled AND safety check triggers:\n- Prompt user for confirmation before pushing\n- Show them what would be pushed\n\nFor users who have been burned and want extra safety. Most users will not need this.\n\nLocation: internal/config/ and internal/syncbranch/worktree.go\nParent issue: bd-3s8","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-02T19:31:00.927907-08:00","updated_at":"2025-12-02T19:31:00.927907-08:00","dependencies":[{"issue_id":"bd-4u8","depends_on_id":"bd-7ch","type":"blocks","created_at":"2025-12-02T19:31:09.134795-08:00","created_by":"daemon"}]}
{"id":"bd-53c","title":"bd sync corrupts issues.jsonl in multi-clone environments","description":"During parallel swarm operations on 2025-11-29, bd sync corrupted the issues database. Commit 93718056 purged all 80 issues from issues.jsonl.\n\nReproduction:\n1. Multiple clones of same repo (polecat swarm)\n2. Each clone runs bd sync in parallel\n3. One sync overwrites others, resulting in data loss\n\nEven in single-clone scenarios (~/src/beads), running bd sync after git pull seems to nuke the JSONL.\n\nWorkaround: Use bd import -i .beads/issues.jsonl --no-git-history instead of bd sync.\n\nRoot cause investigation needed. Options:\n1. Pessimistic locking (flock)\n2. Single point of merge (polecats on ephemeral branches)\n3. Beads-level locking (bd sync --lock)","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-29T16:30:30.592507-08:00","updated_at":"2025-11-29T23:19:57.254217-08:00","closed_at":"2025-11-29T23:15:02.435084-08:00"}
{"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-63l","title":"bd hooks install fails in git worktrees","description":"When bd is used in a git worktree, bd hooks install fails with 'mkdir .git: not a directory' because .git is a file (gitdir pointer) not a directory. Beads should detect and follow the .git gitdir pointer to install hooks in the correct location. This blocks normal worktree workflows.\n\n## Symptoms of this bug:\n- Git hooks don't install automatically\n- Auto-sync doesn't run (5-second debounce)\n- Hash mismatch warnings in bd output\n- Daemon fails to start with 'auto_start_failed'\n\n## Workaround:\nUse `git rev-parse --git-dir` to find the actual hooks directory and copy hooks manually:\n```bash\nmkdir -p $(git rev-parse --git-dir)/hooks\ncp -r .beads-hooks/* $(git rev-parse --git-dir)/hooks/\n```","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-29T00:27:59.111163003-07:00","updated_at":"2025-11-29T23:20:04.196608-08:00","closed_at":"2025-11-29T23:20:01.394894-08:00"}
{"id":"bd-6ic","title":"Second worktree test","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-30T00:40:28.768125-08:00","updated_at":"2025-11-30T00:40:58.06615-08:00","closed_at":"2025-11-30T00:40:58.06615-08:00"}
{"id":"bd-6l8","title":"Auto-resolve all field conflicts in merge.go","description":"Eliminate manual conflict resolution by adding deterministic auto-resolve rules for all fields:\n\n- Priority: higher priority wins (lower number = more urgent)\n- IssueType: local wins\n- Notes: concatenate both sides with separator\n- Title: side with latest updated_at on the issue wins\n- Description: side with latest updated_at on the issue wins\n\nCurrently true conflicts (both sides changed same field to different values) fail sync. With this change, NO conflicts ever require manual resolution.\n\nLocation: internal/merge/merge.go\nParent issue: bd-3s8","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-02T19:30:59.244181-08:00","updated_at":"2025-12-02T19:49:51.570143-08:00","closed_at":"2025-12-02T19:49:51.570143-08:00"}
{"id":"bd-6rf","title":"bd doctor: detect and fix stale beads-sync branch","description":"## Problem\n\nWhen beads-sync diverges significantly from main (on source code, not just .beads/), it needs to be reset. After a force-push reset, other clones/contributors will have orphaned local beads-sync branches.\n\n## Symptoms\n- Local beads-sync is many commits behind main on source files\n- Local beads-sync doesn't share recent history with remote beads-sync (after force-push)\n- bd sync may behave unexpectedly\n\n## Proposed bd doctor checks\n\n1. **Check beads-sync alignment with main**\n - If beads-sync exists and is \u003eN commits behind main on non-.beads/ files, warn\n - Suggests: reset beads-sync to main\n\n2. **Check beads-sync alignment with remote**\n - If local beads-sync has diverged from origin/beads-sync (no common recent ancestor)\n - This happens after someone force-pushed a reset\n - Suggests: reset local beads-sync to origin/beads-sync\n\n## Proposed fixes (--fix)\n\n- Reset local beads-sync branch to origin/beads-sync or main\n- Handle worktree if present (git worktree remove, then recreate on next sync)\n\n## Context\nDiscovered when beads-sync drifted 126 commits behind main. Required manual reset and force-push. Contributors will need to reset their local branches too.","status":"open","priority":2,"issue_type":"feature","created_at":"2025-12-02T23:45:40.607538-08:00","updated_at":"2025-12-02T23:45:40.607538-08:00"}
{"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"}
{"id":"bd-73u","title":"Refactor daemon local-only sync functions to reduce duplication","description":"PR #433 added three new local-only sync functions (createLocalSyncFunc, createLocalExportFunc, createLocalAutoImportFunc) that are largely copy-paste of existing ones with git operations removed. Refactor to use a single implementation with a skipGit bool parameter or extract shared logic into helper functions to reduce ~200 lines of duplication.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-01T17:38:02.632264-08:00","updated_at":"2025-12-02T23:28:48.752202-08:00","closed_at":"2025-12-01T21:08:11.952459-08:00"}
{"id":"bd-7ch","title":"Auto-push after merge with safety check","description":"Make bd sync a true one-command solution by auto-pushing after successful content merge.\n\nBehavior:\n- After successful content merge, auto-push by default\n- Safety check: detect when \u003e50% issues vanished AND \u003e5 existed before\n- On safety check trigger: warn but still push (do not block happy path)\n\nVanished means issues removed from issues.jsonl entirely, NOT status=closed (closed is legitimate swarm completion).\n\nLocation: internal/syncbranch/worktree.go\nParent issue: bd-3s8","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-02T19:30:59.540636-08:00","updated_at":"2025-12-02T19:30:59.540636-08:00"}
{"id":"bd-81a","title":"Add programmatic tip injection API","description":"Allow tips to be programmatically injected at runtime based on detected conditions. This enables dynamic tips (not just pre-defined ones) to be shown with custom priority and frequency.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-11T23:29:46.645583-08:00","updated_at":"2025-11-25T17:52:35.096882-08:00","closed_at":"2025-11-25T17:52:35.096882-08:00","dependencies":[{"issue_id":"bd-81a","depends_on_id":"bd-d4i","type":"blocks","created_at":"2025-11-11T23:29:46.646327-08:00","created_by":"daemon"}]}
{"id":"bd-8a5","title":"Refactor: deduplicate FindJSONLInDir and FindJSONLPath","description":"## Background\n\nAfter fixing bd-tqo, we now have two nearly identical functions for finding the JSONL file:\n- `autoimport.FindJSONLInDir(dbDir string)` in internal/autoimport/autoimport.go\n- `beads.FindJSONLPath(dbPath string)` in internal/beads/beads.go\n\nBoth implement the same logic:\n1. Prefer issues.jsonl\n2. Fall back to beads.jsonl for legacy support\n3. Skip deletions.jsonl and merge artifacts\n4. Default to issues.jsonl if nothing found\n\n## Problem\n\nCode duplication means bug fixes need to be applied in multiple places (as we just experienced with bd-tqo).\n\n## Proposed Solution\n\nExtract shared logic to a utility package that both can import. Options:\n1. Create `internal/jsonlpath` package with the core logic\n2. Have `autoimport` import `beads` and call `FindJSONLPath` (but APIs differ slightly)\n3. Move to `internal/utils` if appropriate\n\nNeed to verify no import cycles would be created.\n\n## Affected Files\n- internal/autoimport/autoimport.go\n- internal/beads/beads.go","status":"closed","priority":4,"issue_type":"task","created_at":"2025-11-26T23:45:18.974339-08:00","updated_at":"2025-11-29T22:06:06.330185-08:00","closed_at":"2025-11-28T23:07:08.912247-08:00"}
{"id":"bd-8an","title":"bd import auto-detects wrong prefix from directory name instead of issue IDs","description":"When importing issues.jsonl into a fresh database, 'bd import' prints:\n\n ✓ Initialized database with prefix 'beads' (detected from issues)\n\nBut the issues all have prefix 'bd-' (e.g., bd-03r). It appears to be detecting the prefix from the directory name (.beads/) rather than from the actual issue IDs in the JSONL.\n\nThis causes import to fail with:\n validate ID prefix for bd-03r: issue ID 'bd-03r' does not match configured prefix 'beads'\n\nWorkaround: Run 'bd config set issue_prefix bd' before import, or use 'bd init --prefix bd'.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:01.582564-08:00","updated_at":"2025-11-28T22:17:12.607316-08:00","closed_at":"2025-11-27T22:38:48.971617-08:00"}
{"id":"bd-8ib","title":"Update git hooks to be sync.branch aware","description":"## Problem\n\nThe pre-push hook blocks pushes when .beads/issues.jsonl has uncommitted changes. But with sync.branch configured, those changes are intentionally NOT committed to main - they go to the sync branch via worktree.\n\n## Current Behavior\n\n1. User configures sync.branch=beads-sync\n2. bd sync commits changes to beads-sync via worktree \n3. Local .beads/issues.jsonl is updated (needed for import)\n4. git push to main triggers pre-push hook\n5. Hook sees uncommitted .beads changes and blocks push\n6. User must use --no-verify to push\n\n## Expected Behavior\n\nWhen sync.branch is configured, the pre-push hook should:\n1. Check if sync.branch is set (bd config get sync.branch)\n2. If set, skip the .beads uncommitted check OR\n3. Verify changes are committed to the sync branch instead\n\n## Affected Files\n\n- examples/git-hooks/pre-push\n- examples/git-hooks/pre-commit (may also need update)\n\n## Workaround\n\nUse git push --no-verify","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-30T00:43:40.991951-08:00","updated_at":"2025-11-30T11:12:09.91242-08:00","closed_at":"2025-11-30T11:12:09.91242-08:00"}
{"id":"bd-8nz","title":"Merge timestamp tie-breaker should prefer local (left)","description":"In mergeFieldByUpdatedAt, when timestamps are exactly equal, right wins. For consistency with IssueType (where local/left wins), equal timestamps should prefer left. Minor inconsistency.","status":"open","priority":4,"issue_type":"task","created_at":"2025-12-02T20:14:59.898345-08:00","updated_at":"2025-12-02T20:14:59.898345-08:00"}
{"id":"bd-8q0","title":"Add Claude Code web installation docs to README","description":"GH #439 reported installation issues in Claude Code web environment. The go install fallback works, but users need guidance. Add a section to README documenting the workaround: go install + PATH export.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-12-01T21:02:24.511955-08:00","updated_at":"2025-12-01T21:10:10.587639-08:00","closed_at":"2025-12-01T21:10:10.587639-08:00"}
{"id":"bd-8uk","title":"Missing test for PullResult.SafetyWarnings population","description":"","status":"closed","priority":4,"issue_type":"task","created_at":"2025-12-02T21:56:08.413387-08:00","updated_at":"2025-12-02T22:11:17.630494-08:00","closed_at":"2025-12-02T22:11:17.630494-08:00"}
{"id":"bd-91x","title":"Fix dependency naming inconsistencies (GH #440)","description":"Parent-child dependency documentation is backwards and UI labels are confusing.\\n\\nProblems:\\n1. DEPENDENCIES.md says 'bd dep add PARENT CHILD' but this is rejected\\n2. bd show displays epic children under 'Blocks' instead of 'Children'\\n3. bd dep tree EPIC shows nothing (need --direction=up)\\n4. Inconsistent with 'bd epic status' which uses 'children'\\n\\nSee: https://github.com/steveyegge/beads/issues/440","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-01T21:01:41.63295-08:00","updated_at":"2025-12-01T21:06:17.866688-08:00","closed_at":"2025-12-01T21:06:17.866688-08:00"}
{"id":"bd-93d","title":"Jira export script (jsonl2jira.py)","description":"Create a Python script to push beads issues to Jira.\n\n**Requires**: Jira import script to be complete first (need external_ref matching logic working)\n\n**Features needed**:\n- Create new Jira issues from beads issues without external_ref\n- Update existing Jira issues matched by external_ref\n- Map beads fields back to Jira fields\n- Handle Jira workflow transitions (status changes may need transitions)\n- Support custom field mapping for design/acceptance_criteria/notes\n\n**Challenges**:\n- Jira status changes often require workflow transitions, not direct updates\n- Need to discover valid transitions via API\n- Custom fields vary by Jira instance\n\n**Usage**:\n```bash\nbd export | python jsonl2jira.py --create-only # Only create, don't update\nbd export | python jsonl2jira.py # Create and update\n```\n\n**After creation**: Sets external_ref on beads issue to link back","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-30T12:56:14.266357-08:00","updated_at":"2025-11-30T15:19:40.264737-08:00","closed_at":"2025-11-30T15:19:40.264737-08:00","dependencies":[{"issue_id":"bd-93d","depends_on_id":"bd-qvj","type":"parent-child","created_at":"2025-11-30T12:56:44.652391-08:00","created_by":"stevey"},{"issue_id":"bd-93d","depends_on_id":"bd-tjn","type":"blocks","created_at":"2025-11-30T12:56:54.941116-08:00","created_by":"stevey"}]}
{"id":"bd-9cc","title":"bd doctor: export diagnostics history for debugging","description":"Add ability to save doctor diagnostics to a file (e.g., diagnostics.json) for historical analysis and bug reporting. This would help track intermittent issues and provide context when filing bug reports. Could integrate with --perf output for comprehensive system snapshots.","status":"open","priority":4,"issue_type":"feature","created_at":"2025-12-02T12:52:23.711572-08:00","updated_at":"2025-12-02T12:52:23.711572-08:00"}
{"id":"bd-9e23","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":"closed","priority":4,"issue_type":"chore","created_at":"2025-11-02T15:32:30.242357-08:00","updated_at":"2025-11-26T11:14:49.172418-08:00","closed_at":"2025-11-26T11:14:49.172418-08:00"}
{"id":"bd-9li4","title":"Create Docker image for Agent Mail","description":"Containerize Agent Mail server for easy deployment.\n\nAcceptance Criteria:\n- Dockerfile with Python 3.14\n- Health check endpoint\n- Volume mount for storage\n- Environment variable configuration\n- Multi-arch builds (amd64, arm64)\n\nFile: deployment/agent-mail/Dockerfile","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-07T22:43:43.231964-08:00","updated_at":"2025-11-25T17:47:30.777486-08:00","closed_at":"2025-11-25T17:47:30.777486-08:00"}
{"id":"bd-a5z","title":"bd doctor: add --dry-run flag to preview fixes without applying","description":"Currently bd doctor --fix applies all fixes. Add a --dry-run flag to preview what would be fixed without making changes. This helps users understand the impact before committing to repairs.","status":"open","priority":3,"issue_type":"feature","created_at":"2025-12-02T12:52:10.106929-08:00","updated_at":"2025-12-02T12:52:10.106929-08:00"}
{"id":"bd-a6m","title":"isLikelyHash rejects 3-char all-letter base36 hashes","description":"ExtractIssuePrefix fails for multi-hyphen prefixes when the 3-char hash suffix has no digits.\n\nExample: `xa-adt-bat` returns prefix `xa` instead of `xa-adt`.\n\nRoot cause: `isLikelyHash()` requires at least one digit to distinguish hashes from English words, but base36 hashes can be all-letters by chance.\n\nAffected: 20 issues in xa-adapt with suffixes like bat, dev, fbi, oil, etc.","design":"Fix: Accept all-letter suffixes for 3-char only, keep digit requirement for 4+.\n\nRationale (word collision probability by length):\n- 3-char: 36³ = 46K hashes, ~1000 common words = ~2% collision (too high to ignore)\n- 4-char: 36⁴ = 1.6M hashes, ~3000 words = ~0.2% collision (acceptable)\n- 5+ char: collision rate negligible\n\nChange in isLikelyHash():\n```go\nhasDigit := len(s) == 3 // 3-char gets free pass\n```","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-12-02T17:11:19.783336327-05:00","updated_at":"2025-12-02T17:12:37.634260315-05:00","closed_at":"2025-12-02T17:12:37.634260315-05:00","external_ref":"https://github.com/steveyegge/beads/issues/446"}
{"id":"bd-alz","title":"bd doctor: add configuration value validation","description":"Currently bd doctor checks for missing config files but doesn't validate config values. Add validation for: invalid priority values, malformed sync intervals, invalid branch names, unsupported storage backends, etc. This would catch misconfigurations before they cause runtime errors.","status":"open","priority":3,"issue_type":"feature","created_at":"2025-12-02T12:52:31.852532-08:00","updated_at":"2025-12-02T12:52:31.852532-08:00"}
{"id":"bd-azh","title":"Fix bd doctor --fix recursive message for deletions manifest","description":"When running bd doctor --fix, if the deletions manifest check fails but there are no deleted issues in git history, the fix succeeds but doesn't create the file. The check then runs again and tells user to run bd doctor --fix - the same command they just ran.\n\nFix: Create empty deletions.jsonl when hydration finds no deletions, and recognize empty file as valid in the check.\n\nFixes: https://github.com/steveyegge/beads/issues/403","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-27T12:41:09.426143-08:00","updated_at":"2025-11-27T12:41:23.521981-08:00","closed_at":"2025-11-27T12:41:23.521981-08:00"}
{"id":"bd-b8h","title":"Refactor check-health DB access to avoid repeated path resolution","description":"The runCheckHealth lightweight checks (hintsDisabled, checkVersionMismatch, checkSyncBranchQuick) each have duplicated database path resolution logic. Extract a helper function to DRY this up.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T19:27:35.075929-08:00","updated_at":"2025-11-25T19:50:21.272961-08:00","closed_at":"2025-11-25T19:50:21.272961-08:00"}
{"id":"bd-bgs","title":"Git history fallback doesn't escape regex special chars in IDs","description":"## Problem\n\nIn `batchCheckGitHistory`, IDs are directly interpolated into a regex pattern:\n\n```go\npatterns = append(patterns, fmt.Sprintf(\\`\"id\":\"%s\"\\`, id))\nsearchPattern := strings.Join(patterns, \"|\")\ncmd := exec.Command(\"git\", \"log\", \"--all\", \"-G\", searchPattern, ...)\n```\n\nIf an ID contains regex special characters (e.g., `bd-foo.bar` or `bd-test+1`), the pattern will be malformed or match unintended strings.\n\n## Location\n`internal/importer/importer.go:923-926`\n\n## Impact\n- False positives: IDs with `.` could match any character\n- Regex errors: IDs with `[` or `(` could cause git to fail\n- Security: potential for regex injection (low risk since IDs are validated)\n\n## Fix\nEscape regex special characters:\n\n```go\nimport \"regexp\"\n\nescapedID := regexp.QuoteMeta(id)\npatterns = append(patterns, fmt.Sprintf(\\`\"id\":\"%s\"\\`, escapedID))\n```","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-25T12:50:30.132232-08:00","updated_at":"2025-11-25T15:04:06.217695-08:00","closed_at":"2025-11-25T15:04:06.217695-08:00"}
{"id":"bd-bhd","title":"Git history fallback assumes .beads is direct child of repo root","description":"## Problem\n\n`checkGitHistoryForDeletions` assumes the repo structure:\n\n```go\nrepoRoot := filepath.Dir(beadsDir) // Assumes .beads is in repo root\njsonlPath := filepath.Join(\".beads\", \"beads.jsonl\")\n```\n\nBut `.beads` could be in a subdirectory (monorepo, nested project), and the actual JSONL filename could be different (configured via `metadata.json`).\n\n## Location\n`internal/importer/importer.go:865-869`\n\n## Impact\n- Git search will fail silently for repos with non-standard structure\n- Monorepo users won't get deletion propagation\n\n## Fix\n1. Use `git rev-parse --show-toplevel` to find actual repo root\n2. Compute relative path from repo root to JSONL\n3. Or use `git -C \u003cdir\u003e` to run from beadsDir directly","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-25T12:51:03.46856-08:00","updated_at":"2025-11-25T15:05:40.754716-08:00","closed_at":"2025-11-25T15:05:40.754716-08:00"}
{"id":"bd-bok","title":"bd doctor --fix needs non-interactive mode (-y/--yes flag)","description":"When running `bd doctor --fix` in non-interactive mode (scripts, CI, Claude Code), it prompts 'Continue? (Y/n):' and fails with EOF.\n\n**Expected**: A `-y` or `--yes` flag to auto-confirm fixes.\n\n**Workaround**: Currently have to run `bd init` instead, but that's not discoverable from the doctor output.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-27T20:21:10.290649-08:00","updated_at":"2025-11-28T22:17:12.607642-08:00","closed_at":"2025-11-28T21:56:14.708313-08:00"}
{"id":"bd-bt6y","title":"Improve compact/daemon/merge documentation and UX","description":"Multiple documentation and UX issues encountered:\n1. \"bd compact --analyze\" fails with misleading \"requires SQLite storage\" error when daemon is running. Needs --no-daemon or better error.\n2. \"bd merge\" help text is outdated (refers to 3-way merge instead of issue merging).\n3. Daemon mode purpose isn't clear to local-only users.\n4. Compact/cleanup commands are hard to discover.\n\nProposed fixes:\n- Fix compact+daemon interaction or error message.\n- Update \"bd merge\" help text.\n- Add \"when to use daemon\" section to docs.\n- Add maintenance section to quickstart.\n","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T18:55:43.637047-05:00","updated_at":"2025-11-29T22:06:06.330457-08:00","closed_at":"2025-11-28T23:10:43.884784-08:00"}
{"id":"bd-bx9","title":"bd init --contributor should configure sync.remote=upstream for fork workflows","description":"When running `bd init --contributor` in a fork workflow (where `upstream` remote points to the original repo), the wizard should configure beads to sync from `upstream/main` rather than `origin/main`.\n\n**Current behavior:**\n- Contributor mode detects the fork setup (upstream remote exists)\n- Sets up planning repo and auto-routing\n- Does NOT configure sync remote\n- `bd sync` on feature branches shows \"No upstream configured, using --from-main mode\" and syncs from `origin/main`\n\n**Expected behavior:**\n- Contributor mode should also set `sync.remote = upstream` (or similar config)\n- `bd sync` should pull beads from `upstream/main` (source of truth)\n\n**Why this matters:**\n- The fork's `origin/main` may be behind `upstream/main`\n- Contributors want the latest issues from the source repo\n- Code PRs go: local -\u003e origin -\u003e upstream, but beads should come FROM upstream\n\n**Suggested fix:**\nAdd to `runContributorWizard()` after detecting fork:\n```go\nif isFork {\n store.SetConfig(ctx, \"sync.remote\", \"upstream\")\n}\n```","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-29T00:39:05.137488727-05:00","updated_at":"2025-11-29T23:23:01.219117-08:00","closed_at":"2025-11-29T23:22:57.631519-08:00","labels":["contributor","sync"]}
{"id":"bd-c362","title":"Extract database search logic into helper function","description":"The logic for finding a database in a beads directory is duplicated:\n- FindDatabasePath() BEADS_DIR section (beads.go:141-169)\n- findDatabaseInTree() (beads.go:248-280)\n\nBoth implement the same search order:\n1. Check config.json first (single source of truth)\n2. Fall back to canonical beads.db\n3. Search for *.db files, filtering backups and vc.db\n\nRefactoring suggestion:\nExtract to a helper function like:\n func findDatabaseInBeadsDir(beadsDir string) string\n\nBenefits:\n- Single source of truth for database search logic\n- Easier to maintain and update search order\n- Reduces code duplication\n\nRelated to [deleted:bd-e16b] implementation.","status":"closed","priority":3,"issue_type":"chore","created_at":"2025-11-02T18:34:02.831543-08:00","updated_at":"2025-11-25T22:27:33.794656-08:00","closed_at":"2025-11-25T22:27:33.794656-08:00"}
{"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":"closed","priority":3,"issue_type":"chore","created_at":"2025-11-20T20:17:45.119583-05:00","updated_at":"2025-11-29T22:06:06.330716-08:00","closed_at":"2025-11-28T23:37:52.276192-08:00"}
{"id":"bd-c5m","title":"Safety check tests use string(rune()) which only works for single digits","description":"","status":"closed","priority":4,"issue_type":"bug","created_at":"2025-12-02T21:55:41.688857-08:00","updated_at":"2025-12-02T22:10:15.616882-08:00","closed_at":"2025-12-02T22:10:15.616882-08:00"}
{"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":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-27T22:10:41.992686-08:00","updated_at":"2025-11-28T22:17:12.607956-08:00","closed_at":"2025-11-28T22:15:55.878353-08:00"}
{"id":"bd-ciu","title":"formatVanishedIssues output order is non-deterministic","description":"","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-12-02T21:55:32.897206-08:00","updated_at":"2025-12-02T22:07:23.677332-08:00","closed_at":"2025-12-02T22:07:23.677332-08:00"}
{"id":"bd-clg","title":"bd jira sync command","description":"Add a built-in bd command for Jira synchronization.\n\n**Requires**: Both import and export scripts working\n\n**Features**:\n- `bd jira sync --pull` - Import from Jira to beads\n- `bd jira sync --push` - Export from beads to Jira\n- `bd jira sync` - Bidirectional (pull then push, with conflict resolution)\n- `bd jira status` - Show sync status and last sync time\n\n**Conflict resolution**:\n- Timestamp-based: newer update wins\n- Option for --prefer-local or --prefer-jira to override\n- Interactive mode for manual conflict resolution (optional)\n\n**Integration**:\n- Uses jira.* config settings from bd config\n- Stores last sync timestamp in config\n- Logs sync activity for audit\n\n**Stretch goals**:\n- Webhook integration for real-time sync\n- Selective sync by JQL filter","status":"closed","priority":3,"issue_type":"feature","created_at":"2025-11-30T12:56:27.716537-08:00","updated_at":"2025-11-30T15:25:37.896045-08:00","closed_at":"2025-11-30T15:25:37.896045-08:00","dependencies":[{"issue_id":"bd-clg","depends_on_id":"bd-qvj","type":"parent-child","created_at":"2025-11-30T12:56:49.796568-08:00","created_by":"stevey"},{"issue_id":"bd-clg","depends_on_id":"bd-tjn","type":"blocks","created_at":"2025-11-30T12:57:00.075288-08:00","created_by":"stevey"},{"issue_id":"bd-clg","depends_on_id":"bd-93d","type":"blocks","created_at":"2025-11-30T12:57:05.206431-08:00","created_by":"stevey"}]}
{"id":"bd-co0","title":"Imperator does not know its own mail identity","description":"","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-30T22:53:49.963803-08:00","updated_at":"2025-12-02T23:28:48.752455-08:00","closed_at":"2025-12-01T22:01:26.953199-08:00"}
{"id":"bd-d0t","title":"Priority 0 in merge may incorrectly win over set priorities","description":"In mergePriority(), priority 0 (which may mean 'unset' due to Go's zero value) beats any explicitly set priority like P1, P2, etc. Should probably treat 0 as 'no priority set' and not let it win conflicts.","status":"open","priority":3,"issue_type":"bug","created_at":"2025-12-02T20:14:58.906543-08:00","updated_at":"2025-12-02T20:14:58.906543-08:00"}
{"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":"2025-11-27T22:40:11.654051-08:00","closed_at":"2025-11-27T22:40:11.654051-08:00"}
{"id":"bd-dmd","title":"Duplicate safety check message when confirmation required","description":"","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-12-02T21:55:50.204007-08:00","updated_at":"2025-12-02T22:08:09.569984-08:00","closed_at":"2025-12-02T22:08:09.569984-08:00"}
{"id":"bd-dtm","title":"Inconsistent stderr printing: bd-feh warning still prints directly","description":"","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-12-02T21:55:25.212867-08:00","updated_at":"2025-12-02T22:05:53.14012-08:00","closed_at":"2025-12-02T22:05:53.14012-08:00"}
{"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-e3w","title":"bd sync: use worktree for sync.branch commits (non-daemon mode)","description":"## Summary\n\nWhen `sync.branch` is configured (e.g., `beads-sync`), `bd sync` should commit beads changes to that branch via git worktree, even when the user's working directory is on a different branch (e.g., `main`).\n\nCurrently:\n- `bd sync` always commits to the current branch\n- Daemon with `--auto-commit` uses worktrees to commit to sync branch\n- Gap: `bd sync` ignores sync.branch config\n\n## Goal\n\nWorkers stay on `main` (or feature branches) while beads metadata automatically flows to `beads-sync` branch. No daemon required.\n\n## Design Considerations\n\n1. **Worktree lifecycle**: Create on first use, reuse thereafter\n2. **Daemon interaction**: Ensure daemon and bd sync don't conflict\n3. **MCP server**: Uses daemon or direct mode - needs same behavior\n4. **Pull semantics**: Pull from sync branch, not current branch\n5. **Push semantics**: Push to sync branch remote\n6. **Error handling**: Worktree corruption, missing branch, etc.\n\n## Affected Components\n\n- `cmd/bd/sync.go` - Main changes\n- `cmd/bd/daemon_sync_branch.go` - Reuse existing functions\n- `internal/git/worktree.go` - Already implemented\n- MCP server (if it bypasses daemon)\n\n## Edge Cases\n\n- Fresh clone (no sync branch exists yet)\n- Worktree exists but is corrupted\n- Concurrent bd sync from multiple processes\n- sync.branch configured but remote doesn't have that branch\n- User switches sync.branch config mid-session","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-11-30T00:31:20.026356-08:00","updated_at":"2025-11-30T12:10:32.798348-08:00","closed_at":"2025-11-30T00:41:35.335791-08:00"}
{"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":"closed","priority":3,"issue_type":"feature","created_at":"2025-11-28T18:21:47.789887-08:00","updated_at":"2025-11-28T22:17:12.608286-08:00","closed_at":"2025-11-28T21:56:57.608777-08:00"}
{"id":"bd-e92","title":"Add test coverage for internal/autoimport package","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:22.338577-05:00","updated_at":"2025-11-28T22:17:12.608565-08:00","closed_at":"2025-11-28T21:52:34.222127-08:00","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"}]}
{"id":"bd-emg","title":"bd init should refuse when JSONL already has issues (safety guard)","description":"When running `bd init` in a directory with an existing JSONL containing issues, bd should refuse and suggest the correct action instead of proceeding.\n\n## The Problem\n\nCurrent behavior when database is missing but JSONL exists:\n```\n$ bd create \"test\"\nError: no beads database found\nHint: run 'bd init' to create a database...\n```\n\nThis leads users (and AI agents) to reflexively run `bd init`, which can cause:\n- Prefix mismatch if wrong prefix specified\n- Data corruption if JSONL is damaged\n- Confusion about what actually happened\n\n## Proposed Behavior\n\n```\n$ bd init --prefix bd\n\n⚠ Found existing .beads/issues.jsonl with 76 issues.\n\nThis appears to be a fresh clone, not a new project.\n\nTo hydrate the database from existing JSONL:\n bd doctor --fix\n\nTo force re-initialization (may cause data loss):\n bd init --prefix bd --force\n\nAborting.\n```\n\n## Trigger Conditions\n\n- `.beads/issues.jsonl` or `.beads/beads.jsonl` exists\n- File contains \u003e 0 valid issue lines\n- No `--force` flag provided\n\n## Edge Cases\n\n- Empty JSONL (0 issues) → allow init (new project)\n- Corrupted JSONL → warn but allow with confirmation\n- Existing `.db` file → definitely refuse (weird state)\n\n## Related\n\n- bd-dmb: Fresh clone should suggest hydration (better error messages)\n- bd-4ew: bd doctor should detect fresh clone\n\nThis issue is about the safety guard on `bd init` itself, not the error messages from other commands.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-28T18:21:41.149304-08:00","updated_at":"2025-11-28T22:17:18.849507-08:00","closed_at":"2025-11-28T22:17:18.849507-08:00"}
{"id":"bd-f0n","title":"Git history fallback missing timeout - could hang on large repos","description":"## Problem\n\nThe git commands in `checkGitHistoryForDeletions` have no timeout. On large repos with extensive history, `git log --all -S` or `git log --all -G` can take a very long time (minutes).\n\n## Location\n`internal/importer/importer.go:899` and `:930`\n\n## Impact\n- Import could hang indefinitely\n- User has no feedback that git search is running\n- No way to cancel except killing the process\n\n## Fix\nAdd context with timeout to git commands:\n\n```go\nctx, cancel := context.WithTimeout(context.Background(), 30*time.Second)\ndefer cancel()\ncmd := exec.CommandContext(ctx, \"git\", ...)\n```\n\nAlso consider adding a `--since` flag to bound the git history search.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-25T12:48:24.388639-08:00","updated_at":"2025-11-25T15:04:53.669714-08:00","closed_at":"2025-11-25T15:04:53.669714-08:00"}
{"id":"bd-f2f","title":"CRITICAL: bd sync exports before pull, allowing stale DB to corrupt JSONL statuses","description":"## Root Cause\n\nThe fix in bd-53c (reverse ZFC check) only checks COUNTS, not content. The real corruption happens when:\n\n1. Polecat A has stale DB with old status values (e.g., status=closed for issues that are now open on remote)\n2. Polecat A runs bd sync:\n - **Export FIRST**: DB (status=closed) → JSONL (overwrites correct status=open)\n - Commit: Stale JSONL committed\n - Pull: 3-way merge with remote\n - Merge uses 'closed wins' rule → status stays closed\n3. Polecat A pushes → Remote now corrupted with status=closed\n\n## Why bd-53c didn't fix it\n\nThe reverse ZFC check compares COUNTS:\n```go\nif jsonlCount \u003e dbCount // Only catches count mismatch\n```\n\nBut in the corruption scenario:\n- JSONL count = 5, DB count = 5 (same count!)\n- Only the STATUS field differs\n\n## The Real Fix\n\n**PULL BEFORE EXPORT**. The sync order must be:\n1. Pull from remote (get latest state)\n2. Import merged JSONL to DB\n3. THEN export DB changes (if any)\n\nCurrent order is: Export → Commit → Pull → Import → Push\n\nThis is a fundamental architecture change to the sync flow.\n\n## Workaround\n\nUse --no-auto-flush and manually control the sync order, or disable daemon auto-export.\n\n## Evidence\n\nFrom user investigation:\n- At 595b7943 (13:20:30): 5 open issues\n- At 10239812 (13:28:39): 0 open issues\n- All 5 issues had their status changed from open to closed\n- Count stayed at 5 (not a deletion issue)","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-29T17:33:26.744766-08:00","updated_at":"2025-11-29T19:24:31.010075-08:00","closed_at":"2025-11-29T19:24:31.010075-08:00"}
{"id":"bd-fl4","title":"Test sync branch setup","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-30T00:26:47.520507-08:00","updated_at":"2025-11-30T00:33:23.105998-08:00","closed_at":"2025-11-30T00:33:23.105998-08:00"}
{"id":"bd-fmc","title":"string(rune()) pattern in other test files still only works for single digits","description":"The bd-c5m fix only addressed worktree_divergence_test.go, but several other test files have the same issue:\n\n- cmd/bd/stale_test.go:218, 234\n- cmd/bd/export_integrity_integration_test.go:45-47, 279-280\n- internal/storage/sqlite/comments_test.go:146, 165\n- internal/storage/sqlite/blocked_cache_test.go:292\n- internal/storage/sqlite/compact_bench_test.go:117\n- internal/storage/sqlite/cycle_detection_test.go:418\n\nThese use string(rune('0'+i)) which produces wrong characters when i \u003e= 10.\nShould use strconv.Itoa(i) instead.","status":"closed","priority":4,"issue_type":"bug","created_at":"2025-12-02T22:29:12.355705-08:00","updated_at":"2025-12-02T22:39:51.844638-08:00","closed_at":"2025-12-02T22:39:51.844638-08:00"}
{"id":"bd-ge7","title":"Improve Beads test coverage from 46% to 80%","description":"","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-11-20T21:21:03.700271-05:00","updated_at":"2025-11-28T22:17:12.608871-08:00","closed_at":"2025-11-28T21:56:04.085939-08:00"}
{"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":"closed","priority":3,"issue_type":"feature","created_at":"2025-11-26T23:22:45.486584-08:00","updated_at":"2025-11-28T22:17:12.609134-08:00","closed_at":"2025-11-28T21:55:06.895066-08:00"}
{"id":"bd-gmf","title":"Update flake.nix vendorHash after dependency bumps","description":"The Nix flake CI is failing due to stale vendorHash.\n\nError from CI:\n```\nerror: hash mismatch in fixed-output derivation beads-0.24.4-go-modules.drv\n```\n\nRoot cause: go.mod/go.sum was updated by dependabot (wazero, anthropic-sdk-go, etc.) but flake.nix vendorHash wasn't updated.\n\n## Immediate Fix\nRun `nix build` locally, get the correct hash from the error message, update flake.nix.\n\n## Long-term Fix\nAdd a GitHub Action that auto-updates vendorHash when go.mod/go.sum changes:\n1. Trigger on push to main when go.mod/go.sum changes\n2. Run `nix build` to get the new hash from the error\n3. Update flake.nix with the correct hash\n4. Commit and push","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-02T23:16:06.851696-08:00","updated_at":"2025-12-02T23:21:39.917239-08:00","closed_at":"2025-12-02T23:21:39.917239-08:00"}
{"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":"closed","priority":3,"issue_type":"feature","created_at":"2025-11-21T18:55:07.534304-05:00","updated_at":"2025-11-29T22:06:06.330972-08:00","closed_at":"2025-11-28T23:10:19.946063-08:00"}
{"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-hm8","title":"Add uninstall documentation (GH #445)","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-01T21:04:30.313637-08:00","updated_at":"2025-12-01T21:04:57.943192-08:00","closed_at":"2025-12-01T21:04:57.943192-08:00","labels":["docs"]}
{"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-in6","title":"CONFIG.md docs for sync.require_confirmation_on_mass_delete missing threshold detail","description":"The docs say 'if \u003e50% of issues vanish' but the actual code (worktree.go:380) also requires '\u003e5 issues existed before'. The docs should mention both conditions for completeness.","status":"closed","priority":4,"issue_type":"task","created_at":"2025-12-02T22:29:56.753032-08:00","updated_at":"2025-12-02T22:40:37.385126-08:00","closed_at":"2025-12-02T22:40:37.385126-08:00"}
{"id":"bd-io0","title":"sync.branch config lost on clone - should be in config.yaml","description":"## Problem\n\nThe sync.branch configuration is stored in the SQLite database, which is gitignored. When contributors clone a repo that uses beads:\n\n1. They get .beads/issues.jsonl (tracked)\n2. They don't get .beads/beads.db (gitignored)\n3. They lose the sync.branch config\n\nWhen they run 'bd init' or 'bd doctor --fix', sync.branch gets auto-set to the current branch (usually 'main'), but if the project uses a dedicated sync branch like 'beads-sync', they'll be committing to the wrong branch.\n\n## Root Cause\n\nsyncbranch.Get() only checks:\n1. BEADS_SYNC_BRANCH env var\n2. Database config (store.GetConfig)\n\nIt never reads from config.yaml, which IS tracked in git and persists across clones.\n\n## Proposed Solution\n\nAdd sync-branch support to config.yaml with this precedence:\n1. BEADS_SYNC_BRANCH env var (highest)\n2. config.yaml sync-branch setting\n3. Database config (legacy/local override)\n4. Auto-detect from current branch (lowest)\n\nChanges needed:\n1. Update syncbranch.Get() to check config.GetString('sync-branch') between env and database\n2. Update config.yaml template in init.go to include sync-branch\n3. Update docs to recommend setting sync-branch in config.yaml for team projects\n4. Consider: bd init --branch should also write to config.yaml, not just database","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-30T10:51:29.594627-08:00","updated_at":"2025-11-30T10:54:14.198025-08:00","closed_at":"2025-11-30T10:54:14.198025-08:00"}
{"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"}
{"id":"bd-k2n","title":"PushSyncBranch may fail if worktree was cleaned up","description":"","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-12-02T21:56:00.209253-08:00","updated_at":"2025-12-02T22:09:09.552051-08:00","closed_at":"2025-12-02T22:09:09.552051-08:00"}
{"id":"bd-k4b","title":"Enhance dep tree to show full dependency graph","description":"When running `bd dep tree \u003cissue-id\u003e`, the current output only shows the issue itself without its dependency relationships.\n\n## Current Behavior\n\n```\n$ bd dep tree gt-0iqq\n🌲 Dependency tree for gt-0iqq:\n\n→ gt-0iqq: Implement Boss (global overseer) [P2] (open)\n```\n\nThis doesn't show any of the dependency structure.\n\n## Desired Behavior\n\nShow the full dependency DAG rooted at the given issue. For example:\n\n```\n$ bd dep tree gt-0iqq\n🌲 Dependency tree for gt-0iqq:\n\ngt-0iqq: Implement Boss (global overseer) [P2] (open)\n├── gt-0xh4: Boss session management [P2] (open) [READY]\n│ ├── gt-le7c: Boss mail identity [P2] (open)\n│ │ ├── gt-r8fe: Boss human escalation queue [P2] (open)\n│ │ └── gt-vdak: Boss dispatch loop [P2] (open)\n│ │ └── gt-kgy6: Boss resource management [P2] (open)\n│ │ └── gt-93iv: Boss wake daemon [P2] (open)\n│ └── gt-vdak: (shown above)\n```\n\n## Suggested Options\n\n- `--direction=down|up|both` - Show dependents (what this blocks), dependencies (what blocks this), or both\n- `--status=open` - Filter to only show issues with a given status\n- `--depth=N` - Limit tree depth\n- Handle DAG cycles gracefully (show \"(shown above)\" or similar for already-displayed nodes)\n\n## Use Case\n\nWhen reorganizing a set of related issues (like I just did with the Boss implementation), being able to visualize the full dependency graph helps verify the structure is correct before syncing.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-25T19:18:18.750649-08:00","updated_at":"2025-11-25T19:50:46.863319-08:00","closed_at":"2025-11-25T19:31:55.312314-08:00"}
{"id":"bd-kig","title":"Test worktree sync branch commit","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-30T00:38:13.906936-08:00","updated_at":"2025-11-30T00:40:23.609537-08:00","closed_at":"2025-11-30T00:40:23.609537-08:00"}
{"id":"bd-l7u","title":"Duplicate DefaultRetentionDays constants","description":"## Problem\n\nThere are now two constants for the same value:\n\n1. `deletions.DefaultRetentionDays = 7` in `internal/deletions/deletions.go:184`\n2. `configfile.DefaultDeletionsRetentionDays = 7` in `internal/configfile/configfile.go:102`\n\n## Impact\n- DRY violation\n- Risk of values getting out of sync\n- Confusing which one to use\n\n## Fix\nRemove the constant from `deletions` package and have it import from `configfile`, or create a shared constants package.","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-25T12:49:38.356211-08:00","updated_at":"2025-11-25T15:15:21.964842-08:00","closed_at":"2025-11-25T15:15:21.964842-08:00"}
{"id":"bd-l954","title":"Performance Testing Framework","description":"Add comprehensive performance testing for beads focusing on optimization guidance and validating 10K+ database scale. Uses standard Go tooling, follows existing patterns, minimal complexity.\n\nComponents:\n- Benchmark suite for critical operations at 10K-20K scale\n- Fixture generator for realistic test data (epic hierarchies, cross-links)\n- User diagnostics via bd doctor --perf\n- Always-on profiling integration\n\nGoals:\n- Identify bottlenecks for optimization work\n- Validate performance at 10K+ issue scale\n- Enable users to collect diagnostics for bug reports\n- Support both SQLite and JSONL import paths","status":"closed","priority":2,"issue_type":"epic","created_at":"2025-11-13T22:22:11.203467-08:00","updated_at":"2025-11-29T22:06:06.331232-08:00","closed_at":"2025-11-28T23:07:57.285628-08:00"}
{"id":"bd-lsa","title":"Mass deletion logging for forensics","description":"Log detailed information when the safety check triggers during auto-push.\n\nWhen \u003e50% issues vanish AND \u003e5 existed:\n- Log which issues vanished\n- Log the before/after counts\n- Log timestamp for forensic analysis\n\nThis gives users visibility into what happened if something goes wrong, without blocking the sync.\n\nLocation: internal/syncbranch/worktree.go\nParent issue: bd-3s8","status":"open","priority":2,"issue_type":"task","created_at":"2025-12-02T19:30:59.835398-08:00","updated_at":"2025-12-02T19:30:59.835398-08:00","dependencies":[{"issue_id":"bd-lsa","depends_on_id":"bd-7ch","type":"blocks","created_at":"2025-12-02T19:31:08.254087-08:00","created_by":"daemon"}]}
{"id":"bd-m0w","title":"Add test coverage for internal/validation package","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:24.129559-05:00","updated_at":"2025-11-28T22:17:12.609385-08:00","closed_at":"2025-11-28T21:52:34.198974-08:00","dependencies":[{"issue_id":"bd-m0w","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.350477-05:00","created_by":"daemon"}]}
{"id":"bd-m7ge","title":"Add .beads/README.md during 'bd init' for project documentation and promotion","description":"When 'bd init' is run, automatically generate a .beads/README.md file that:\n\n1. Briefly explains what Beads is (AI-native issue tracking that lives in your repo)\n2. Links to the main repository: https://github.com/steveyegge/beads\n3. Provides a quick reference of essential commands:\n - bd create: Create new issues\n - bd list: View all issues\n - bd update: Modify issue status/details\n - bd show: View issue details\n - bd sync: Sync with git remote\n4. Highlights key benefits for AI coding agents and developers\n5. Encourages developers to try it out\n\nThe README should be enthusiastic and compelling to get open source contributors excited about using Beads for their AI-assisted development workflows.","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-16T22:32:50.478681-08:00","updated_at":"2025-11-25T17:49:42.558381-08:00","closed_at":"2025-11-25T17:49:42.558381-08:00"}
{"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":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T18:56:30.124918-05:00","updated_at":"2025-11-29T22:06:06.331473-08:00","closed_at":"2025-11-28T23:37:52.199294-08:00"}
{"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":"2025-11-28T18:36:52.087768-08:00","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":"closed","priority":3,"issue_type":"feature","created_at":"2025-11-28T17:59:37.918686-08:00","updated_at":"2025-11-29T22:06:06.331709-08:00","closed_at":"2025-11-28T23:09:06.171564-08:00"}
{"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":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-28T17:06:26.266097-08:00","updated_at":"2025-11-28T21:52:13.632029-08:00","closed_at":"2025-11-28T21:52:13.632029-08:00"}
{"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":"2025-11-28T18:36:52.088427-08:00","closed_at":"2025-11-28T17:42:49.92251-08:00"}
{"id":"bd-qn5","title":"bd doctor: handle missing daemon registry gracefully","description":"When no daemon has ever been started, bd doctor shows an error parsing the registry: 'failed to parse registry: invalid character 0 after top-level value'. The doctor should handle the case where ~/.bd/daemon/registry.json doesn't exist, treating it as 'no daemon running' rather than an error.","status":"open","priority":2,"issue_type":"bug","created_at":"2025-12-02T12:51:56.300983-08:00","updated_at":"2025-12-02T12:52:02.949424-08:00"}
{"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-qvj","title":"Jira import/export integration","description":"Add ability to import issues from Jira and export beads issues to Jira. See GitHub discussion #430 for user request.\n\n**Background**: User @kaihendry configured jira.* settings but found bd sync doesn't sync with Jira - only with git. The config namespace exists but the integration doesn't.\n\n**Existing infrastructure**:\n- external_ref field for linking to external systems\n- Import logic matches by external_ref first (priority over ID matching)\n- Config namespace jira.* documented in CONFIG.md\n- GitHub import example (examples/github-import/gh2jsonl.py) provides pattern\n\n**Schema mapping challenges**:\n- Jira workflows are highly customizable (status mapping)\n- Jira has more field types (components, versions, custom fields)\n- Two-way sync needs conflict resolution\n- Jira Cloud vs Server/Data Center have different APIs\n\n**Approach**: Phased implementation starting with import, then export, then bidirectional sync.","status":"closed","priority":2,"issue_type":"epic","created_at":"2025-11-30T12:55:44.835009-08:00","updated_at":"2025-12-01T10:44:53.454483-08:00","closed_at":"2025-12-01T10:44:53.454483-08:00"}
{"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":"closed","priority":4,"issue_type":"task","created_at":"2025-11-24T00:28:57.248959-08:00","updated_at":"2025-11-29T22:06:06.332176-08:00","closed_at":"2025-11-28T23:28:00.886536-08:00"}
{"id":"bd-t3b","title":"Add test coverage for internal/config package","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:22.91657-05:00","updated_at":"2025-11-28T22:17:12.609614-08:00","closed_at":"2025-11-28T21:54:15.009889-08:00","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-t5m","title":"CRITICAL: git-history-backfill purges entire database when JSONL reset","description":"When a clone gets reset (git reset --hard origin/main), the git-history-backfill logic incorrectly adds ALL issues to the deletions manifest, then sync purges the entire database.\\n\\nFix adds safety guard: never delete more than 50% of issues via git-history-backfill. If threshold exceeded, abort with warning message.","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-11-30T21:24:47.397394-08:00","updated_at":"2025-11-30T21:24:52.710971-08:00","closed_at":"2025-11-30T21:24:52.710971-08:00"}
{"id":"bd-tjn","title":"Jira import script (jira2jsonl.py)","description":"Create a Python script to import Jira issues into beads JSONL format.\n\n**Pattern**: Follow examples/github-import/gh2jsonl.py\n\n**Features needed**:\n- Fetch issues via Jira REST API with JQL queries\n- Pagination handling (100 issues per request)\n- Map Jira fields to beads fields (see schema mapping in epic)\n- Set external_ref to Jira issue URL for re-sync\n- Support both Jira Cloud and Server/Data Center APIs\n- Read config from bd config (jira.url, jira.project, jira.api_token)\n\n**Config-driven mapping**:\n- jira.status_map.* for status conversion\n- jira.type_map.* for issue type conversion\n- jira.priority_map.* for priority conversion\n\n**Usage**:\n```bash\npython jira2jsonl.py --project PROJ | bd import\n# or\npython jira2jsonl.py --jql 'project=PROJ AND status\\!=Done' | bd import\n```\n\n**Output**: JSONL with external_ref set to Jira issue URL","status":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-30T12:55:59.517985-08:00","updated_at":"2025-11-30T15:11:56.692594-08:00","closed_at":"2025-11-30T15:11:56.692594-08:00","dependencies":[{"issue_id":"bd-tjn","depends_on_id":"bd-qvj","type":"parent-child","created_at":"2025-11-30T12:56:39.507643-08:00","created_by":"stevey"}]}
{"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-tok","title":"Upgrade notification persists after running suggested commands","description":"The upgrade notification kept showing even after running 'bd upgrade review' and 'bd doctor' as suggested.\n\nExpected: Notification should be dismissed after running either/both commands\nActual: Notification persisted on every bd command\n\nInvestigation findings:\n- metadata.json correctly shows last_bd_version=0.28.0\n- The notification stopped appearing after a few more invocations\n- May be related to daemon caching or a race condition\n- The 'upgradeAcknowledged' flag in version_tracking.go:115 only persists per-session (in-memory)\n\nPossible causes:\n1. Daemon vs direct mode inconsistency - daemon may have stale version info\n2. The version is checked/updated before daemon connection, but daemon has cached state\n3. Race between trackBdVersion() and daemon startup\n\nStatus: May have resolved itself, but root cause unclear. Close if no longer reproducible.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-12-02T23:23:04.652453-08:00","updated_at":"2025-12-02T23:38:09.310731-08:00","closed_at":"2025-12-02T23:38:09.310731-08:00"}
{"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":"2025-11-28T19:50:01.116426-08:00","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":"2025-11-28T18:36:52.088915-08:00","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":"closed","priority":2,"issue_type":"feature","created_at":"2025-11-27T20:21:21.049215-08:00","updated_at":"2025-11-28T22:17:12.609841-08:00","closed_at":"2025-11-28T21:57:11.164293-08:00"}
{"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"}
{"id":"bd-wmo","title":"PruneDeletions iterates map non-deterministically","description":"## Problem\n\n`PruneDeletions` iterates over `loadResult.Records` which is a map. Go maps iterate in random order, so:\n\n1. `result.PrunedIDs` order is non-deterministic\n2. `kept` slice order is non-deterministic → `WriteDeletions` output order varies\n\n## Location\n`internal/deletions/deletions.go:213`\n\n## Impact\n- Git diffs are noisy (file changes order on each prune)\n- Tests could be flaky if they depend on order\n- Harder to debug/audit\n\n## Fix\nSort by ID or timestamp before iterating:\n\n```go\n// Convert map to slice and sort\nvar records []DeletionRecord\nfor _, r := range loadResult.Records {\n records = append(records, r)\n}\nsort.Slice(records, func(i, j int) bool {\n return records[i].ID \u003c records[j].ID\n})\n```","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-11-25T12:49:11.290916-08:00","updated_at":"2025-11-25T15:15:21.903649-08:00","closed_at":"2025-11-25T15:15:21.903649-08:00"}
{"id":"bd-x2i","title":"Add bd deleted command for audit trail","description":"Parent: bd-imj\n\nAdd command to view deletion history.\n\nUsage:\n bd deleted # Show recent deletions (last 7 days)\n bd deleted --since=30d # Show deletions in last 30 days\n bd deleted --all # Show all tracked deletions\n bd deleted bd-xxx # Show deletion details for specific issue\n\nOutput format:\n bd-xxx 2025-11-25 10:00 stevey duplicate of bd-yyy\n bd-yyy 2025-11-25 10:05 claude cleanup\n\nAcceptance criteria:\n- List deletions with timestamp, actor, reason\n- Filter by time range\n- Lookup specific issue ID\n- JSON output option for scripting","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T09:57:21.113861-08:00","updated_at":"2025-11-25T15:13:53.781519-08:00","closed_at":"2025-11-25T15:13:53.781519-08:00"}
{"id":"bd-xo9","title":"Document sync.require_confirmation_on_mass_delete config option","description":"","status":"closed","priority":4,"issue_type":"task","created_at":"2025-12-02T21:56:25.580287-08:00","updated_at":"2025-12-02T22:13:43.992387-08:00","closed_at":"2025-12-02T22:13:43.992387-08:00"}
{"id":"bd-xyc","title":"Consolidate check-health DB opens into single connection","description":"The --check-health flag opens the database 3 separate times (once per quick check). Consolidate into a single DB open for better performance, especially on slower filesystems.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-25T19:27:42.034178-08:00","updated_at":"2025-11-25T19:50:21.32375-08:00","closed_at":"2025-11-25T19:50:21.32375-08:00"}
{"id":"bd-ybv5","title":"Refactor AGENTS.md to use external references","description":"Suggestion to use external references (e.g., \"ALWAYS REFER TO ./beads/prompt.md\") instead of including all instructions directly within AGENTS.md.\nReasons:\n1. Agents can follow external references.\n2. Prevents context pollution/stuffing in AGENTS.md as more tools append instructions.\n","status":"closed","priority":3,"issue_type":"task","created_at":"2025-11-20T18:55:53.259144-05:00","updated_at":"2025-11-26T22:25:57.772875-08:00","closed_at":"2025-11-26T22:25:57.772875-08:00"}
{"id":"bd-ye0d","title":"troubleshoot GH#278 daemon exits every few secs","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-13T06:27:23.39509215-07:00","updated_at":"2025-11-25T17:48:43.62418-08:00","closed_at":"2025-11-25T17:48:43.62418-08:00"}
{"id":"bd-zai","title":"bd init resets metadata.json jsonl_export to beads.jsonl, ignoring existing issues.jsonl","description":"When running 'bd init --prefix bd' in a repo that already has .beads/issues.jsonl, the init command overwrites metadata.json and sets jsonl_export back to 'beads.jsonl' instead of detecting and respecting the existing issues.jsonl file.\n\nSteps to reproduce:\n1. Have a repo with .beads/issues.jsonl (canonical) and metadata.json pointing to issues.jsonl\n2. Delete beads.db and run 'bd init --prefix bd'\n3. Check metadata.json - it now says jsonl_export: beads.jsonl\n\nExpected: Init should detect existing issues.jsonl and use it.\n\nWorkaround: Manually edit metadata.json after init.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:27:41.653287-08:00","updated_at":"2025-11-28T22:17:12.610089-08:00","closed_at":"2025-11-28T21:54:32.52461-08:00"}
{"id":"bd-zj8e","title":"Performance Testing Documentation","description":"Create docs/performance-testing.md documenting the performance testing framework.\n\nSections:\n1. Overview - What the framework does, goals\n2. Running Benchmarks\n - make bench command\n - Running specific benchmarks\n - Interpreting output (ns/op, allocs/op)\n3. Profiling and Analysis\n - Viewing CPU profiles with pprof\n - Reading flamegraphs\n - Memory profiling\n - Finding hotspots\n4. User Diagnostics\n - bd doctor --perf usage\n - Sharing profiles with bug reports\n - Understanding the report output\n5. Comparing Performance\n - Using benchstat for before/after comparisons\n - Detecting regressions\n6. Tips for Optimization\n - Common patterns\n - When to profile vs benchmark\n\nStyle:\n- Concise, practical examples\n- Screenshots/examples of pprof output\n- Clear command-line examples\n- Focus on workflow, not theory","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-13T22:23:38.99897-08:00","updated_at":"2025-11-29T22:06:06.332423-08:00","closed_at":"2025-11-28T23:37:52.227831-08:00"}
{"id":"bd-zsz","title":"Add --parent flag to bd onboard output","description":"bd onboard didn't document --parent flag for epic subtasks, causing AI agents to guess wrong syntax. Added --parent example and CLI help section pointing to bd \u003ccmd\u003e --help.\n\nFixes: https://github.com/steveyegge/beads/issues/402","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-27T13:01:51.366625-08:00","updated_at":"2025-11-27T13:02:02.018003-08:00","closed_at":"2025-11-27T13:02:02.018003-08:00"}
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