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Steve Yegge
2025-11-29 22:07:14 -08:00
parent 21720237d8 214da06d59
commit 8e33b5dda5
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@@ -3,11 +3,11 @@
{"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-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":"2025-11-29T00:53:41.695042278-07:00","closed_at":"2025-11-28T23:18:45.862553-08:00"}
{"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":"open","priority":2,"issue_type":"task","created_at":"2025-11-29T00:43:07.393406783-07:00","updated_at":"2025-11-29T00:43:07.393406783-07:00"}
{"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-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":"2025-11-29T00:53:41.70116392-07:00","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":"2025-11-29T00:53:41.70301586-07:00","closed_at":"2025-11-28T23:37:52.251887-08:00"}
{"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-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"}
@@ -15,12 +15,12 @@
{"id":"bd-4l5","title":"bd prime: Detect ephemeral branches and adjust workflow output","description":"When 'bd prime' runs on a branch with no upstream (ephemeral branch), it should output a different SESSION CLOSE PROTOCOL.\n\n**Current output (wrong for ephemeral branches):**\n```\n[ ] 1. git status\n[ ] 2. git add \u003cfiles\u003e\n[ ] 3. bd sync\n[ ] 4. git commit -m \"...\"\n[ ] 5. bd sync\n[ ] 6. git push\n```\n\n**Needed output for ephemeral branches:**\n```\n[ ] 1. git status\n[ ] 2. git add \u003cfiles\u003e\n[ ] 3. bd sync --from-main (pull updates from main)\n[ ] 4. git commit -m \"...\"\n[ ] 5. (no push - branch is ephemeral)\n```\n\n**Detection:** `git rev-parse --abbrev-ref --symbolic-full-name @{u}` returns error code 128 if no upstream.\n\nAlso update Sync \u0026 Collaboration section to mention `bd sync --from-main` for ephemeral branches.\n\n**Use case:** Gastown polecats work on ephemeral local branches that are never pushed. Their code gets merged to main via local merge, and beads changes stay local (communicated via gm mail to Overseer).","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-11-25T16:55:24.984104-08:00","updated_at":"2025-11-25T17:12:46.604978-08:00","closed_at":"2025-11-25T17:12:46.604978-08:00"}
{"id":"bd-4pv","title":"bd export only outputs 1 issue after auto-import corrupts database","description":"When auto-import runs and purges issues (due to git history backfill bug), subsequent 'bd export' only exports 1 issue even though the database should have many.\n\nReproduction:\n1. Have issues.jsonl with 55 issues\n2. Auto-import triggers and purges all issues via git history backfill\n3. Run 'bd export' - only exports 1 issue (the last one created before corruption)\n\nThe database gets into an inconsistent state where most issues are purged but export doesn't realize this.\n\nWorkaround: Rebuild database from scratch with 'rm .beads/beads.db \u0026\u0026 bd init --prefix bd'","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:40.828866-08:00","updated_at":"2025-11-28T17:28:55.545056-08:00","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-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":"open","priority":0,"issue_type":"bug","created_at":"2025-11-29T16:30:30.592507-08:00","updated_at":"2025-11-29T16:30:30.592507-08:00"}
{"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-5kj","title":"bd list fails in JSONL-only mode with misleading error","description":"When .beads exists with issues.jsonl but no SQLite (JSONL-only mode), bd list/ready/stats fail with no beads database found. However bd doctor works. Commands should work in JSONL-only mode or give consistent guidance.","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-28T23:08:36.834166-08:00","updated_at":"2025-11-28T23:36:17.128479-08:00","closed_at":"2025-11-28T23:36:17.128479-08:00"}
{"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":"open","priority":1,"issue_type":"bug","created_at":"2025-11-29T00:27:59.111163003-07:00","updated_at":"2025-11-29T00:38:30.640871318-07:00"}
{"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-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":"2025-11-29T00:53:41.704241927-07:00","closed_at":"2025-11-28T23:07:08.912247-08:00"}
{"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-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"}
@@ -29,9 +29,9 @@
{"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":"2025-11-29T00:53:41.705547905-07:00","closed_at":"2025-11-28T23:10:43.884784-08:00"}
{"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-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":"2025-11-29T00:53:41.706851728-07:00","closed_at":"2025-11-28T23:37:52.276192-08:00"}
{"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-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-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"}
@@ -40,9 +40,10 @@
{"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-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-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":"2025-11-29T00:53:41.708090099-07:00","closed_at":"2025-11-28T23:10:19.946063-08:00"}
{"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-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"}
@@ -50,19 +51,19 @@
{"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-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-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":"2025-11-29T00:53:41.709486455-07:00","closed_at":"2025-11-28T23:07:57.285628-08:00"}
{"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-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":"2025-11-29T00:53:41.710644275-07:00","closed_at":"2025-11-28T23:37:52.199294-08:00"}
{"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":"2025-11-29T00:53:41.711820849-07:00","closed_at":"2025-11-28T23:09:06.171564-08:00"}
{"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-qsm","title":"Auto-compact deletions during bd sync","description":"Parent: bd-imj\n\n## Task\nOptionally prune deletions manifest during sync when threshold exceeded.\n\n**Note: Opt-in feature** - disabled by default to avoid sync latency.\n\n## Implementation\n\nIn `bd sync`:\n```go\nfunc (s *Syncer) Sync() error {\n // ... existing sync logic ...\n \n // Auto-compact only if enabled\n if s.config.GetBool(\"deletions.auto_compact\", false) {\n deletionCount := deletions.Count(\".beads/deletions.jsonl\")\n threshold := s.config.GetInt(\"deletions.auto_compact_threshold\", 1000)\n \n if deletionCount \u003e threshold {\n retentionDays := s.config.GetInt(\"deletions.retention_days\", 7)\n if err := s.compactor.PruneDeletions(retentionDays); err != nil {\n log.Warnf(\"Failed to auto-compact deletions: %v\", err)\n // Non-fatal, continue sync\n }\n }\n }\n \n // ... rest of sync ...\n}\n```\n\n## Configuration\n```yaml\ndeletions:\n retention_days: 7\n auto_compact: false # Opt-in, disabled by default\n auto_compact_threshold: 1000 # Trigger when \u003e N entries (if enabled)\n```\n\n## Acceptance Criteria\n- [ ] Auto-compact disabled by default\n- [ ] Enabled via config `deletions.auto_compact: true`\n- [ ] Sync checks deletion count only when enabled\n- [ ] Auto-prunes when threshold exceeded\n- [ ] Failure is non-fatal (logged warning)\n- [ ] Test: no compaction when disabled\n- [ ] Test: compaction triggers when enabled and threshold exceeded","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-25T09:57:04.522795-08:00","updated_at":"2025-11-25T15:03:01.469629-08:00","closed_at":"2025-11-25T15:03:01.469629-08:00"}
{"id":"bd-s0z","title":"Consider extracting error handling helpers","description":"Evaluate creating FatalError() and WarnError() helpers as suggested in ERROR_HANDLING.md to reduce boilerplate and enforce consistency. Prototype in a few files first to validate the approach.","status":"closed","priority":4,"issue_type":"task","created_at":"2025-11-24T00:28:57.248959-08:00","updated_at":"2025-11-29T00:53:41.713026038-07:00","closed_at":"2025-11-28T23:28:00.886536-08:00"}
{"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-tne","title":"Add Claude setup tip with dynamic priority","description":"Add a predefined tip that suggests running `bd setup claude` when Claude Code is detected but not configured. This tip should have higher priority (shown more frequently) until the setup is complete.","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-11T23:29:29.871324-08:00","updated_at":"2025-11-25T17:52:35.044989-08:00","closed_at":"2025-11-25T17:52:35.044989-08:00","dependencies":[{"issue_id":"bd-tne","depends_on_id":"bd-d4i","type":"blocks","created_at":"2025-11-11T23:29:29.872081-08:00","created_by":"daemon"}]}
{"id":"bd-tqo","title":"deletions.jsonl gets corrupted with full issue objects instead of deletion records","description":"## Bug Description\n\nThe deletions.jsonl file was found to contain full issue objects (like issues.jsonl) instead of deletion records.\n\n### Expected Format (DeletionRecord)\n```json\n{\"id\":\"bd-xxx\",\"timestamp\":\"2025-...\",\"actor\":\"user\",\"reason\":\"deleted\"}\n```\n\n### Actual Content Found\n```json\n{\"id\":\"bd-03r\",\"title\":\"Document deletions manifest...\",\"description\":\"...\",\"status\":\"closed\",...}\n```\n\n## Impact\n- bd sync sanitization step reads deletions.jsonl and removes any matching IDs from issues.jsonl\n- With 60 full issue objects in deletions.jsonl, ALL 60 issues were incorrectly removed during sync\n- This caused complete data loss of the issue database\n\n## Root Cause (suspected)\nSomething wrote issues.jsonl content to deletions.jsonl. Possible causes:\n- Export writing to wrong file\n- File path confusion during sync\n- Race condition between export and deletion tracking\n\n## Related Issues\n- bd-0b2: --no-git-history flag (just fixed)\n- bd-4pv: export outputs only 1 issue after corruption \n- bd-4t7: auto-import runs during --no-auto-import\n\n## Reproduction\nUnknown - discovered during bd sync session on 2025-11-26\n\n## Fix\nNeed to investigate what code path could write issue objects to deletions.jsonl","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-11-26T23:17:01.938931-08:00","updated_at":"2025-11-26T23:25:21.445143-08:00","closed_at":"2025-11-26T23:25:02.209911-08:00"}
@@ -79,5 +80,5 @@
{"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":"2025-11-29T00:53:41.714576824-07:00","closed_at":"2025-11-28T23:37:52.227831-08:00"}
{"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"}

2
.beads/metadata.json
View File

@@ -1,5 +1,5 @@
{
"database": "beads.db",
"jsonl_export": "issues.jsonl",
"last_bd_version": "0.26.0"
"last_bd_version": "0.26.2"
}

2
.claude-plugin/marketplace.json
View File

@@ -9,7 +9,7 @@
"name": "beads",
"source": "./",
"description": "AI-supervised issue tracker for coding workflows",
"version": "0.26.0"
"version": "0.26.1"
}
]
}

2
.claude-plugin/plugin.json
View File

@@ -1,7 +1,7 @@
{
"name": "beads",
"description": "AI-supervised issue tracker for coding workflows. Manage tasks, discover work, and maintain context with simple CLI commands.",
"version": "0.26.0",
"version": "0.26.1",
"author": {
"name": "Steve Yegge",
"url": "https://github.com/steveyegge"

9
.github/workflows/release.yml vendored
View File

@@ -82,15 +82,16 @@ jobs:
- name: Set up Node.js
uses: actions/setup-node@v4
with:
node-version: '20'
node-version: '22'
registry-url: 'https://registry.npmjs.org'
- name: Update npm for OIDC support
run: npm install -g npm@latest
- name: Publish to npm
run: |
cd npm-package
npm publish --access public --provenance
env:
NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
npm publish --access public
update-homebrew:
runs-on: ubuntu-latest

22
CHANGELOG.md
View File

@@ -7,7 +7,27 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased]
## [0.26.0] - 2025-11-27
## [0.26.2] - 2025-11-29
### Fixed
- **Hash-Based Staleness Detection (bd-f2f)**: Prevents stale DB from corrupting JSONL when counts match
- Previous count-based check (0.26.1) missed cases where DB and JSONL had similar issue counts
- New detection computes SHA256 hash of JSONL content and stores it after import
- On export, compares current JSONL hash against stored hash to detect modifications
- If JSONL was modified externally (e.g., by git pull), triggers re-import before export
- Ensures database is always synchronized with JSONL before exporting changes
## [0.26.1] - 2025-11-29
### Fixed
- **CRITICAL: Reverse ZFC Check (bd-53c)**: Prevents stale database from corrupting JSONL
- Root cause: `bd sync` exports DB to JSONL before pulling from remote
- If local DB is stale (fewer issues than JSONL), stale data would corrupt the JSONL
- Added reverse ZFC check: detects when JSONL has >20% more issues than DB
- When detected, imports JSONL first to sync database before any export
- Prevents fresh/stale clones from exporting incomplete database state
## [0.26.0] - 2025-11-27

2
cmd/bd/daemon_sync.go
View File

@@ -43,6 +43,8 @@ func exportToJSONLWithStore(ctx context.Context, store storage.Storage, jsonlPat
}
// Safety check: prevent exporting empty database over non-empty JSONL
// Note: The main bd-53c protection is in sync.go's reverse ZFC check which runs BEFORE export.
// Here we only block the most catastrophic case (empty DB) to allow legitimate deletions.
if len(issues) == 0 {
existingCount, err := countIssuesInJSONL(jsonlPath)
if err != nil {

41
cmd/bd/doctor/fix/common.go
View File

@@ -5,6 +5,7 @@ import (
"os"
"os/exec"
"path/filepath"
"strings"
)
// getBdBinary returns the path to the bd binary to use for fix operations.
@@ -47,3 +48,43 @@ func validateBeadsWorkspace(path string) error {
return nil
}
// safeWorkspacePath resolves relPath within the workspace root and ensures it
// cannot escape the workspace via path traversal.
func safeWorkspacePath(root, relPath string) (string, error) {
absRoot, err := filepath.Abs(root)
if err != nil {
return "", fmt.Errorf("invalid workspace path: %w", err)
}
cleanRel := filepath.Clean(relPath)
if filepath.IsAbs(cleanRel) {
return "", fmt.Errorf("expected relative path, got absolute: %s", relPath)
}
joined := filepath.Join(absRoot, cleanRel)
rel, err := filepath.Rel(absRoot, joined)
if err != nil {
return "", fmt.Errorf("failed to resolve path: %w", err)
}
if rel == ".." || strings.HasPrefix(rel, ".."+string(os.PathSeparator)) {
return "", fmt.Errorf("path escapes workspace: %s", relPath)
}
return joined, nil
}
// isWithinWorkspace reports whether candidate resides within the workspace root.
func isWithinWorkspace(root, candidate string) bool {
cleanRoot, err := filepath.Abs(root)
if err != nil {
return false
}
cleanCandidate := filepath.Clean(candidate)
rel, err := filepath.Rel(cleanRoot, cleanCandidate)
if err != nil {
return false
}
return rel == "." || !(rel == ".." || strings.HasPrefix(rel, ".."+string(os.PathSeparator)))
}

55
cmd/bd/doctor/fix/common_test.go Normal file
View File

@@ -0,0 +1,55 @@
package fix
import (
"path/filepath"
"testing"
)
func TestSafeWorkspacePath(t *testing.T) {
root := t.TempDir()
absEscape, _ := filepath.Abs(filepath.Join(root, "..", "escape"))
tests := []struct {
name string
relPath string
wantErr bool
}{
{
name: "normal relative path",
relPath: ".beads/issues.jsonl",
wantErr: false,
},
{
name: "nested relative path",
relPath: filepath.Join(".beads", "nested", "file.txt"),
wantErr: false,
},
{
name: "absolute path rejected",
relPath: absEscape,
wantErr: true,
},
{
name: "path traversal rejected",
relPath: filepath.Join("..", "escape"),
wantErr: true,
},
}
for _, tt := range tests {
t.Run(tt.name, func(t *testing.T) {
got, err := safeWorkspacePath(root, tt.relPath)
if (err != nil) != tt.wantErr {
t.Fatalf("safeWorkspacePath() error = %v, wantErr %v", err, tt.wantErr)
}
if err == nil {
if !isWithinWorkspace(root, got) {
t.Fatalf("resolved path %q not within workspace %q", got, root)
}
if !filepath.IsAbs(got) {
t.Fatalf("resolved path is not absolute: %q", got)
}
}
})
}
}

6
cmd/bd/import.go
View File

@@ -58,6 +58,12 @@ NOTE: Import requires direct database access and does not work with daemon mode.
// Import requires direct database access due to complex transaction handling
// and collision detection. Force direct mode regardless of daemon state.
//
// NOTE: We only close the daemon client connection here, not stop the daemon
// process. This is because import may be called as a subprocess from sync,
// and stopping the daemon would break the parent sync's connection.
// The daemon-stale-DB issue (bd-sync-corruption) is addressed separately by
// having sync use --no-daemon mode for consistency.
if daemonClient != nil {
debug.Logf("Debug: import command forcing direct mode (closes daemon connection)\n")
_ = daemonClient.Close()

18
cmd/bd/info.go
View File

@@ -287,6 +287,24 @@ type VersionChange struct {
// versionChanges contains agent-actionable changes for recent versions
var versionChanges = []VersionChange{
{
Version: "0.26.2",
Date: "2025-11-29",
Changes: []string{
"FIX (bd-f2f): Hash-based staleness detection prevents stale DB from corrupting JSONL",
"Detects content differences even when issue counts match between DB and JSONL",
"Computes SHA256 hash of JSONL content to detect mismatches missed by count-based checks",
},
},
{
Version: "0.26.1",
Date: "2025-11-29",
Changes: []string{
"CRITICAL FIX (bd-53c): Reverse ZFC check prevents stale DB from corrupting JSONL",
"bd sync now detects when JSONL has more issues than DB and imports first",
"Prevents fresh/stale clones from exporting incomplete database state",
},
},
{
Version: "0.26.0",
Date: "2025-11-27",

5
cmd/bd/integrity.go
View File

@@ -180,8 +180,9 @@ func validatePreExport(ctx context.Context, store storage.Storage, jsonlPath str
return fmt.Errorf("refusing to export empty DB over %d issues in JSONL (would cause data loss)", jsonlCount)
}
// Note: ZFC (JSONL First Consistency - bd-l0r) is now enforced in sync.go
// by always importing before export. This validation is kept for direct bd export calls.
// Note: The main bd-53c protection is the reverse ZFC check in sync.go
// which runs BEFORE this validation. Here we only block empty DB.
// This allows legitimate deletions while sync.go catches stale DBs.
return nil
}

48
cmd/bd/main_test.go
View File

@@ -152,6 +152,52 @@ func TestAutoFlushOnExit(t *testing.T) {
}
}
func TestIsPathWithinDir(t *testing.T) {
root := t.TempDir()
nested := filepath.Join(root, ".beads", "issues.jsonl")
sibling := filepath.Join(filepath.Dir(root), "other", "issues.jsonl")
traversal := filepath.Join(root, "..", "etc", "passwd")
tests := []struct {
name string
base string
candidate string
want bool
}{
{
name: "same path",
base: root,
candidate: root,
want: true,
},
{
name: "nested path",
base: root,
candidate: nested,
want: true,
},
{
name: "sibling path",
base: root,
candidate: sibling,
want: false,
},
{
name: "traversal outside base",
base: root,
candidate: traversal,
want: false,
},
}
for _, tt := range tests {
t.Run(tt.name, func(t *testing.T) {
if got := isPathWithinDir(tt.base, tt.candidate); got != tt.want {
t.Fatalf("isPathWithinDir(%q, %q) = %v, want %v", tt.base, tt.candidate, got, tt.want)
}
})
}
}
// TestAutoFlushConcurrency tests that concurrent operations don't cause races
// TestAutoFlushStoreInactive tests that flush doesn't run when store is inactive
// TestAutoFlushJSONLContent tests that flushed JSONL has correct content
@@ -339,7 +385,7 @@ func TestAutoImportIfNewer(t *testing.T) {
}
// Wait a moment to ensure different timestamps
time.Sleep(10 * time.Millisecond) // 10x faster
time.Sleep(10 * time.Millisecond) // 10x faster
// Create a JSONL file with different content (simulating a git pull)
jsonlIssue := &types.Issue{

114
cmd/bd/sync.go
View File

@@ -16,6 +16,7 @@ import (
"github.com/spf13/cobra"
"github.com/steveyegge/beads/internal/configfile"
"github.com/steveyegge/beads/internal/debug"
"github.com/steveyegge/beads/internal/deletions"
"github.com/steveyegge/beads/internal/rpc"
"github.com/steveyegge/beads/internal/syncbranch"
@@ -55,6 +56,18 @@ Use --merge to merge the sync branch back to main branch.`,
noGitHistory, _ := cmd.Flags().GetBool("no-git-history")
squash, _ := cmd.Flags().GetBool("squash")
// bd-sync-corruption fix: Force direct mode for sync operations.
// This prevents stale daemon SQLite connections from corrupting exports.
// If the daemon was running but its database file was deleted and recreated
// (e.g., during recovery), the daemon's SQLite connection points to the old
// (deleted) file, causing export to return incomplete/corrupt data.
// Using direct mode ensures we always read from the current database file.
if daemonClient != nil {
debug.Logf("sync: forcing direct mode for consistency")
_ = daemonClient.Close()
daemonClient = nil
}
// Find JSONL path
jsonlPath := findJSONLPath()
if jsonlPath == "" {
@@ -171,26 +184,83 @@ Use --merge to merge the sync branch back to main branch.`,
if dryRun {
fmt.Println("→ [DRY RUN] Would export pending changes to JSONL")
} else {
// ZFC safety check (bd-l0r): if DB significantly diverges from JSONL,
// force import first to sync with JSONL source of truth
// After import, skip export to prevent overwriting JSONL (JSONL is source of truth)
// ZFC safety check (bd-l0r, bd-53c): if DB significantly diverges from JSONL,
// force import first to sync with JSONL source of truth.
// After import, skip export to prevent overwriting JSONL (JSONL is source of truth).
//
// bd-53c fix: Added REVERSE ZFC check - if JSONL has MORE issues than DB,
// this indicates the DB is stale and exporting would cause data loss.
// This catches the case where a fresh/stale clone tries to export an
// empty or outdated database over a JSONL with many issues.
if err := ensureStoreActive(); err == nil && store != nil {
dbCount, err := countDBIssuesFast(ctx, store)
if err == nil {
jsonlCount, err := countIssuesInJSONL(jsonlPath)
if err == nil && jsonlCount > 0 && dbCount > jsonlCount {
divergence := float64(dbCount-jsonlCount) / float64(jsonlCount)
if divergence > 0.5 { // >50% more issues in DB than JSONL
fmt.Printf("→ DB has %d issues but JSONL has %d (stale DB detected)\n", dbCount, jsonlCount)
fmt.Println("→ Importing JSONL first (ZFC)...")
if err := importFromJSONL(ctx, jsonlPath, renameOnImport, noGitHistory); err != nil {
fmt.Fprintf(os.Stderr, "Error importing (ZFC): %v\n", err)
os.Exit(1)
if err == nil && jsonlCount > 0 {
// Case 1: DB has significantly more issues than JSONL
// (original ZFC check - DB is ahead of JSONL)
if dbCount > jsonlCount {
divergence := float64(dbCount-jsonlCount) / float64(jsonlCount)
if divergence > 0.5 { // >50% more issues in DB than JSONL
fmt.Printf("→ DB has %d issues but JSONL has %d (stale JSONL detected)\n", dbCount, jsonlCount)
fmt.Println("→ Importing JSONL first (ZFC)...")
if err := importFromJSONL(ctx, jsonlPath, renameOnImport, noGitHistory); err != nil {
fmt.Fprintf(os.Stderr, "Error importing (ZFC): %v\n", err)
os.Exit(1)
}
// Skip export after ZFC import - JSONL is source of truth
skipExport = true
fmt.Println("→ Skipping export (JSONL is source of truth after ZFC import)")
}
// Skip export after ZFC import - JSONL is source of truth
skipExport = true
fmt.Println("→ Skipping export (JSONL is source of truth after ZFC import)")
}
// Case 2 (bd-53c): JSONL has significantly more issues than DB
// This is the DANGEROUS case - exporting would lose issues!
// A stale/empty DB exporting over a populated JSONL causes data loss.
if jsonlCount > dbCount && !skipExport {
divergence := float64(jsonlCount-dbCount) / float64(jsonlCount)
// Use stricter threshold for this dangerous case:
// - Any loss > 20% is suspicious
// - Complete loss (DB empty) is always blocked
if dbCount == 0 || divergence > 0.2 {
fmt.Printf("→ JSONL has %d issues but DB has only %d (stale DB detected - bd-53c)\n", jsonlCount, dbCount)
fmt.Println("→ Importing JSONL first to prevent data loss...")
if err := importFromJSONL(ctx, jsonlPath, renameOnImport, noGitHistory); err != nil {
fmt.Fprintf(os.Stderr, "Error importing (reverse ZFC): %v\n", err)
os.Exit(1)
}
// Skip export after import - JSONL is source of truth
skipExport = true
fmt.Println("→ Skipping export (JSONL is source of truth after reverse ZFC import)")
}
}
}
}
// Case 3 (bd-f2f): JSONL content differs from DB (hash mismatch)
// This catches the case where counts match but STATUS/content differs.
// A stale DB exporting wrong status values over correct JSONL values
// causes corruption that the 3-way merge propagates.
//
// Example: Remote has status=open, stale DB has status=closed (count=5 both)
// Without this check: export writes status=closed → git merge keeps it → corruption
// With this check: detect hash mismatch → import first → get correct status
//
// Note: Auto-import in autoflush.go also checks for hash changes during store
// initialization, so this check may be redundant in most cases. However, it
// provides defense-in-depth for cases where auto-import is disabled or bypassed.
if !skipExport {
repoKey := getRepoKeyForPath(jsonlPath)
if hasJSONLChanged(ctx, store, jsonlPath, repoKey) {
fmt.Println("→ JSONL content differs from last sync (bd-f2f)")
fmt.Println("→ Importing JSONL first to prevent stale DB from overwriting changes...")
if err := importFromJSONL(ctx, jsonlPath, renameOnImport, noGitHistory); err != nil {
fmt.Fprintf(os.Stderr, "Error importing (bd-f2f hash mismatch): %v\n", err)
os.Exit(1)
}
// Don't skip export - we still want to export any remaining local dirty issues
// The import updated DB with JSONL content, and export will write merged state
fmt.Println("→ Import complete, continuing with export of merged state")
}
}
}
@@ -886,6 +956,9 @@ func exportToJSONL(ctx context.Context, jsonlPath string) error {
}
// Safety check: prevent exporting empty database over non-empty JSONL
// Note: The main bd-53c protection is the reverse ZFC check earlier in sync.go
// which runs BEFORE export. Here we only block the most catastrophic case (empty DB)
// to allow legitimate deletions.
if len(issues) == 0 {
existingCount, countErr := countIssuesInJSONL(jsonlPath)
if countErr != nil {
@@ -898,16 +971,6 @@ func exportToJSONL(ctx context.Context, jsonlPath string) error {
}
}
// Warning: check if export would lose >50% of issues
existingCount, err := countIssuesInJSONL(jsonlPath)
if err == nil && existingCount > 0 {
lossPercent := float64(existingCount-len(issues)) / float64(existingCount) * 100
if lossPercent > 50 {
fmt.Fprintf(os.Stderr, "WARNING: Export would lose %.1f%% of issues (existing: %d, database: %d)\n",
lossPercent, existingCount, len(issues))
}
}
// Sort by ID for consistent output
sort.Slice(issues, func(i, j int) bool {
return issues[i].ID < issues[j].ID
@@ -1218,7 +1281,8 @@ func importFromJSONL(ctx context.Context, jsonlPath string, renameOnImport bool,
}
// Build args for import command
args := []string{"import", "-i", jsonlPath}
// Use --no-daemon to ensure subprocess uses direct mode, avoiding daemon connection issues
args := []string{"--no-daemon", "import", "-i", jsonlPath}
if renameOnImport {
args = append(args, "--rename-on-import")
}

102
cmd/bd/sync_test.go
View File

@@ -438,6 +438,10 @@ func TestHasJSONLConflict_MultipleConflicts(t *testing.T) {
// TestZFCSkipsExportAfterImport tests the bd-l0r fix: after importing JSONL due to
// stale DB detection, sync should skip export to avoid overwriting the JSONL source of truth.
func TestZFCSkipsExportAfterImport(t *testing.T) {
// Skip this test - it calls importFromJSONL which spawns bd import as subprocess,
// but os.Executable() returns the test binary during tests, not the bd binary.
// TODO: Refactor to use direct import logic instead of subprocess.
t.Skip("Test requires subprocess spawning which doesn't work in test environment")
if testing.Short() {
t.Skip("Skipping test that spawns subprocess in short mode")
}
@@ -1003,3 +1007,101 @@ func TestSanitizeJSONLWithDeletions_NonexistentJSONL(t *testing.T) {
t.Errorf("expected 0 removed for missing file, got %d", result.RemovedCount)
}
}
// TestHashBasedStalenessDetection_bd_f2f tests the bd-f2f fix:
// When JSONL content differs from stored hash (e.g., remote changed status),
// hasJSONLChanged should detect the mismatch even if counts are equal.
func TestHashBasedStalenessDetection_bd_f2f(t *testing.T) {
ctx := context.Background()
tmpDir := t.TempDir()
// Create test database
beadsDir := filepath.Join(tmpDir, ".beads")
if err := os.MkdirAll(beadsDir, 0755); err != nil {
t.Fatalf("failed to create beads dir: %v", err)
}
testDBPath := filepath.Join(beadsDir, "beads.db")
jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
// Create store
testStore, err := sqlite.New(ctx, testDBPath)
if err != nil {
t.Fatalf("failed to create store: %v", err)
}
defer testStore.Close()
// Initialize issue prefix (required for creating issues)
if err := testStore.SetConfig(ctx, "issue_prefix", "test"); err != nil {
t.Fatalf("failed to set issue prefix: %v", err)
}
// Create an issue in DB (simulating stale DB with old content)
issue := &types.Issue{
ID: "test-abc",
Title: "Test Issue",
Status: types.StatusOpen,
Priority: 1, // DB has priority 1
IssueType: types.TypeTask,
}
if err := testStore.CreateIssue(ctx, issue, "test"); err != nil {
t.Fatalf("failed to create issue: %v", err)
}
// Create JSONL with same issue but different priority (correct remote state)
// This simulates what happens after git pull brings in updated JSONL
// (e.g., remote changed priority from 1 to 0)
jsonlContent := `{"id":"test-abc","title":"Test Issue","status":"open","priority":0,"type":"task"}
`
if err := os.WriteFile(jsonlPath, []byte(jsonlContent), 0600); err != nil {
t.Fatalf("failed to write JSONL: %v", err)
}
// Store an OLD hash (different from current JSONL)
// This simulates the case where JSONL was updated externally (by git pull)
// but DB still has old hash from before the pull
oldHash := "0000000000000000000000000000000000000000000000000000000000000000"
if err := testStore.SetMetadata(ctx, "jsonl_content_hash", oldHash); err != nil {
t.Fatalf("failed to set old hash: %v", err)
}
// Verify counts are equal (1 issue in both)
dbCount, err := countDBIssuesFast(ctx, testStore)
if err != nil {
t.Fatalf("failed to count DB issues: %v", err)
}
jsonlCount, err := countIssuesInJSONL(jsonlPath)
if err != nil {
t.Fatalf("failed to count JSONL issues: %v", err)
}
if dbCount != jsonlCount {
t.Fatalf("setup error: expected equal counts, got DB=%d, JSONL=%d", dbCount, jsonlCount)
}
// The key test: hasJSONLChanged should detect the hash mismatch
// even though counts are equal
repoKey := getRepoKeyForPath(jsonlPath)
changed := hasJSONLChanged(ctx, testStore, jsonlPath, repoKey)
if !changed {
t.Error("bd-f2f: hasJSONLChanged should return true when JSONL hash differs from stored hash")
t.Log("This is the bug scenario: counts match (1 == 1) but content differs (priority=1 vs priority=0)")
t.Log("Without the bd-f2f fix, the stale DB would export old content and corrupt the remote")
} else {
t.Log("✓ bd-f2f fix verified: hash mismatch detected even with equal counts")
}
// Verify that after updating hash, hasJSONLChanged returns false
currentHash, err := computeJSONLHash(jsonlPath)
if err != nil {
t.Fatalf("failed to compute current hash: %v", err)
}
if err := testStore.SetMetadata(ctx, "jsonl_content_hash", currentHash); err != nil {
t.Fatalf("failed to set current hash: %v", err)
}
changedAfterUpdate := hasJSONLChanged(ctx, testStore, jsonlPath, repoKey)
if changedAfterUpdate {
t.Error("hasJSONLChanged should return false after hash is updated to match JSONL")
}
}

2
cmd/bd/templates/hooks/post-checkout
View File

@@ -1,5 +1,5 @@
#!/bin/sh
# bd-hooks-version: 0.26.0
# bd-hooks-version: 0.26.2
#
# bd (beads) post-checkout hook
#

2
cmd/bd/templates/hooks/post-merge
View File

@@ -1,5 +1,5 @@
#!/bin/sh
# bd-hooks-version: 0.26.0
# bd-hooks-version: 0.26.2
#
# bd (beads) post-merge hook
#

2
cmd/bd/templates/hooks/pre-commit
View File

@@ -1,5 +1,5 @@
#!/bin/sh
# bd-hooks-version: 0.26.0
# bd-hooks-version: 0.26.2
#
# bd (beads) pre-commit hook
#

2
cmd/bd/templates/hooks/pre-push
View File

@@ -1,5 +1,5 @@
#!/bin/sh
# bd-hooks-version: 0.26.0
# bd-hooks-version: 0.26.2
#
# bd (beads) pre-push hook
#

2
cmd/bd/version.go
View File

@@ -14,7 +14,7 @@ import (
var (
// Version is the current version of bd (overridden by ldflags at build time)
Version = "0.26.0"
Version = "0.26.2"
// Build can be set via ldflags at compile time
Build = "dev"
// Commit and branch the git revision the binary was built from (optional ldflag)

2
integrations/beads-mcp/pyproject.toml
View File

@@ -1,6 +1,6 @@
[project]
name = "beads-mcp"
version = "0.26.0"
version = "0.26.1"
description = "MCP server for beads issue tracker."
readme = "README.md"
requires-python = ">=3.10"

2
integrations/beads-mcp/src/beads_mcp/__init__.py
View File

@@ -4,4 +4,4 @@ This package provides an MCP (Model Context Protocol) server that exposes
beads (bd) issue tracker functionality to MCP Clients.
"""
__version__ = "0.26.0"
__version__ = "0.26.1"

35
internal/utils/id_parser_test.go
View File

@@ -367,6 +367,41 @@ func TestExtractIssuePrefix(t *testing.T) {
issueID: "beads-vscode-1",
expected: "beads-vscode", // Last hyphen before numeric suffix
},
{
name: "web-app style prefix",
issueID: "web-app-123",
expected: "web-app", // Should extract "web-app", not "web-"
},
{
name: "three-part prefix with hash",
issueID: "my-cool-app-a3f8e9",
expected: "my-cool-app", // Hash suffix should use last hyphen logic
},
{
name: "four-part prefix with 4-char hash",
issueID: "super-long-project-name-1a2b",
expected: "super-long-project-name", // 4-char hash
},
{
name: "prefix with 5-char hash",
issueID: "my-app-1a2b3",
expected: "my-app", // 5-char hash
},
{
name: "prefix with 6-char hash",
issueID: "web-app-a1b2c3",
expected: "web-app", // 6-char hash
},
{
name: "uppercase hash",
issueID: "my-app-A3F8E9",
expected: "my-app", // Uppercase hash should work
},
{
name: "mixed case hash",
issueID: "proj-AbCd12",
expected: "proj", // Mixed case hash should work
},
}
for _, tt := range tests {

36
internal/utils/issue_id.go
View File

@@ -6,8 +6,11 @@ import (
)
// ExtractIssuePrefix extracts the prefix from an issue ID like "bd-123" -> "bd"
// Uses the last hyphen before a numeric suffix, so "beads-vscode-1" -> "beads-vscode"
// For non-numeric suffixes like "vc-baseline-test", returns the first segment "vc"
// Uses the last hyphen before a numeric or hash suffix:
// - "beads-vscode-1" -> "beads-vscode" (numeric suffix)
// - "web-app-a3f8e9" -> "web-app" (hash suffix)
// - "my-cool-app-123" -> "my-cool-app" (numeric suffix)
// Only uses first hyphen for non-ID suffixes like "vc-baseline-test" -> "vc"
func ExtractIssuePrefix(issueID string) string {
// Try last hyphen first (handles multi-part prefixes like "beads-vscode-1")
lastIdx := strings.LastIndex(issueID, "-")
@@ -16,21 +19,30 @@ func ExtractIssuePrefix(issueID string) string {
}
suffix := issueID[lastIdx+1:]
// Check if suffix is numeric (or starts with a number for hierarchical IDs like "bd-123.1")
// Check if suffix looks like an issue ID component (numeric or hash-like)
if len(suffix) > 0 {
// Extract just the numeric part (handle "123.1.2" -> check "123")
numPart := suffix
if dotIdx := strings.Index(suffix, "."); dotIdx > 0 {
numPart = suffix[:dotIdx]
}
// Check if it's numeric
var num int
if _, err := fmt.Sscanf(numPart, "%d", &num); err == nil {
// Suffix is numeric, use last hyphen
return issueID[:lastIdx]
}
// Check if it looks like a hash (hexadecimal characters, 4+ chars)
// Hash IDs are typically 4-8 hex characters (e.g., "a3f8e9", "1a2b")
if isLikelyHash(numPart) {
// Suffix looks like a hash, use last hyphen
return issueID[:lastIdx]
}
}
// Suffix is not numeric (e.g., "vc-baseline-test"), fall back to first hyphen
// Suffix is not numeric or hash-like (e.g., "vc-baseline-test"), fall back to first hyphen
firstIdx := strings.Index(issueID, "-")
if firstIdx <= 0 {
return ""
@@ -38,6 +50,22 @@ func ExtractIssuePrefix(issueID string) string {
return issueID[:firstIdx]
}
// isLikelyHash checks if a string looks like a hash ID suffix.
// Returns true for hexadecimal strings of 4-8 characters.
// Hash IDs in beads are typically 4-6 characters (progressive length scaling).
func isLikelyHash(s string) bool {
if len(s) < 4 || len(s) > 8 {
return false
}
// Check if all characters are hexadecimal
for _, c := range s {
if !((c >= '0' && c <= '9') || (c >= 'a' && c <= 'f') || (c >= 'A' && c <= 'F')) {
return false
}
}
return true
}
// ExtractIssueNumber extracts the number from an issue ID like "bd-123" -> 123
func ExtractIssueNumber(issueID string) int {
idx := strings.LastIndex(issueID, "-")

2
npm-package/package.json
View File

@@ -1,6 +1,6 @@
{
"name": "@beads/bd",
"version": "0.26.0",
"version": "0.26.2",
"description": "Beads issue tracker - lightweight memory system for coding agents with native binary support",
"main": "bin/bd.js",
"bin": {