bd sync: 2025-11-27 20:21:31

.beads/issues.jsonl

@@ -7,6 +7,7 @@
 {"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":"open","priority":3,"issue_type":"task","created_at":"2025-11-24T00:28:55.890991-08:00","updated_at":"2025-11-24T00:28:55.890991-08:00"}
 {"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":"open","priority":2,"issue_type":"feature","created_at":"2025-11-27T20:21:15.691764-08:00","updated_at":"2025-11-27T20:21:15.691764-08:00"}
 {"id":"bd-4h3","title":"Add test coverage for internal/git package","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:23.497486-05:00","updated_at":"2025-11-20T21:21:23.497486-05:00","dependencies":[{"issue_id":"bd-4h3","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.277639-05:00","created_by":"daemon"}]}
 {"id":"bd-4l5","title":"bd prime: Detect ephemeral branches and adjust workflow output","description":"When 'bd prime' runs on a branch with no upstream (ephemeral branch), it should output a different SESSION CLOSE PROTOCOL.\n\n**Current output (wrong for ephemeral branches):**\n```\n[ ] 1. git status\n[ ] 2. git add \u003cfiles\u003e\n[ ] 3. bd sync\n[ ] 4. git commit -m \"...\"\n[ ] 5. bd sync\n[ ] 6. git push\n```\n\n**Needed output for ephemeral branches:**\n```\n[ ] 1. git status\n[ ] 2. git add \u003cfiles\u003e\n[ ] 3. bd sync --from-main  (pull updates from main)\n[ ] 4. git commit -m \"...\"\n[ ] 5. (no push - branch is ephemeral)\n```\n\n**Detection:** `git rev-parse --abbrev-ref --symbolic-full-name @{u}` returns error code 128 if no upstream.\n\nAlso update Sync \u0026 Collaboration section to mention `bd sync --from-main` for ephemeral branches.\n\n**Use case:** Gastown polecats work on ephemeral local branches that are never pushed. Their code gets merged to main via local merge, and beads changes stay local (communicated via gm mail to Overseer).","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-11-25T16:55:24.984104-08:00","updated_at":"2025-11-25T17:12:46.604978-08:00","closed_at":"2025-11-25T17:12:46.604978-08:00"}
 {"id":"bd-4pv","title":"bd export only outputs 1 issue after auto-import corrupts database","description":"When auto-import runs and purges issues (due to git history backfill bug), subsequent 'bd export' only exports 1 issue even though the database should have many.\n\nReproduction:\n1. Have issues.jsonl with 55 issues\n2. Auto-import triggers and purges all issues via git history backfill\n3. Run 'bd export' - only exports 1 issue (the last one created before corruption)\n\nThe database gets into an inconsistent state where most issues are purged but export doesn't realize this.\n\nWorkaround: Rebuild database from scratch with 'rm .beads/beads.db \u0026\u0026 bd init --prefix bd'","status":"open","priority":2,"issue_type":"bug","created_at":"2025-11-26T22:28:40.828866-08:00","updated_at":"2025-11-26T22:28:40.828866-08:00"}
@@ -22,10 +23,12 @@
 {"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":"open","priority":2,"issue_type":"feature","created_at":"2025-11-27T20:21:10.290649-08:00","updated_at":"2025-11-27T20:21:10.290649-08:00"}
 {"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":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T18:55:43.637047-05:00","updated_at":"2025-11-20T18:55:43.637047-05:00"}
 {"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":"open","priority":3,"issue_type":"chore","created_at":"2025-11-20T20:17:45.119583-05:00","updated_at":"2025-11-20T20:17:45.119583-05:00"}
 {"id":"bd-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":"open","priority":1,"issue_type":"feature","created_at":"2025-11-27T20:21:04.947959-08:00","updated_at":"2025-11-27T20:21:04.947959-08:00"}
 {"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-e92","title":"Add test coverage for internal/autoimport package","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:22.338577-05:00","updated_at":"2025-11-20T21:21:22.338577-05:00","dependencies":[{"issue_id":"bd-e92","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.128625-05:00","created_by":"daemon"}]}
 {"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"}
@@ -51,6 +54,7 @@
 {"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-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-v0x","title":"Auto-detect issue prefix from existing JSONL in 'bd init'","description":"When running `bd init` in a fresh clone with existing JSONL, it should auto-detect the issue prefix from the JSONL file instead of requiring `--prefix`.\n\nCurrently you must specify `--prefix ef` manually. But the JSONL file already contains issues like `ef-1it`, `ef-1jp` etc., so the prefix is known.\n\n**Ideal UX**:\n```\n$ bd init\nDetected issue prefix 'ef' from existing JSONL (38 issues).\n✓ Database initialized...\n```\n\nThis would make fresh clone hydration a single command: `bd init` with no flags.","status":"open","priority":2,"issue_type":"feature","created_at":"2025-11-27T20:21:21.049215-08:00","updated_at":"2025-11-27T20:21:21.049215-08:00"}
 {"id":"bd-v29","title":"Deletions pruning doesn't include results in JSON output","description":"## Problem\n\nWhen `bd compact --json` runs with deletions pruning, the prune results are silently discarded:\n\n```go\n// Only report if there were deletions to prune\nif result.PrunedCount \u003e 0 {\n    if jsonOutput {\n        // JSON output will be included in the main response\n        return  // \u003c-- BUG: results are NOT included anywhere\n    }\n    ...\n}\n```\n\n## Location\n`cmd/bd/compact.go:925-929`\n\n## Impact\n- JSON consumers don't know deletions were pruned\n- No way to audit pruning via automation\n\n## Fix\nReturn prune results and include in JSON output structure:\n\n```json\n{\n  \"success\": true,\n  \"compacted\": {...},\n  \"deletions_pruned\": {\n    \"count\": 5,\n    \"retention_days\": 7\n  }\n}\n```","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-11-25T12:48:59.730979-08:00","updated_at":"2025-11-25T15:11:54.363653-08:00","closed_at":"2025-11-25T15:11:54.363653-08:00"}
 {"id":"bd-wcl","title":"Document CLI + hooks as recommended approach over MCP","description":"Update documentation to position CLI + bd prime hooks as the primary recommended approach over MCP server, explaining why minimizing context matters even with large context windows (compute cost, energy, environment, latency).","status":"closed","priority":2,"issue_type":"task","created_at":"2025-11-12T00:15:25.923025-08:00","updated_at":"2025-11-26T20:13:52.891053-08:00","closed_at":"2025-11-26T18:06:51.020351-08:00"}
 {"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"}