When not in a git repository:
- Daemon startup now shows clear message immediately instead of waiting
5 seconds: "Note: No git repository initialized — running without
background sync"
- Added new doctor check "Git Sync Setup" that explains the situation
Doctor check now shows three states:
1. No git repo → Warning with fix: "Run 'git init' to enable background sync"
2. Git repo, no sync-branch → OK with hint about team collaboration benefits
3. Git repo + sync-branch → OK, fully configured
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Review findings addressed:
1. Fixed HasSyncBranchGitignoreFlags() - now correctly returns (hasAnyFlag,
hasSkipWorktree) since skip-worktree takes precedence in git ls-files -v
2. Added interactions.jsonl to list of files to hide (was only issues.jsonl)
3. Added idempotency check - skips setting flags if already set (checks for S)
4. Made output conditional - only prints when flags actually changed
5. Fixed addToGitExclude() pattern matching - now uses exact line match
instead of substring to prevent false positives
6. Refactored to use setGitIndexFlags() helper to reduce duplication
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
When sync.branch is configured, issues.jsonl appears modified in git status
even though changes go to the sync branch. This is confusing for users and
risks accidental commits to the wrong branch.
Implementation:
- Added SyncBranchGitignore() to set git index flags (assume-unchanged,
skip-worktree) on issues.jsonl when sync.branch is configured
- For untracked files, adds to .git/info/exclude instead
- Called automatically from bd sync after successful sync-branch sync
- Added bd doctor check and fix for this issue
- Added HasSyncBranchGitignoreFlags() to check current flag state
- Added ClearSyncBranchGitignore() to remove flags when sync.branch disabled
Fixes: GH#870 (duplicate of GH#797, GH#801)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
When daemon fails to start due to legacy database or fingerprint validation,
the error was only logged to daemon.log. Users saw "Daemon took too long"
with no hint about the actual problem.
Changes:
- Write validation errors to .beads/daemon-error file before daemon exits
- Check for daemon-error file in autostart and display contents on timeout
- Elevate legacy database check in bd doctor from warning to error
Now when daemon fails due to legacy database, users see:
"LEGACY DATABASE DETECTED!
...
Run 'bd migrate --update-repo-id' to add fingerprint"
Instead of just "Daemon took too long to start".
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When sync-branch is configured, JSONL files are intentionally untracked
in working branches and only committed to the dedicated sync branch.
The CheckIssuesTracking and CheckUntrackedBeadsFiles checks now detect
sync-branch mode via GetFromYAML() and return OK status instead of
false warnings.
Add support for Gemini CLI hook-based integration, similar to Claude Code:
- bd setup gemini: Install SessionStart/PreCompress hooks
- bd setup gemini --check: Verify installation
- bd setup gemini --remove: Remove hooks
- bd setup gemini --project: Project-only installation
- bd setup gemini --stealth: Use bd prime --stealth
Also adds Gemini CLI integration check to bd doctor.
Gemini CLI's hook system is nearly identical to Claude Code's,
making this a clean, low-maintenance addition.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The last-touched file was accidentally removed from GitignoreTemplate
in commit 310d374 (GH#814 fix). This restores it and adds it to
requiredPatterns so bd doctor will detect outdated gitignores.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds #nosec G204 annotations to exec.Command calls that use
hardcoded paths. Fixes pre-existing lint failure exposed by PR #832.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
- Add redirect to GitignoreTemplate with explanatory comment
- Add redirect to requiredPatterns for outdated gitignore detection
- Add CheckRedirectNotTracked() to detect already-tracked redirect files
- Add FixRedirectTracking() to untrack via git rm --cached
- Register check in bd doctor under Git Integration category
- Add 6 tests for the new functionality
The redirect file contains a relative path that only works in the
original worktree. When committed, it causes warnings in other clones:
"Warning: redirect target does not exist"
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When bd worktree creates a worktree, it writes a .beads/redirect file
pointing back to the main repo's .beads/. If this file is accidentally
committed (e.g., via git add .), it causes "redirect target does not exist"
warnings when cloned or used in other worktrees.
Changes:
- Add 'redirect' to GitignoreTemplate to prevent future accidental commits
- Add 'redirect' to requiredPatterns so bd doctor detects outdated .gitignore
- Add CheckRedirectNotTracked() to detect already-tracked redirect files
- Add FixRedirectTracking() to untrack accidentally committed redirects
Tests: 8 new tests covering template, detection, and fix scenarios
The prefix mismatch check in bd doctor was reporting warnings when
issues were created via molecule workflows (bd mol pour), which
intentionally use a different prefix pattern (<base>-mol instead
of just <base>).
Added recognition of valid workflow prefix variants:
- <prefix>-mol (molecules from bd mol pour)
- <prefix>-wisp (ephemeral wisps)
- <prefix>-eph (ephemeral issues)
These are intentional prefix extensions for visual distinction, not
actual mismatches. The check now only warns for truly mismatched
prefixes (e.g., different project entirely).
Added comprehensive regression tests for all prefix variant cases.
Fixes#811
Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When no issue ID is provided to `bd update` or `bd close`, use the last
touched issue from the most recent create, update, show, or close operation.
This addresses the common workflow where you create an issue and then
immediately want to add more details (like changing priority from P2 to P4)
without re-typing the issue ID.
Implementation:
- New file last_touched.go with Get/Set/Clear functions
- Store last touched ID in .beads/last-touched (gitignored)
- Track on create, update, show, and close operations
- Allow update/close with zero args to use last touched
(bd-s2t)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Post-merge cleanup of PR #805:
1. Extract duplicate error classification logic into classifyDatabaseError()
helper function (was duplicated in two places in database.go)
2. Fix semantic conflict between --force and --source=db flags:
- --force implies "database is broken, rebuild from JSONL"
- --source=db implies "use database as source of truth"
- These are contradictory; now errors with clear message
- --force with --source=auto or --source=jsonl works as expected
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Executed-By: beads/crew/dave
Rig: beads
Role: crew
Apply the same enhanced error classification to PRAGMA integrity_check
failures as we do for database open failures.
This ensures users see detailed, actionable recovery steps regardless of
which stage the corruption is detected (open vs integrity check).
Tested with real corruption scenarios - all error paths now provide
specific recovery guidance with exact commands.
Add comprehensive database corruption recovery capabilities to bd doctor.
## Changes
### New Command Flags
- --force: Force repair mode that bypasses database validation
- --source: Choose source of truth (auto/jsonl/db) for recovery
### Enhanced Error Classification
Improved CheckDatabaseIntegrity() to detect and classify:
- Database locked errors (suggests killing processes, removing locks)
- Invalid SQLite files (suggests JSONL recovery with exact commands)
- Migration/validation failures (orphaned dependencies, etc.)
- Generic database errors (context-aware suggestions)
Each error type provides:
- Specific diagnosis
- Step-by-step recovery instructions
- Appropriate command examples with new flags
### Force Recovery Implementation
New DatabaseCorruptionRecoveryWithOptions() function:
- Bypasses database validation when --force is used
- Supports explicit source of truth selection
- Auto-detects best recovery path when source=auto
- Comprehensive rollback on failure
- Uses --force --no-git-history in import during force mode
### Integration
Updated fix orchestration to pass force and source flags to recovery.
## Usage Examples
```bash
# Unopenable database with validation errors
bd doctor --fix --force --source=jsonl
# Choose specific source of truth
bd doctor --fix --source=jsonl # Trust JSONL
bd doctor --fix --source=db # Trust database
bd doctor --fix --source=auto # Auto-detect (default)
# Force recovery with auto-detection
bd doctor --fix --force
```
## Problem Solved
Before: When database had validation errors (orphaned dependencies,
foreign key violations), all bd commands failed in a catch-22 situation.
Could not open database to fix database. Users had to manually delete
database files and reinit.
After: bd doctor --fix --force detects unopenable databases, provides
clear recovery steps, and forces rebuild from JSONL even when database
validation fails.
## Backward Compatibility
- All new flags are optional with safe defaults
- --source defaults to 'auto' (existing behavior)
- --force is opt-in only
- Existing bd doctor behavior unchanged when flags not used
- DatabaseCorruptionRecovery() still exists for compatibility
Fixes: bd-pgza
Safeguard for users with global gitignore patterns like *.jsonl that
could cause issues.jsonl to be ignored, breaking bd sync.
The check runs git check-ignore and warns if issues.jsonl would be
ignored by any gitignore rule (global, parent directory, etc).
The CheckSyncBranchHookCompatibility was checking core.hooksPath first,
while CheckGitHooks always uses .git/hooks/. This caused inconsistent
results when core.hooksPath was set globally.
Fix: Remove core.hooksPath check from CheckSyncBranchHookCompatibility
to match CheckGitHooks behavior. Both now consistently use .git/hooks/.
Note: A future improvement could make both respect core.hooksPath.
The negation patterns (!issues.jsonl, !interactions.jsonl, etc.) in
.beads/.gitignore had higher precedence than the fork protection
exclusion in .git/info/exclude, effectively defeating fork protection.
Contributors could accidentally stage and commit upstream issue
databases because:
1. Fork protection added .beads/issues.jsonl to .git/info/exclude
2. .beads/.gitignore had !issues.jsonl which overrode the exclusion
3. .gitignore files have higher precedence than .git/info/exclude
The negation patterns were unnecessary anyway since no pattern in
.beads/.gitignore matches those files. Added a comment explaining
why negations should not be added.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Rename followRedirect to FollowRedirect in internal/beads (export it)
- Update doctor/maintenance.go to use beads.FollowRedirect
- Update doctor/fix/common.go to use beads.FollowRedirect
- Remove 66 lines of duplicated code across 3 implementations
This ensures consistent redirect handling with path canonicalization,
chain prevention, and proper error warnings.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add resolveBeadsDir helper to fix/common.go to follow redirect files
- Update OrphanedDependencies, ChildParentDependencies, and MergeArtifacts
to use resolveBeadsDir instead of hardcoded .beads path
- Add --verbose/-v flag to bd doctor command
- Only print individual items if verbose or count < 20, always show summary
(bd-dq74, bd-v55y)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Strip (bd-xxx), (gt-xxx) suffixes from code comments and changelog
entries. The descriptions remain meaningful without the ephemeral
issue IDs.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add a --deep flag to bd doctor that runs comprehensive graph integrity
checks on the beads database:
- Parent consistency: verify parent-child deps point to existing issues
- Dependency integrity: all dependencies reference valid issues
- Epic completeness: find epics ready to close (all children closed)
- Agent bead integrity: validate agent beads have valid state values
- Mail thread integrity: verify thread_id references exist
- Molecule integrity: check molecules have valid parent-child structures
The deep validation mode warns about potential slowness on large databases
and provides both human-readable and JSON output formats.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add Phase field to Formula type to indicate recommended instantiation phase
- Add warning in 'bd mol pour' when formula has phase="vapor"
- Improve pour/wisp help text with clear comparison of when to use each
- Add CheckPersistentMolIssues doctor check to detect mol- issues in JSONL
- Update beads-release.formula.json with phase="vapor"
This helps prevent accidental persistence of ephemeral workflow issues.
Extended bd-tvus fix to all doctor check functions that access .beads/
directory. In Gas Town multi-clone setups, crew/polecat clones use
.beads/redirect files to point to the shared mayor/rig beads directory.
Doctor checks now use resolveBeadsDir() to follow these redirects:
- daemon.go: CheckDaemonStatus
- git.go: CheckSyncBranchConfig, FindOrphanedIssues, CheckOrphanedIssues
- installation.go: CheckMultipleDatabases, CheckPermissions
- integrity.go: CheckIDFormat, CheckDependencyCycles, CheckTombstones,
CheckDeletionsManifest, CheckRepoFingerprint
- jsonl_integrity.go: CheckJSONLIntegrity
- legacy.go: CheckFreshClone
- maintenance.go: CheckStaleClosedIssues, CheckExpiredTombstones,
CheckCompactionCandidates
- perf.go: RunPerformanceDiagnostics, CollectPlatformInfo
- validation.go: CheckMergeArtifacts, CheckOrphanedDependencies,
CheckDuplicateIssues, CheckTestPollution, CheckChildParentDependencies,
CheckGitConflicts
- version.go: CheckMetadataVersionTracking
Intentionally NOT changed (check local files):
- CheckInstallation: checks local .beads/ exists
- CheckUntrackedBeadsFiles: checks git tracking of local files
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The bug was that doctor's database checks used the local .beads/beads.db
file directly, while import followed the redirect to the actual database.
This caused confusing output showing 0 issues when the actual database
had hundreds. Fixed by using resolveBeadsDir() in all database checks.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add nolint:unparam for readOnly param in sqlite_open.go
- Handle cmd.Help() error in wisp.go
- Handle rows.Close() error in migration 028
- Handle targetStore.Close() error in create.go
- Update Nix vendorHash for current dependencies
Cherry-picked from PR #769
Implements the 'bd orphans' command to identify issues referenced in commits
but still open in the database, and refactors to eliminate code duplication.
- Creates cmd/bd/orphans.go with Cobra command structure
- Identifies orphaned issues (referenced in git commits but still open/in_progress)
- Supports multiple output formats (human, JSON, detailed)
- Auto-close with --fix flag
DRY refactoring:
- Extracted FindOrphanedIssues() to cmd/bd/doctor/git.go as shared core logic
- Moved OrphanIssue type to cmd/bd/doctor/types.go
- Refactored CheckOrphanedIssues() to use FindOrphanedIssues()
Cherry-picked from PR #767
Co-authored-by: Amp <amp@ampcode.com>
- Add --check flag to doctor for specific check modes
- Add --check=pollution to run detailed pollution detection
- Add --clean flag to delete detected test issues
- Mark detect-pollution command as hidden (deprecated)
- Update fix messages to point to new doctor --check=pollution
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Analysis found these commands are dead code:
- gt never calls `bd pin` - uses `bd update --status=pinned` instead
- Beads.Pin() wrapper exists but is never called
- bd hook functionality duplicated by gt mol status
- Code comment says "pinned field is cosmetic for bd hook visibility"
Removed:
- cmd/bd/pin.go
- cmd/bd/unpin.go
- cmd/bd/hook.go
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Modern git (2.28+) uses 'main' as default branch, not 'master'.
Tests were failing because they assumed 'master' branch exists.
Changes:
- Use 'git init --initial-branch=main' instead of bare 'git init'
- Change 'git checkout master' to 'git checkout main'
- Add git.ResetCaches() after os.Chdir() to clear cached git state
- Ensures test isolation when changing directories
Adds automatic database recovery when bd doctor --fix detects corruption:
- Detects SQLite corruption (malformed database, SQLITE_CORRUPT errors)
- Backs up corrupted database before recovery attempt
- Rebuilds from JSONL if available (issues.jsonl, deletions.jsonl)
- Falls back to fresh database if JSONL unavailable
- Reports recovery results (issues imported, success/failure)
Recovery is triggered automatically by --fix when corruption is detected.
No manual intervention required.
The CheckChildParentDependencies detection and ChildParentDependencies fix
were flagging ALL child→parent dependencies, including legitimate
'parent-child' type structural hierarchy relationships.
Now only blocking types (blocks, conditional-blocks, waits-for) are
detected as anti-patterns. The 'parent-child' type is a legitimate
hierarchy marker used for:
- Tracking parent-child relationships
- Transitive block propagation (if parent blocked, children blocked)
- Hierarchy visualization in external tools
Changes:
- Add type filter to SELECT queries (only blocking types)
- Add type filter to DELETE statement (preserve parent-child)
- Add regression test TestChildParentDependencies_PreservesParentChildType
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Claude Code's installed_plugins.json changed from v1 (plugins as structs)
to v2 (plugins as arrays). Update GetClaudePluginVersion() to handle both.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
GH#740: bd doctor --fix was auto-removing child→parent dependencies,
calling them an 'anti-pattern'. While these often indicate modeling
mistakes (deadlock), they may be intentional in some workflows.
Changes:
- Add --fix-child-parent flag (required to remove child→parent deps)
- Remove ChildParentDependencies from default --fix set
- Update warning message to reference new flag
- Update comments to reflect more nuanced understanding
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extends bd doctor to detect complete-but-unclosed molecules (epics where
all children are closed but root is still open).
- Added CheckStaleMolecules() to doctor/maintenance.go
- Added resolveBeadsDir() helper to follow Gas Town redirect files
- Check appears in Maintenance category with warning severity
- Shows example IDs and suggests 'bd mol stale' for review
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
