Strip (bd-xxx), (gt-xxx) suffixes from code comments and changelog
entries. The descriptions remain meaningful without the ephemeral
issue IDs.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When beads is redirected (e.g., in Gas Town crew clones), bd prime now
shows a notice about the redirect. This helps agents understand why
they share issues with other clones.
CLI mode shows:
> ⚠️ **Redirected**: Local .beads → /path/to/target/.beads
> You share issues with other clones using this redirect.
MCP mode shows:
**Note**: Beads redirected to /path/to/target/.beads (shared with other clones)
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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
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
In git worktrees, any bd command was slow with a 2-3s pause because:
- git.IsWorktree() was called 4+ times per command
- Each call spawned 2 git processes (git-dir and git-common-dir)
- git.GetRepoRoot() and git.GetMainRepoRoot() also called multiple times
Fix: Cache results using sync.Once since these values do not change during
a single command execution:
- IsWorktree() - caches worktree detection
- GetRepoRoot() - caches repo root path
- GetMainRepoRoot() - caches main repo root for worktrees
Added ResetCaches() for test cleanup between subtests that change directories.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Wisps now use Wisp=true flag in the main database. The separate
.beads-wisp/ directory is no longer needed.
Removed:
- WispDirName constant
- FindWispDir()
- FindWispDatabasePath()
- NewWispStorage()
- EnsureWispGitignore()
- IsWispDatabase()
- All related tests
- .beads-wisp/ from .gitignore
- Remove cross-store squash logic from mol_squash.go
- Delete runWispSquash() and squashWispToPermanent() functions
- Simplify runMolSquash() to work with main store only
- Update mol_burn.go to work with main database
- Remove .beads-wisp/ directory references
- Look for Wisp=true issues in main store instead
- Update mol_bond.go to use Wisp flag instead of separate store
- --wisp now creates issues with Wisp=true in main store
- --pour creates issues with Wisp=false (persistent)
- Update bondProtoMol signature to accept both flags
- Deprecate wisp storage functions in beads.go
- WispDirName, FindWispDir, FindWispDatabasePath
- NewWispStorage, EnsureWispGitignore, IsWispDatabase
- All marked deprecated with reference to bd-bkul
- Remove obsolete cross-store squash tests
- TestSquashWispToPermanent
- TestSquashWispToPermanentWithSummary
- TestSquashWispToPermanentKeepChildren
All tests pass. Build succeeds.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The TestMain in beads_hash_multiclone_test.go was running `go build ./cmd/bd`
from the package directory (internal/beads) instead of the module root, causing
the build to fail with "directory not found".
Now uses `go list -m -f '{{.Dir}}'` to locate the module root and sets cmd.Dir
appropriately before building.
This fixes the integration test setup that was preventing TestRoutingIntegration
from running. (bd-g9eu)
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Conditional bonds now work as documented: "B runs only if A fails".
Implementation:
- Add DepConditionalBlocks dependency type to types.go
- Add IsFailureClose() helper to detect failure keywords in close_reason
- Update blocked cache to handle conditional-blocks:
- B is blocked while A is open
- B stays blocked if A closes with success
- B becomes unblocked if A closes with failure
Failure keywords: failed, rejected, wontfix, cancelled, abandoned,
blocked, error, timeout, aborted (case-insensitive)
Updated bondProtoProto, bondProtoMol, bondMolMol to use
DepConditionalBlocks for conditional bond type.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add git.GetRepoRoot() with Windows path normalization
- Update beads.findGitRoot() to delegate to git.GetRepoRoot()
- Replace findBeadsDir() with beads.FindBeadsDir() across 8 files
- Remove duplicate findBeadsDir() and findGitRoot() function definitions
- Remove dead test code (TestInfoCommand, TestInfoWithNoDaemon)
- Update tests to work with consolidated APIs
Part of Code Health Review Dec 2025 epic (bd-tggf).
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(doctor): UX improvements for diagnostics and daemon
- Add Repo Fingerprint check to detect when database belongs to a
different repository (copied .beads dir or git remote URL change)
- Add interactive fix for repo fingerprint with options: update repo ID,
reinitialize database, or skip
- Add visible warning when daemon takes >5s to start, recommending
'bd doctor' for diagnosis
- Detect install method (Homebrew vs script) and show only relevant
upgrade command
- Improve WARNINGS section:
- Add icons (⚠ or ✖) next to each item
- Color numbers by severity (yellow for warnings, red for errors)
- Render entire error lines in red
- Sort by severity (errors first)
- Fix alignment with checkmarks above
- Use heavier fail icon (✖) for better visibility
- Add integration and validation tests for doctor fixes
* fix(lint): address errcheck and gosec warnings
- mol_bond.go: explicitly ignore ephStore.Close() error
- beads.go: add nosec for .gitignore file permissions (0644 is standard)
- Add wisp detection in mol squash: checks wisp storage if not in main
- squashWispToPermanent: creates digest in permanent, deletes from wisp
- Fix directory naming: .beads-wisps → .beads-wisp (singular, matches doc)
- Add comprehensive tests for wisp squash scenarios
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Standardize terminology for ephemeral molecule storage:
- .beads-ephemeral/ → .beads-wisps/
- --ephemeral flag → --wisp flag
- All Ephemeral* functions → Wisp*
Wisps are the "steam" in Gas Town's engine metaphor - ephemeral
molecules that evaporate after squash.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add .beads-ephemeral/ storage support for ephemeral molecule tracking:
- FindEphemeralDir: locate ephemeral directory (sibling to .beads/)
- FindEphemeralDatabasePath: get DB path, create directory if needed
- NewEphemeralStorage: open ephemeral SQLite database
- EnsureEphemeralGitignore: add .beads-ephemeral/ to .gitignore
- IsEphemeralDatabase: check if a path is ephemeral storage
Part of the wisp storage epic for Gas Town patrol cycles.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add 'deferred' as a valid issue status for issues that are deliberately
put on ice - not blocked by dependencies, just postponed for later.
Changes:
- Add StatusDeferred constant and update IsValid() validation
- Add DeferredIssues to Statistics struct with counting in both SQLite
and memory storage
- Add 'bd defer' command to set status to deferred
- Add 'bd undefer' command to restore status to open
- Update help text across list, search, count, dep, stale, and config
- Update MCP server models and tools to accept deferred status
- Add deferred to blocker status checks (schema, cache, ready, compact)
- Add StatusDeferred to public API exports (beads.go, internal/beads)
- Add snowflake styling for deferred in dep tree and graph views
Semantics:
- deferred vs blocked: deferred is a choice, blocked is forced
- deferred vs closed: deferred will be revisited, closed is done
- Deferred issues excluded from 'bd ready' (already works since
default filter only includes open/in_progress)
- Deferred issues still block dependents (they are not done!)
- Deferred issues visible in 'bd list' and 'bd stale'
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add support for template molecules (is_template field and TypeMolecule type):
- Add IsTemplate field to Issue type with JSON support
- Add TypeMolecule constant to IssueType constants
- Add IsTemplate filter to IssueFilter for querying
- Update all SQL queries to include is_template column
- Add migration 024 for is_template column
- Add FindMoleculesJSONLInDir helper for molecules.jsonl path detection
This enables treating certain issues as read-only templates that can be
instantiated to create work items. The template flag allows separating
template molecules from regular work items in queries and exports.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
In multi-workspace setups like Gas Town, nested .beads directories are
intentional and separate:
- Town level: ~/gt/.beads
- Rig level: ~/gt/gastown/.beads
Previously, FindAllDatabases() walked up the entire directory tree
and warned about "multiple databases detected" even though these are
unrelated beads instances for different scopes.
Now FindAllDatabases() stops as soon as it finds the first (closest)
.beads directory. Parent directories are out of scope.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update default.nix vendorHash to match current go.mod dependencies
- Fix NewSQLiteStorage calls to include required context.Context parameter
- Rename duplicate runCmd to runGitCmd in routing_integration_test.go
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds comprehensive Git worktree support for beads issue tracking:
Core changes:
- New internal/git/gitdir.go package for worktree detection
- GetGitDir() returns proper .git location (main repo, not worktree)
- Updated all hooks to use git.GetGitDir() instead of local helper
- BeadsDir() now prioritizes main repository's .beads directory
Features:
- Hooks auto-install in main repo when run from worktree
- Shared .beads directory across all worktrees
- Config option no-install-hooks to disable auto-install
- New bd worktree subcommand for diagnostics
Documentation:
- New docs/WORKTREES.md with setup instructions
- Updated CHANGELOG.md and AGENT_INSTRUCTIONS.md
Testing:
- Updated tests to use exported git.GetGitDir()
- Added worktree detection tests
Co-authored-by: Claude <noreply@anthropic.com>
Closes: #478
Replaces manual working directory save/restore patterns
with Go's built-in `t.Chdir()` helper across 23 test files.
The manual pattern involved calling `os.Getwd()` to save
the original directory, using `defer os.Chdir(origWd)` for
restoration, and manually handling errors during directory
changes. This boilerplate has been replaced with single
`t.Chdir(path)` calls that handle cleanup automatically.
The `t.Chdir()` method automatically restores the working
directory when the test completes, eliminating the need for
manual defer statements and error handling.
Total:
~75 instances replaced (assuming Claude's math is right)
Co-authored-by: Claude <noreply@anthropic.com>
Adds a lightweight redirect mechanism that allows a stub .beads directory
to point to the actual beads location. This solves the workspace problem
where an AI agent runs in one directory but needs to operate on beads
stored elsewhere.
The redirect file is a simple text file containing a path (relative or
absolute) to the target .beads directory. Comments (lines starting with #)
are supported. Redirect chains are prevented - only one level is followed.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Extends the fix from PR #424 to also validate the BEADS_DIR environment
variable. Previously, only the directory tree search was validated, but
BEADS_DIR could still point to a daemon-only directory.
Changes:
- Add validation to BEADS_DIR path using hasBeadsProjectFiles()
- Add comprehensive test for BEADS_DIR validation
- Test verifies both rejection of daemon-only dirs and acceptance of valid dirs
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
FindBeadsDir() now checks for actual beads project files before returning
a .beads directory. This prevents false positives when ~/.beads/ exists
only for daemon registry (registry.json).
Changes:
- Add hasBeadsProjectFiles() helper that checks for:
- metadata.json or config.yaml (project config)
- *.db files (excluding backups and vc.db)
- *.jsonl files (JSONL-only mode)
- Update FindBeadsDir() to validate directories during tree search
- Add comprehensive tests for project file detection
- Update version_tracking_test.go to create project files
Fixes#420🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-authored-by: Claude <noreply@anthropic.com>
Extract shared JSONL file discovery logic to internal/utils/path.go.
Both autoimport and beads packages now use this shared implementation.
Changes:
- Add utils.FindJSONLInDir with common logic
- Update autoimport.go to use utils.FindJSONLInDir
- Update beads.go to delegate to utils.FindJSONLInDir
- Update server_export_import_auto.go to use utils.FindJSONLInDir
- Move FindJSONLInDir test to utils/path_test.go
- Fix pre-existing duplicate countIssuesInJSONLFile in init.go
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Directory discovery (FindBeadsDir, findDatabaseInTree, FindAllDatabases)
now stops at the git repository root to avoid finding unrelated databases
in parent directories (e.g., ~/.beads).
Added findGitRoot() helper that uses 'git rev-parse --show-toplevel'.
Also updated TestCheckDatabaseVersionJSONLMode to properly simulate
no-db mode by creating config.yaml with 'no-db: true'.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Code review follow-up:
- Fix misleading docstring in FindJSONLInDir (does not return empty)
- Fix same bug in beads.FindJSONLPath (also fell back to matches[0])
- Add comprehensive tests for FindJSONLPath skipping deletions
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Change default JSONL filename from beads.jsonl to issues.jsonl
- Add bd doctor check and fix to auto-migrate legacy beads.jsonl configs
- Update FindJSONLPath to prefer issues.jsonl over beads.jsonl
- Add CheckLegacyJSONLConfig and CheckLegacyJSONLFilename checks
- Add LegacyJSONLConfig fix to rename files and update config
- Update .gitattributes to reference issues.jsonl
- Fix tests to expect new canonical filename
- Add bd-6xd to v0.25.1 release notes
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Use utils.CanonicalizePath for BEADS_DB and findDatabaseInTree results
instead of inline filepath.Abs + filepath.EvalSymlinks (bd-736d)
- Extract findDatabaseInBeadsDir helper function that consolidates the
database search logic used by both FindDatabasePath and findDatabaseInTree,
with optional warnings for ambiguous/legacy states (bd-c362)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add Transaction type alias to both internal/beads and public beads packages.
This allows extensions like VC to use RunInTransaction() with the proper
Transaction interface type for atomic issue creation.
bd-m73k
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
## Summary
When metadata.json gets deleted (git clean, merge conflict, rebase), the
version tracking code auto-recreates it using DefaultConfig() which hardcoded
jsonl_export to 'issues.jsonl'. But many repos (including beads itself) use
'beads.jsonl', causing a mismatch between config and actual JSONL file.
## Changes
1. **bd doctor --fix auto-detection** (cmd/bd/doctor/fix/database_config.go)
- New DatabaseConfig() fix function that auto-detects actual JSONL file
- Prefers beads.jsonl over issues.jsonl (canonical name)
- Skips backup files and merge artifacts
- Wired into doctor.go applyFixes()
2. **Version tracking auto-detection** (cmd/bd/version_tracking.go)
- trackBdVersion() now scans for existing JSONL files before defaulting
- Prevents mismatches when metadata.json gets recreated
- Added findActualJSONLFile() helper function
3. **Canonical default name** (internal/configfile/configfile.go)
- DefaultConfig() changed from issues.jsonl to beads.jsonl
- Aligns with canonical naming convention
4. **FindJSONLPath preference** (internal/beads/beads.go)
- Now prefers beads.jsonl over issues.jsonl when scanning
- Default changed from issues.jsonl to beads.jsonl
5. **Test coverage**
- Added comprehensive tests for DatabaseConfig fix
- Updated configfile tests for new default
- Verified backup file skipping logic
## Testing
- All existing tests pass
- New tests verify auto-fix behavior
- Integration tested with simulated mismatches
Closes: bd-afd
Two Windows-specific test failures:
1. TestNewSQLiteStorage - File locking on temp cleanup
- Windows couldn't delete temp database file because connection was still open
- Added defer store.Close() to properly cleanup the database connection
- Without this, Windows file locking prevents TempDir cleanup
2. TestFindAllDatabases - Unexpected nil slice return
- FindAllDatabases could return nil instead of empty slice when os.Getwd() fails
- Changed from var databases to explicit empty slice initialization
- Ensures function always returns non-nil slice, matching test expectations
Both issues are more pronounced on Windows due to stricter file locking
and different filesystem behavior.
Co-Authored-By: Claude <noreply@anthropic.com>
The canonical beads database name is issues.jsonl. Tens of thousands of users
have issues.jsonl, and beads.jsonl was only used by the Beads project itself
due to git history pollution.
Changes:
- Updated bd doctor to warn about beads.jsonl instead of issues.jsonl
- Changed default config from beads.jsonl to issues.jsonl
- Reversed precedence in checkGitForIssues to prefer issues.jsonl
- Updated git merge driver config to use issues.jsonl
- Updated all tests to expect issues.jsonl as the default
issues.jsonl is now the canonical default; beads.jsonl is legacy
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Updates test and documentation to reflect the intentional change from
issues.jsonl to beads.jsonl (commit 7b865eb from Nov 20, 2025).
Fixes GH #356🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fixes a bug where FindAllDatabases() would return the same database
multiple times when symlinks were present in the directory hierarchy.
The issue occurred because the function walked up the directory tree
without resolving symlinks or checking if a database had already been
discovered. This led to confusing warnings about "multiple databases"
even when only one physical database existed.
Changes:
- Added symlink resolution using filepath.EvalSymlinks()
- Implemented deduplication using a seen map with canonical paths
- Added comprehensive tests for symlink scenarios
This ensures that each unique database is reported exactly once,
regardless of how many symlinks point to it in the directory tree.
Resolves duplicate database warnings when symlinks are present.
Updated all test files to pass context.Background() as the first parameter
to sqlite.New() calls to match the updated function signature.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Identified and tagged obviously-slow integration tests with
`//go:build integration` to exclude them from default test runs.
This is step 1 of fixing test performance. The real fix is in
bd-1rh: refactoring tests to use shared DB setup instead of
creating 279 separate databases.
Tagged files:
- cmd/bd: 8 files (CLI tests, git ops, performance benchmarks)
- internal: 8 files (integration tests, E2E tests)
Issues:
- bd-1rh: Main issue tracking test performance
- bd-c49: Audit all tests and create grouping plan (next step)
- bd-y6d: POC refactor of create_test.go
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Complete implementation of signal-aware context propagation for graceful
cancellation across all commands and storage operations.
Key changes:
1. Signal-aware contexts (bd-rtp):
- Added rootCtx/rootCancel in main.go using signal.NotifyContext()
- Set up in PersistentPreRun, cancelled in PersistentPostRun
- Daemon uses same pattern in runDaemonLoop()
- Handles SIGINT/SIGTERM for graceful shutdown
2. Context propagation (bd-yb8):
- All commands now use rootCtx instead of context.Background()
- sqlite.New() receives context for cancellable operations
- Database operations respect context cancellation
- Storage layer propagates context through all queries
3. Cancellation tests (bd-2o2):
- Added import_cancellation_test.go with comprehensive tests
- Added export cancellation test in export_test.go
- Tests verify database integrity after cancellation
- All cancellation tests passing
Fixes applied during review:
- Fixed rootCtx lifecycle (removed premature defer from PersistentPreRun)
- Fixed test context contamination (reset rootCtx in test cleanup)
- Fixed export tests missing context setup
Impact:
- Pressing Ctrl+C during import/export now cancels gracefully
- No database corruption or hanging transactions
- Clean shutdown of all operations
Tested:
- go build ./cmd/bd ✓
- go test ./cmd/bd -run TestImportCancellation ✓
- go test ./cmd/bd -run TestExportCommand ✓
- Manual Ctrl+C testing verified
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
