bondProtoMol was hardcoding Wisp=true, ignoring --pour flag.
Now passes pour parameter through the call chain so --pour
correctly creates persistent (non-wisp) issues.
The --stealth flag was writing absolute paths to global gitignore, but
git pattern matching does not support absolute paths in gitignore files.
Patterns are interpreted relative to the gitignore location, making
absolute paths like /home/user/project/.beads/ never match.
Fix: Use .git/info/exclude which is the git-recommended location for
user-specific, per-repository ignores. Patterns here are relative to
repo root, so .beads/ works correctly.
Benefits:
- Patterns actually work (fixes the bug)
- Per-repo isolation (stealth in one repo does not affect others)
- No global gitignore pollution
- Follows git best practices for user-local ignores
Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add gate operation constants (OpGateCreate, OpGateList, OpGateShow,
OpGateClose, OpGateWait) to protocol.go
- Add Gate*Args and Gate*Result types to protocol.go
- Add gate handler methods (handleGateCreate, handleGateList,
handleGateShow, handleGateClose, handleGateWait) to server_issues_epics.go
- Register gate handlers in handleRequest switch
- Add gate client methods (GateCreate, GateList, GateShow, GateClose,
GateWait) to client.go
- Update cmd/bd/gate.go to use daemon client when available, falling
back to direct store access
Gate commands now work with the daemon, eliminating the need for
--no-daemon flag.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace direct fmt.Fprintf(os.Stderr, "Error:...") + os.Exit(1) patterns with
FatalError() and FatalErrorWithHint() helpers for consistent error handling.
Files updated:
- compact.go: All 48 os.Exit(1) calls converted
- sync.go: All error patterns converted (kept 1 valid summary exit)
- migrate.go: Partial conversion (4 patterns converted)
This is incremental progress on bd-qioh. Remaining work: ~326 error patterns
across other cmd/bd files.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add parity with bd list for filtering:
- Exact priority match with --priority/-p
- Pattern matching: --title-contains, --desc-contains, --notes-contains
- Empty/null checks: --empty-description, --no-assignee, --no-labels
- Allow empty query when filters are provided (e.g., bd search --no-assignee)
All filters work in both direct and daemon mode via RPC.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements on_close hooks in .beads/config.yaml for automation and
notifications. Hooks receive issue data via environment variables
(BEAD_ID, BEAD_TITLE, BEAD_TYPE, BEAD_PRIORITY, BEAD_CLOSE_REASON)
and run via sh -c.
Changes:
- internal/config: Add HookEntry type and GetCloseHooks()
- internal/hooks: Add RunConfigCloseHooks() for executing config hooks
- cmd/bd: Call RunConfigCloseHooks after successful close
- docs/CONFIG.md: Document hooks configuration with examples
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add --verbose/-v flag to show all checks including passed
- Show summary at top with counts (passed/warnings/errors)
- Default mode collapses passed checks with hint to use --verbose
- Group passed checks by category in verbose mode
- Errors shown first, then warnings, then passed
- Visual separators between sections
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
feat(doctor): add count-based database size check
Adds CheckDatabaseSize (Check 29) that warns when closed issues exceed a configurable threshold (default: 5000). The check is informational only - no auto-fix since pruning is destructive.
Also improves fix guidance for sync-branch hook compatibility and legacy JSONL filename checks.
PR #724 by @rsnodgrass
Jira CLIs use --resolution flag (go-jira, jira-cli). Adding this as a
hidden alias improves agent ergonomics - LLMs have a prior for this flag.
Follows same pattern as --body alias for --description (GitHub CLI).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add async gates - coordination primitives for agents to wait on external events
like CI completion, PR merges, timers, or human approval.
Changes:
- Add 'gate' issue type to types.go with gate-specific fields:
- AwaitType: condition type (gh:run, gh:pr, timer, human, mail)
- AwaitID: condition identifier
- Timeout: max wait duration
- Waiters: mail addresses to notify when gate clears
- Add SQLite migration 027_gate_columns for new fields
- Update all SQLite storage queries to handle gate fields
- Add bd gate commands: create, show, list, close, wait
- All commands support --json output and --no-daemon mode
Closes: bd-2v0f, bd-lz49, bd-u66e
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add _ = prefix for ignored Close/Remove return values
- Fix unused cmd parameter in runMoleculeReady
- Add nolint:misspell for intentional British "cancelled" spelling
- Update comments to use US spelling where not intentional
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds release notes for v0.35.0 including:
- Dynamic molecule bonding with --ref flag
- bd activity command for real-time state feed
- waits-for dependency type for fanout gates
- Parallel step detection for molecules
- bd list --parent flag
- Molecule navigation commands
- Performance indexes and bug fixes
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add emitRichMutation() function for events with metadata
- handleClose now emits MutationStatus with old/new status
- handleUpdate detects status changes and emits MutationStatus
- Add comprehensive tests for rich mutation events
Also:
- Add activity.go test coverage (bd-3jcw):
- Tests for parseDurationString, filterEvents, formatEvent
- Tests for all mutation type displays
- Fix silent error handling in --follow mode (bd-csnr):
- Track consecutive daemon failures
- Show warning after 5 failures (rate-limited to 30s)
- Show reconnection message on recovery
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds 'waits-for' dependency type for dynamic molecule bonding:
- DepWaitsFor blocks an issue until spawner's children are closed
- Two gate types: all-children (wait for all) or any-children (first)
- Updated blocked_cache.go CTE to handle waits-for dependencies
- Added --waits-for and --waits-for-gate flags to bd create command
- Added WaitsForMeta struct for gate metadata storage
- Full test coverage for all gate types and dynamic child scenarios
This enables patrol molecules to wait for dynamically-bonded arms to
complete before proceeding (Christmas Ornament pattern).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add --parallel flag to `bd mol show` that analyzes molecule structure
and identifies which steps can run in parallel. Also add --mol flag to
`bd ready` to list ready steps within a specific molecule.
Features:
- `bd mol show <id> --parallel`: Shows parallel group annotations
- `bd ready --mol <id>`: Lists ready steps with parallel opportunities
- Detects steps at same blocking depth that can parallelize
- Groups steps without mutual blocking deps into parallel groups
- JSON output includes full parallel analysis
Algorithm:
- Build dependency graph from blocking deps (blocks, conditional-blocks)
- Calculate blocking depth (distance from unblocked state)
- Group steps at same depth with no mutual blocking into parallel groups
- Mark steps as ready if open/in_progress with no open blockers
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements the Christmas Ornament pattern for patrol molecules:
- Add CloneOptions struct with ParentID and ChildRef for dynamic bonding
- Add generateBondedID() to create custom IDs like "patrol-x7k.arm-ace"
- Add --ref flag to `bd mol bond` for custom child references
- Variable substitution in childRef (e.g., "arm-{{polecat_name}}")
This enables:
bd mol bond mol-polecat-arm bd-patrol --ref arm-{{name}} --var name=ace
# Creates: bd-patrol.arm-ace, bd-patrol.arm-ace.capture, etc.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Filters issues by parent issue ID using parent-child dependencies.
Example: bd list --parent=bd-xyz --status=open
Changes:
- Add ParentID field to IssueFilter type
- Add --parent flag to list command
- Forward parent filter through RPC
- Implement filtering in SQLite and memory storage
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove dual code paths in the autoflush system. FlushManager is now the
only code path for auto-flush operations.
Changes:
- Remove legacy globals: isDirty, needsFullExport, flushTimer
- Remove flushToJSONL() wrapper function (was backward-compat shim)
- Simplify markDirtyAndScheduleFlush/FullExport to just call FlushManager
- Update tests to use FlushManager or flushToJSONLWithState directly
FlushManager handles all flush state internally in its run() goroutine,
eliminating the need for global state. Sandbox mode and tests that do
not need flushing get a no-op when FlushManager is nil.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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 new Maintenance category to bd doctor with checks for:
- Stale closed issues (older than 30 days)
- Expired tombstones (older than TTL)
- Compaction candidates (info only)
Add fix handlers for cleanup and tombstone pruning via bd doctor --fix.
Add deprecation hints to cleanup, compact, and detect-pollution commands
suggesting users try bd doctor instead.
This consolidation reduces cognitive load - users just need to remember
'bd doctor' for health checks and 'bd doctor --fix' for maintenance.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The test was creating an empty .beads/ directory after simulating rm -rf,
but FindBeadsDir() requires some project files (config.yaml, metadata.json,
or *.db/*.jsonl) to recognize a directory as a valid beads directory.
Updated the test to create a minimal config.yaml like bd init actually does
before auto-import runs. This makes the test more realistic and fixes the
flakiness.
When using bd create -f with a running daemon, the command would fail
with 'database not initialized' because it bypassed the daemon RPC path.
The fix adds createIssuesFromMarkdownViaDaemon which:
- Parses the markdown file (no store access needed)
- Converts issue templates to CreateArgs
- Uses daemon Batch RPC to create all issues efficiently
- Preserves all features: labels, dependencies, hooks, JSON output
Tested with daemon and non-daemon modes, verifying priority 0 is
preserved correctly.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
External dependencies (external:project:capability) are now visible in
the dependency tree output. Previously they were invisible because the
recursive CTE only JOINed against the issues table.
Changes:
- GetDependencyTree now fetches external deps and adds them as synthetic
leaf nodes with resolution status (satisfied/blocked)
- formatTreeNode displays external deps with special formatting
- Added helper parseExternalRefParts for parsing external refs
Test coverage added for:
- External deps appearing in dependency tree
- Cycle detection ignoring external refs
- CheckExternalDep when target has no .beads directory
- Various invalid external ref format variations
Closes: bd-vks2, bd-mv6h, bd-d9mu
- Remove TestFindJSONLPathDefault from .test-skip (now passes)
- Add explanatory comments to 24 ignored error locations in cmd/bd:
- Cobra flag methods (MarkHidden, MarkRequired, MarkDeprecated)
- Best-effort cleanup/close operations
- Process signaling operations
Part of code health review epic bd-tggf.
🤖 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).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add bd mol current: Shows current position in molecule workflow
- Displays all steps with status indicators (done/current/ready/blocked/pending)
- Infers molecule from in_progress issues when no ID given
- Supports --for flag to check another agent's molecules
Add bd close --continue: Auto-advances to next molecule step
- After closing, finds parent molecule and next ready step
- Auto-claims next step by default (--no-auto to skip)
- Shows molecule completion message when all steps closed
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The daemon.log was showing duplicate log messages:
- 'File change detected' appeared 4x for a single file change
- 'Git ref change detected' appeared 2x for a single ref update
Root cause:
- fsnotify generates multiple events (Write, Create, Chmod) for single file ops
- Both parent directory and file watchers can trigger for the same change
- Multiple git ref files may be updated simultaneously
Fix:
- Add log deduplication with 500ms window (matching debouncer window)
- Track last log time for file changes and git ref changes separately
- Only log if enough time has passed since last log of same type
- Still trigger debouncer for every event (functionality unchanged)
This reduces log noise while maintaining full functionality.
The error message 'path exists but is not a valid git worktree' was appearing
in daemon.log when the daemon attempted to use an existing worktree that was
in the git worktree list but had other issues (broken sparse checkout, etc.).
Root cause:
- CreateBeadsWorktree only checked isValidWorktree (is it in git worktree list)
- CheckWorktreeHealth was called separately and checked additional things
- If the worktree passed isValidWorktree but failed health check, an error
was logged and repair was attempted
Fix:
- CreateBeadsWorktree now performs a full health check when it finds an
existing worktree that's in the git worktree list
- If the health check fails, it automatically removes and recreates the
worktree
- Removed redundant CheckWorktreeHealth calls in daemon_sync_branch.go and
syncbranch/worktree.go since CreateBeadsWorktree now handles this internally
This eliminates the confusing error message and ensures worktrees are always
in a healthy state after CreateBeadsWorktree returns successfully.
Add --auto-pull flag to control whether the daemon periodically pulls from
remote to check for updates from other clones.
Configuration precedence:
1. --auto-pull CLI flag (highest)
2. BEADS_AUTO_PULL environment variable
3. daemon.auto_pull in database config
4. Default: true when sync.branch is configured
When auto_pull is enabled, the daemon creates a remoteSyncTicker that
periodically calls doAutoImport() to pull remote changes. When disabled,
users must manually run 'git pull' to sync remote changes.
Changes:
- cmd/bd/daemon.go: Add --auto-pull flag and config reading logic
- cmd/bd/daemon_event_loop.go: Gate remoteSyncTicker on autoPull parameter
- cmd/bd/daemon_lifecycle.go: Add auto-pull to status output and spawn args
- internal/rpc/protocol.go: Add AutoPull field to StatusResponse
- internal/rpc/server_core.go: Add autoPull to Server struct and SetConfig
- internal/rpc/server_routing_validation_diagnostics.go: Include in status
- Tests updated to pass autoPull parameter
Closes #TBD
Modernize sorting code to use Go 1.21+ slices package:
- Replace sort.Slice with slices.SortFunc across 16 files
- Use cmp.Compare for orderable types (strings, ints)
- Use time.Time.Compare for time comparisons
- Use cmp.Or for multi-field sorting
- Use slices.SortStableFunc where stability matters
Benefits: cleaner 3-way comparison, slightly better performance,
modern idiomatic Go.
Part of GH#692 refactoring epic.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(daemon): include tombstones in exportToJSONLWithStore for sync propagation
The daemon's exportToJSONLWithStore() function was using an empty
IssueFilter which defaults to IncludeTombstones: false. This caused
deleted issues (tombstones) to be excluded from JSONL exports during
daemon sync cycles.
Bug scenario:
1. User runs `bd delete <issue>` with daemon active
2. Database correctly marks issue as tombstone
3. Main .beads/issues.jsonl correctly shows status:"tombstone"
4. But sync branch worktree JSONL still showed status:"open"
5. Other clones would not see the deletion
The fix adds IncludeTombstones: true to match the behavior of
exportToJSONL() in sync.go, ensuring tombstones propagate to other
clones and prevent resurrection of deleted issues.
Adds regression test TestExportToJSONLWithStore_IncludesTombstones
that verifies tombstones are included in daemon JSONL exports.
* fix: resolve all golangci-lint errors (cherry-pick from fix/linting-errors)
Cherry-picked linting fixes to ensure CI passes.
---------
Co-authored-by: Charles P. Cross <cpdata@users.noreply.github.com>
* fix(daemon): handle diverged sync branch with fetch-rebase-retry on push
When pushing to the sync branch, if the remote has newer commits that
the local worktree doesn't have, the push would fail with "fetch first"
error and the daemon would log the failure without recovery.
Bug scenario:
1. Clone A pushes commit X to sync branch
2. Clone B has local commit Y (not based on X)
3. Clone B's push fails with "fetch first" error
4. Without this fix: daemon logs failure and stops
5. With this fix: daemon fetches, rebases Y on X, and retries push
This fix adds fetch-rebase-retry logic to gitPushFromWorktree():
1. Detect push rejection due to remote having newer commits
2. Fetch the latest remote sync branch
3. Rebase local commits on top of remote
4. Retry the push
If rebase fails (e.g., due to conflicts), the rebase is aborted and
an error is returned with helpful context.
This allows multiple clones to push to the same sync branch without
manual intervention, as long as the changes don't conflict.
Adds integration test TestGitPushFromWorktree_FetchRebaseRetry that
verifies the fetch-rebase-retry behavior with diverged branches.
* fix: resolve all golangci-lint errors (cherry-pick from fix/linting-errors)
Cherry-picked linting fixes to ensure CI passes.
---------
Co-authored-by: Charles P. Cross <cpdata@users.noreply.github.com>
* fix(daemon): add periodic remote sync to event-driven mode
The event-driven daemon mode only triggered imports when the local JSONL
file changed (via file watcher) or when the fallback ticker fired (only
if watcher failed). This meant the daemon wouldn't see updates pushed
by other clones until something triggered a local file change.
Bug scenario:
1. Clone A creates an issue and daemon pushes to sync branch
2. Clone B's daemon only watched local file changes
3. Clone B would not see the new issue until something triggered local change
4. With this fix: Clone B's daemon periodically calls doAutoImport
This fix adds a 30-second periodic remote sync ticker that calls
doAutoImport(), which includes syncBranchPull() to fetch and import
updates from the remote sync branch.
This is essential for multi-clone workflows where:
- Clone A creates an issue and daemon pushes to sync branch
- Clone B's daemon needs to periodically pull to see the new issue
- Without periodic sync, Clone B would only see updates if its local
JSONL file happened to change
The 30-second interval balances responsiveness with network overhead.
Adds integration test TestEventDrivenLoop_PeriodicRemoteSync that
verifies the event-driven loop starts with periodic sync support.
* feat(daemon): add configurable interval for periodic remote sync
- Add BEADS_REMOTE_SYNC_INTERVAL environment variable to configure
the interval for periodic remote sync (default: 30s)
- Add getRemoteSyncInterval() function to parse the env var
- Minimum interval is 5s to prevent excessive load
- Setting to 0 disables periodic sync (not recommended)
- Add comprehensive integration tests for the configuration
Valid duration formats:
- "30s" (30 seconds)
- "1m" (1 minute)
- "5m" (5 minutes)
Tests added:
- TestEventDrivenLoop_HasRemoteSyncTicker
- TestGetRemoteSyncInterval_Default
- TestGetRemoteSyncInterval_CustomValue
- TestGetRemoteSyncInterval_MinimumEnforced
- TestGetRemoteSyncInterval_InvalidValue
- TestGetRemoteSyncInterval_Zero
- TestSyncBranchPull_FetchesRemoteUpdates
* fix: resolve all golangci-lint errors (cherry-pick from fix/linting-errors)
Cherry-picked linting fixes to ensure CI passes.
* feat(daemon): add config.yaml support for remote-sync-interval
- Add remote-sync-interval to .beads/config.yaml as alternative to
BEADS_REMOTE_SYNC_INTERVAL environment variable
- Environment variable takes precedence over config.yaml (follows
existing pattern for flush-debounce)
- Add config binding in internal/config/config.go
- Update getRemoteSyncInterval() to use config.GetDuration()
- Add doctor validation for remote-sync-interval in config.yaml
Configuration sources (in order of precedence):
1. BEADS_REMOTE_SYNC_INTERVAL environment variable
2. remote-sync-interval in .beads/config.yaml
3. DefaultRemoteSyncInterval (30s)
Example config.yaml:
remote-sync-interval: "1m"
---------
Co-authored-by: Charles P. Cross <cpdata@users.noreply.github.com>
The interactions.jsonl file is an append-only audit log that should be
tracked in git (synced with bd sync), but it was missing from the
negation patterns in .beads/.gitignore.
This adds !interactions.jsonl alongside !issues.jsonl and !metadata.json
for consistency and clarity that this file should be committed.
Co-authored-by: Christian Catalan <crcatala@gmail.com>
