When the database has orphaned dependencies or labels, the migration
invariant check fails and prevents the database from opening. This
creates a chicken-and-egg problem where bd doctor --fix cannot run.
The new bd repair command:
- Opens SQLite directly, bypassing invariant checks
- Deletes orphaned dependencies (issue_id or depends_on_id not in issues)
- Deletes orphaned labels (issue_id not in issues)
- Runs WAL checkpoint to persist changes
- Supports --dry-run to preview what would be cleaned
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Eliminate code duplication between importFromGit and importFromLocalJSONL
by extracting the common JSONL parsing and import logic.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds --from-jsonl flag that imports from the current working tree's
.beads/issues.jsonl file instead of scanning git history. This prevents
deleted issues from being resurrected during re-initialization.
Use case: After running bd compact --purge-tombstones and committing
the cleaned JSONL, a subsequent bd init would previously re-import
all historical issues from git, defeating the cleanup.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Unlike --prune which removes tombstones by age, --purge-tombstones removes
tombstones that have no open issues depending on them, regardless of age.
Also cleans stale deps from closed issues to tombstones.
Usage:
bd compact --purge-tombstones --dry-run # Preview what would be purged
bd compact --purge-tombstones # Actually purge
Note: Use --no-daemon to prevent daemon from re-exporting after cleanup.
- Add findExistingSwarm helper and duplicate swarm check with --force flag
- Add bd swarm list command for discovering swarm molecules with progress stats
- Fix empty coordinator display in swarm create output
- Allow swarm status to accept swarm molecule ID (follows relates-to link)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add EpicChildren struct and getEpicChildren() helper function
- Define SwarmStore interface for dependency injection
- Refactor analyzeEpicForSwarm to use shared helper
- Refactor getSwarmStatus to use shared helper
- Eliminates duplicate code for fetching epic children and building
dependency maps across both functions
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Displays each issue on a single line with format:
<id> [<status>] P<priority> <type>: <title>
Example:
bd show bd-nlzv --short
bd-nlzv [open] P2 feature: bd show --short flag for compact output
Useful for quick status checks of multiple issues. (bd-nlzv)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Build status map upfront from childIssues instead of calling
GetIssue for each dependency. Reduces queries from O(issues * deps)
to O(issues).
Also removes unused GetIssue from the interface.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements `bd swarm create <epic-id>` to create a swarm molecule
that orchestrates parallel work on an epic.
Features:
- Creates molecule with mol_type=swarm for discovery
- Links to epic via relates-to dependency
- Validates epic structure before creation
- Auto-wraps single issues in an epic when needed
- Optional --coordinator flag to specify coordinator agent
- Supports JSON output for machine consumption
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Show current swarm status computed from beads:
- Completed: closed issues with timestamps
- Active: in_progress issues with assignees
- Ready: open issues with all deps satisfied
- Blocked: open issues waiting on deps
- Progress percentage
State is COMPUTED from beads, not stored separately.
Supports --json for programmatic use.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add mol_type field to beads for swarm coordination:
- Values: 'swarm' (multi-polecat), 'patrol' (recurring ops), 'work' (default)
- Nullable, defaults to empty string (treated as 'work')
Changes:
- Add mol_type column to SQLite schema and migration 031
- Add MolType type with IsValid() validation in types.go
- Update insertIssue/GetIssue to handle mol_type
- Add --mol-type flag to create command
- Add mol_type filtering to list and ready commands
- Update RPC protocol for daemon mode support
- Update test schema in migrations_test.go
🤝 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds validation of epic structure for swarm execution:
- Computes ready fronts (waves of parallel work)
- Detects structural issues (cycles, orphans, missing deps)
- Reports estimated worker-sessions and max parallelism
- Warns about potential dependency inversions
- Returns exit code for CI integration
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extract init.go into multiple focused files:
- init_git_hooks.go: Git hooks installation and merge driver setup (~480 lines)
- init_stealth.go: Stealth mode and fork/exclude configuration (~310 lines)
- init_agent.go: AGENTS.md and Claude settings setup (~170 lines)
- init_templates.go: config.yaml and README.md templates (~180 lines)
This reduces init.go from 1928 lines to 705 lines, meeting the <800 line target.
Each extracted file handles a cohesive set of functionality.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Created 7 new beads to track TODOs that were previously inline comments:
- bd-7l27: Integrate migration detection into bd doctor (5 files)
- bd-6x6g: Add multi-repo target repo switching in bd create
- bd-ag35: Add daemon RPC endpoints for config and stale check
- bd-2dwo: Remove deprecated daemon logger function
- bd-0qx5: Implement Jira issue timestamp comparison for sync
- bd-7zka: Implement formula features (repeat, for_each, branch, gate, split)
- bd-h048: Refactor sync_test to use direct import logic
Updated 16 TODO comments to include bead ID references for tracking.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extracted 8 helper functions from the monolithic flushToJSONLWithState:
- recordFlushFailure/recordFlushSuccess: Failure tracking and counter management
- readExistingJSONL: Parse existing JSONL file for incremental merging
- fetchAndMergeIssues: Fetch dirty issues from DB and merge into map
- filterWisps: Remove ephemeral (wisp) issues from export
- filterByMultiRepoPrefix: Multi-repo prefix filtering for non-primary repos
- updateFlushExportMetadata: Store hashes and timestamps after export
- getIssuesToExport: Determine full vs incremental export issue list
Main function now reads as a clear pipeline:
1. Validate integrity -> 2. Get issues -> 3. Read existing JSONL
4. Merge from DB -> 5. Filter wisps -> 6. Filter by prefix
7. Write atomically -> 8. Update metadata
Benefits:
- Each helper is single-responsibility and testable
- Main function reduced from ~280 to ~94 lines
- Logic is clearly separated and documented
- Easier to understand and maintain
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replaced three near-identical functions with a single unified collectSteps()
that uses a callback strategy for label handling:
- Removed collectStepsRecursive() (DB version)
- Removed collectStepsToSubgraph() (in-memory version)
- Removed collectStepIDMappings() (now handled by unified function)
The new collectSteps() function:
- Takes optional labelHandler callback for DB path (extracts labels separately)
- Takes optional issueMap for in-memory path
- Always builds idMapping for dependency resolution
- Eliminates ~60 lines of duplicated code
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extracted duplicated switch statement for mapping step type strings to
types.IssueType into a single helper function. This removes code
duplication between collectStepsToSubgraph() and collectStepsRecursive().
The new stepTypeToIssueType() function:
- Converts 'task', 'bug', 'feature', 'epic', 'chore' to types
- Returns types.TypeTask for empty or unrecognized types
- Used by both functions with children-override-to-epic logic preserved
- migrate-* commands → subcommands of `bd migrate`
- relate/unrelate → subcommands of `bd dep`
- daemons subcommands → available under `bd daemon`
- comment alias → hidden with deprecation warning
All old commands still work with deprecation warnings for backwards
compatibility. Reduces visible top-level commands from ~73 to 66.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
New commands and features:
- bd worktree for parallel development
- bd slot commands for agent bead slot management
- bd agent state for ZFC-compliant state reporting
- bd doctor --deep for full graph integrity validation
- Agent bead support (type=agent, type=role, migration 030)
- Computed .parent field in JSON output
- Auto-bypass daemon for wisp operations
- Pour warning for vapor-phase formulas
Performance:
- O(2^n) → O(V+E) cycle detection (GH#775)
Fixes:
- Import hash mismatch warnings
- Test updates for version tracking thresholds
- Migration test updated for new agent schema fields
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Now shows:
- Truncated title (40 chars max) after issue ID
- Assignee with @ prefix when present
- Format: 'bd-xxx completed · Title here... @assignee'
Also changed 'in_progress' to 'started' for cleaner output.
🤖 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>
Wisp operations (mol wisp *, mol burn, mol squash) and commands operating on
ephemeral issue IDs (bd-eph-*, gt-eph-*, eph-*) now auto-bypass the daemon.
Since wisps are ephemeral (Ephemeral=true) and never exported to JSONL,
the daemon cannot help with them anyway. This eliminates the need to manually
add --no-daemon for every wisp operation.
Changes:
- Add isWispOperation() helper to detect wisp commands and ephemeral IDs
- Add FallbackWispOperation constant for daemon status tracking
- Insert wisp detection in PersistentPreRunE daemon connection logic
- Update error messages in wisp.go, mol_burn.go, mol_squash.go
- Add comprehensive unit tests for isWispOperation()
Add agent commands for self-reporting state:
- bd agent state <agent> <state>: Update agent state and last_activity
- bd agent heartbeat <agent>: Update last_activity timestamp only
- bd agent show <agent>: Display agent bead details
States: idle, spawning, running, working, stuck, done, stopped, dead
Also adds AgentState and LastActivity fields to UpdateArgs in RPC protocol.
🤖 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.
- Add CheckReadonly calls to create/remove commands
- Add cleanup on partial failure (remove worktree if beads setup fails)
- Prevent removing main repository as worktree
- Fix gitignore entry to use relative path from repo root
- Remove misleading stash check (stashes are repo-wide, not per-worktree)
- Populate Name field in WorktreeInfo struct
- Add #nosec comments for exec.Command and file reads
🤖 Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds user-facing worktree management commands:
- bd worktree create <name> - creates worktree with beads redirect
- bd worktree list - shows all worktrees and their beads state
- bd worktree remove <name> - removes worktree with safety checks
- bd worktree info - shows current worktree info
The create command automatically sets up .beads/redirect to point to
the main repos .beads directory, ensuring all worktrees share
the same issue database. This enables parallel development with
multiple agents or features.
🤖 Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add slot management commands:
- bd slot set <agent> <slot> <bead> - set slot (error if occupied)
- bd slot clear <agent> <slot> - clear slot
- bd slot show <agent> - show all slots
These enforce cardinality constraints for agent bead slots.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update ParseIssueType to use canonical types.IsValid() (includes agent, role, gate, message)
- Add ValidateAgentID function to validate gt-<role>[-<rig>[-<name>]] pattern
- Wire up validation in create.go when --type=agent with explicit ID
- Update --type flag help text to include agent and role types
- Add comprehensive test coverage for agent ID validation
The import command was only updating jsonl_content_hash, not jsonl_file_hash.
After sync imports JSONL but skips re-export (because DB matches JSONL),
the jsonl_file_hash remained stale, causing validateJSONLIntegrity() to
emit spurious "JSONL file hash mismatch" warnings on subsequent operations.
Now import also calls SetJSONLFileHash with the same hash value, keeping
both hashes in sync and eliminating the false warnings.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The limit wasn't enforced by init/create, so users could create issues
with longer prefixes but couldn't use rename-prefix to consolidate them.
Since the DB handles longer prefixes fine, just remove the limit.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Allows reparenting issues to a different epic/parent:
bd update bd-xyz --parent=bd-epic
Implementation:
- Add Parent field to UpdateArgs in protocol.go
- Handle reparenting in RPC handler (server_issues_epics.go)
- Add --parent flag to updateCmd with both daemon and direct mode support
- Remove old parent-child dependency before adding new one
- Pass empty string to remove parent entirely
🤖 Generated with [Claude Code](https://claude.com/claude-code)
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)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds a new command that shows the active .beads directory path,
including redirect information for debugging. Supports --json output.
Example:
bd where
→ /Users/stevey/gt/beads/mayor/rig/.beads
(via redirect from /Users/stevey/gt/beads/crew/emma/.beads)
prefix: bd
database: /Users/stevey/gt/beads/mayor/rig/.beads/beads.db
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
Move cleanup, compact, and reset commands under `bd admin` namespace.
Creates hidden aliases for backwards compatibility that show deprecation
notice when used.
- Create cmd/bd/admin.go with parent command
- Create cmd/bd/admin_aliases.go for hidden backwards-compat aliases
- Update cleanup.go, compact.go, reset.go to remove rootCmd.AddCommand
- Update all documentation to use `bd admin <cmd>` syntax
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.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>
