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.
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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.
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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.
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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
Agent identity fields on Issue struct:
- HookBead: reference to current work (0..1 cardinality)
- RoleBead: reference to role definition bead
- AgentState: self-reported state (idle|spawning|running|working|stuck|done|stopped|dead)
- LastActivity: timestamp for heartbeat/timeout detection
- RoleType: agent type (polecat|crew|witness|refinery|mayor|deacon)
- Rig: rig name (empty for town-level agents)
Also adds:
- AgentState type with IsValid() method
- Validation for agent state in Issue.Validate()
- Agent fields included in content hash
This enables the agent-as-bead architecture where agents are tracked
as first-class beads with self-reported state.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add TypeAgent and TypeRole to IssueType enum in types.go
- Update IsValid() to include new types
- Add UI styles with distinct colors (cyan for agent, green for role)
- Add RenderType cases for consistent display
This enables creating agent beads (identity) and role beads (behavior
definitions) as part of the agent-as-bead architecture.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When running the release workflow, users often stage CHANGELOG.md and info.go
changes before running bump-version.sh. Previously, the script would error
on uncommitted changes with --commit.
Now:
- --allow-staged permits pre-staged CHANGELOG.md and cmd/bd/info.go
- Script detects these as expected release files and includes them in commit
- Provides helpful error message if other files are staged
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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>
Documents the .beads/redirect feature for sharing databases across
multiple clones, and the new `bd where` command for debugging.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replaced 3 separate caches (isWorktree, mainRepoRoot, repoRoot) with a
single gitContext struct populated by one git call. This reduces git
subprocess calls from up to 4 down to 1 and simplifies ResetCaches().
🤖 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>
Changed from "preserved for reference" to "suppresses resurrections"
which better reflects the actual purpose.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Document all 7 issue statuses:
- open, in_progress, blocked, deferred, closed, tombstone, pinned
The pinned status was previously undocumented but is used by Gas Town
for hook management and persistent work items.
🤖 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>
docs: fix README and PLUGIN.md documentation issues
- Clarify that bd ready shows issues ready to work on (#512)
- Update git hooks install command from deprecated script to bd hooks install (#513)
- Fix Claude Code plugin local install: use ./beads not ., clarify shell vs CC commands (#514)
Fixes#512, #513, #514
Update docs to reflect CLI command restructuring:
- migrate-tombstones → migrate tombstones
- bd quickstart is now hidden, point to docs/QUICKSTART.md
- Add CLI consolidation section to CHANGELOG.md
- Remove quickstart from command tables
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.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>
