Orphan detection was reporting tombstoned issues (already deleted) as
orphans, causing repeated warnings during sync. Filter out status='tombstone'
from the orphan query.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove the entire YAML-based workflow system in preparation for
redesigning templates as native Beads.
Removed:
- cmd/bd/templates/workflows/*.yaml
- cmd/bd/workflow.go
- internal/types/workflow.go (WorkflowTemplate types)
The new design will use regular Beads with a template label,
and a clone-with-substitution operation for instantiation.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds `bd workflow` command group that creates epics with dependent child tasks
from YAML templates. This enables structured multi-step workflows like version
bumps where agents can work through tasks with verification and dependencies.
Commands:
- `bd workflow list` - List available workflow templates
- `bd workflow show <name>` - Show template details and task graph
- `bd workflow create <name> --var key=value` - Instantiate workflow
- `bd workflow status <epic-id>` - Show workflow progress
- `bd workflow verify <task-id>` - Run verification command
Features:
- Variable substitution with {{var}} syntax
- Built-in variables: {{today}}, {{user}}
- Preflight checks before workflow creation
- Hierarchical task IDs under epic (bd-xxx.1, bd-xxx.2)
- Dependency graph between tasks
- Verification commands embedded in task descriptions
Includes built-in `version-bump` template with 21 tasks covering:
- All 10+ version files
- check-versions.sh verification
- Git commit, tag, push
- CI monitoring (goreleaser, npm, pypi, homebrew)
- Local machine upgrades
- Final verification
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove ClearDirtyIssues() which had a race condition that could lose
dirty issues if export failed partway through. All callers now use
ClearDirtyIssuesByID() which only clears specific exported issues.
- Remove from Storage interface
- Remove from SQLite and Memory implementations
- Update 6 test call sites to use ClearDirtyIssuesByID()
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Three changes to fix deleted issues resurrecting during bd sync:
1. daemon handleDelete now uses CreateTombstone instead of DeleteIssue
- internal/rpc/server_issues_epics.go
2. sync.go exportToJSONL now includes IncludeTombstones:true
- cmd/bd/sync.go
3. server_export_import_auto.go handleExport and auto-export now include
tombstones in SearchIssues filter
- internal/rpc/server_export_import_auto.go
Also adds README.md documentation for sync.branch mode (bd-dsdh):
- Explains "always dirty" working tree behavior
- Shell alias tip: gs='git status -- ":!.beads/"'
- When to use bd sync --merge
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Move runHook into build-tagged implementations (unix/windows) to keep unix syscalls off Windows builds.
- In unix implementation, guard nil Process, return wrapped kill errors except ESRCH, and document linkage to TestRunSync_KillsDescendants.
- On Windows, best-effort kill on timeout retains prior behavior.
- In tests, move testing.Short earlier and keep descendant-kill coverage on Linux.
Root cause: The merge driver matched issues by IssueKey (ID+CreatedAt+CreatedBy).
When timestamp precision differed (e.g., with/without nanoseconds), the same
issue was treated as two different issues, causing both tombstone and closed
versions to appear in the merge result.
Fix: Added ID-based fallback matching in merge3WayWithTTL. When key-based
matching fails but the same ID exists in the other side, use that for merging.
Also track processed IDs to prevent duplicates.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- IsExpired(): Negative TTL means immediately expired (for --hard mode)
- IsExpired(): ClockSkewGrace only added for TTLs > 1 hour
- bd cleanup --hard: Use negative TTL to prune freshly created tombstones
- bd delete --hard: New flag to immediately prune tombstones from JSONL
- Import: Add early tombstone check before all phases to prevent resurrection
The early tombstone check prevents ghost issues from being created when
tombstones exist in the DB. However, a deeper git merge issue (bd-ncwo)
can still cause resurrection when remote's status:closed wins the merge.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Ensure RunSync kills the hook process group on timeout so descendant processes (e.g. scripts that ) cannot keep the caller blocked. Add explanatory comment in and a Linux-only unit test in . Trim pid parsing newline in the test. All tests pass locally.
- Add bd cleanup --ephemeral flag for transient message cleanup (bd-kwro.9)
- Add Ephemeral filter to IssueFilter type
- Add ephemeral filtering to SQLite storage queries
Tests (bd-kwro.10):
- Add internal/hooks/hooks_test.go for hook system
- Add cmd/bd/mail_test.go for mail commands
- Add internal/storage/sqlite/graph_links_test.go for graph links
Documentation (bd-kwro.11):
- Add docs/messaging.md for full messaging reference
- Add docs/graph-links.md for graph link types
- Update AGENTS.md with inter-agent messaging section
- Update CHANGELOG.md with all bd-kwro features
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- bd mail reply: reply to messages with thread linking via replies_to
- bd show --thread: display full conversation threads
- bd relate/unrelate: bidirectional relates_to links for knowledge graph
- bd duplicate --of: mark issues as duplicates with auto-close
- bd supersede --with: mark issues as superseded with auto-close
- Hooks system: on_create, on_update, on_close, on_message in .beads/hooks/
- RPC protocol: added Sender, Ephemeral, RepliesTo fields to CreateArgs/UpdateArgs
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add `bd mail send/inbox/read/ack` commands for inter-agent messaging
- Implement GetIdentity() with priority chain: flag > BEADS_IDENTITY env > config.yaml > git user.name > hostname
- Messages are stored as issues with type=message for git-native communication
- Support both daemon and direct mode for all mail operations
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update version in version.go, default.nix, hook templates
- Add CHANGELOG.md entry for v0.30.2
- Add v0.30.1 and v0.30.2 to versionChanges in info.go
- Remove stale internal/deletions import from integration test
(fixes CI failure from bd-fom refactor)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
MemoryStorage.GetStatistics() was returning 0 for blocked_issues and
ready_issues in no-db mode. The SQLite implementation correctly
calculated these based on dependencies, but the memory store only
counted explicit status values.
Changes:
- Reuse getOpenBlockers() helper for dependency-based blocked count
- Calculate ready_issues as open issues with no open blockers
- Add tombstone handling (exclude from TotalIssues)
- Add AverageLeadTime calculation for parity with SQLite
- Add EpicsEligibleForClosure calculation
- Add tests for blocked/ready counts, epics, and tombstones
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Fixes Windows build by adding platform-specific inode handling via build tags. Also fixes gosec lint warnings in migrate_tombstones.go.
Thanks @deblasis!
Refine ExtractIssuePrefix to better distinguish hash IDs from English
words in multi-part issue IDs. Hash suffixes now require digits or be
exactly 3 chars, preventing "test", "gate", "part" from being treated
as hashes. This fixes prefix extraction for IDs like "vc-baseline-test".
Also updates git hooks to use -q flag and adds AGENTS.md documentation.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add TypeMessage issue type for inter-agent communication
- Add 6 new Issue fields: Sender, Ephemeral, RepliesTo, RelatesTo,
DuplicateOf, SupersededBy
- Add 4 new dependency types: replies-to, relates-to, duplicates, supersedes
- Create migration 019_messaging_fields with indexes
- Update all CRUD operations across storage layer
- Fix reset_test.go to use correct function names
- Fix redundant newline lint error in sync.go
Closes: bd-kwro.1
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Two swarm merge bugs fixed:
1. StatusResponse in protocol.go lost daemon config fields (AutoCommit, AutoPush,
LocalMode, SyncInterval, DaemonMode) during merge 60ae6586. These were added in
4e87ae18 but lost when merging bd-zbyb-gusher which had an outdated protocol.go.
2. Duplicate --type flag definition on updateCmd in show.go causing panic on startup.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
The ExtractIssuePrefix function was falling back to first-hyphen
extraction when the suffix didn't look like a hash (e.g., 4+ char
words without digits). This broke prefixes like 'hacker-news' where
an issue ID 'hacker-news-test' would incorrectly extract 'hacker'.
Fix: Always use last-hyphen extraction for alphanumeric suffixes.
Only fall back to first-hyphen for non-alphanumeric suffixes.
Examples:
- 'hacker-news-test' -> 'hacker-news' (was: 'hacker')
- 'me-py-toolkit-abc' -> 'me-py-toolkit' (was: 'me')
- 'vc-baseline-hello' -> 'vc-baseline' (was: 'vc')
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When bd sync pushes from the sync-branch worktree, the pre-push hook
would detect uncommitted JSONL changes and suggest running bd sync -
which is circular since that's what the user is already doing.
Fix: Set BD_SYNC_IN_PROGRESS=1 environment variable when pushing from
worktree, and update pre-push hook to skip checks when this var is set.
Updated files:
- internal/syncbranch/worktree.go: Set env var on push command
- cmd/bd/templates/hooks/pre-push: Check for env var and exit early
- examples/git-hooks/pre-push: Same check
- .beads-hooks/pre-push: Same check
Allow changing an issue type (bug, feature, task, epic, chore) via the
bd update command. The storage layer already supported issue_type in
allowedUpdateFields, this just exposes it through the CLI.
Changes:
- Add --type/-t flag to updateCmd in show.go
- Add IssueType field to UpdateArgs in protocol.go
- Handle issue_type in updatesFromArgs in server_issues_epics.go
- Add validation using ParseIssueType before update
Example usage:
bd update ab-xyz --type epic
Fixes: #522
Claude was using word-based priorities like "medium" instead of numeric
values (0-4 or P0-P4), causing bd create commands to fail in a loop.
Changes:
- Update bd prime output to clearly document priority format with example
- Add explicit note: NOT "high"/"medium"/"low"
- Improve error message to mention that words are not valid
Closes#517🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When sync branch diverges significantly from remote, provide clear
recovery options instead of a confusing rebase conflict error.
- Add CheckDivergence() to detect and report sync branch divergence
- Add ResetToRemote() to reset local sync branch to remote state
- Add --reset-remote and --force-push flags for recovery
- Improve error message when rebase fails to include recovery steps
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Only treat issue IDs as hierarchical (parent.child) when the dot appears
AFTER the first hyphen. This prevents false positives when the project
directory name contains a dot (e.g., "my.project-abc123" was incorrectly
being treated as having parent "my").
Fixes GH#508
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- bd-6pni: Auto-filter tombstoned issues with mismatched prefixes during
import instead of failing. Tombstones from contributor PRs with different
test prefixes are pollution and safe to ignore.
- bd-ffr9: Stop recreating deletions.jsonl after tombstone migration.
Added IsTombstoneMigrationComplete() check to all code paths that write
to the legacy deletions manifest.
- bd-admx: Fix perpetual "JSONL file hash mismatch" warning. Now clears
both export_hashes AND jsonl_file_hash when mismatch detected, so the
warning doesn't repeat.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- bd-8v5o: When doctor --fix hydrates issues from git history, also
remove them from the deletions manifest to prevent perpetual skip
warnings during sync
- bd-wsqt: Remove verbose per-issue "Skipping bd-xxx" messages during
sync. Caller already shows summary of skipped issues.
Added RemoveDeletions() function to deletions package with tests.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When importing issues, if an incoming issue has the same content hash as an
existing issue but a DIFFERENT prefix, this should not be treated as a rename.
Cross-prefix content matches occur when importing issues from other projects
that happen to have identical content.
Previously, the importer would call handleRename which tries to create an issue
with the incoming prefix, failing prefix validation ("does not match configured
prefix" error).
The fix checks if prefixes differ before calling handleRename:
- Same prefix, different ID suffix → true rename, call handleRename
- Different prefix → skip incoming issue, keep existing unchanged
Added test: TestImportCrossPrefixContentMatch reproduces the bug scenario
where alpha-* issues exist but beta-* issues are imported with same content.
Document the intent and nuances of recent fixes:
internal/importer/utils.go:
- RenameImportedIssuePrefixes: explain the three ID formats (sequential,
hash-based, hierarchical) and how prefix renaming preserves identity
- isValidIDSuffix: document why dots are allowed (hierarchical parent-child
relationships) and what characters are rejected
cmd/bd/deletion_tracking.go:
- isIssueNotFoundError: explain why "not found" is success during merge
(issue may be tombstoned, never existed locally, or manually deleted)
- Deletion loop: document what "accepted deletions" means and why we
tolerate missing issues during the pruning phase
The isNumeric function was rejecting valid hierarchical hash IDs like
'6we.2' that contain dots for parent.child notation. This caused
`bd import --rename-on-import` to fail with "non-numeric suffix" errors.
Changes:
- Rename isNumeric to isValidIDSuffix for clarity
- Accept dots (.) in addition to alphanumeric for hierarchical IDs
- Update test cases to cover hierarchical ID formats
* feat: auto-disable daemon in git worktrees for safety
Implement worktree daemon compatibility as proposed in the analysis.
The daemon is now automatically disabled when running in a git worktree
unless sync-branch is configured.
Git worktrees share the same .beads directory, and the daemon commits
to whatever branch its working directory has checked out. This causes
commits to go to the wrong branch when using daemon in worktrees.
- Add shouldDisableDaemonForWorktree() helper that checks:
1. If current directory is a git worktree (via git rev-parse)
2. If sync-branch is configured (env var or config.yaml)
- Modify shouldAutoStartDaemon() to call the helper
- Modify daemon connection logic in main.go to skip connection
- Add FallbackWorktreeSafety constant for daemon status reporting
- Update warnWorktreeDaemon() to skip warning when sync-branch configured
- In worktree WITHOUT sync-branch: daemon auto-disabled, direct mode used
- In worktree WITH sync-branch: daemon enabled (commits go to dedicated branch)
- In regular repo: no change (daemon works as before)
- Added comprehensive unit tests for shouldDisableDaemonForWorktree()
- Added integration tests for shouldAutoStartDaemon() in worktree contexts
- Manual E2E testing verified correct behavior
- Updated WORKTREES.md with new automatic safety behavior
- Updated DAEMON.md with Git Worktrees section
* feat: check database config for sync-branch in worktree safety logic
Previously, the worktree daemon safety check only looked at:
- BEADS_SYNC_BRANCH environment variable
- sync-branch in config.yaml
This meant users who configured sync-branch via `bd config set sync-branch`
(which stores in the database) would still have daemon disabled in worktrees.
Now the check also reads sync.branch from the database config table,
making daemon work in worktrees when sync-branch is configured via any method.
Changes:
- Add IsConfiguredWithDB() function that checks env, config.yaml, AND database
- Add findBeadsDB() to locate database (worktree-aware via git-common-dir)
- Add getMainRepoRoot() helper using git rev-parse
- Add getConfigFromDB() for lightweight database reads
- Update shouldDisableDaemonForWorktree() to use IsConfiguredWithDB()
- Update warnWorktreeDaemon() to use IsConfiguredWithDB()
- Add test case for database config path
* refactor: use existing beads.FindDatabasePath() instead of duplicating code
Remove duplicate getMainRepoRoot() and findBeadsDB() functions from
syncbranch.go and use the existing beads.FindDatabasePath() which is
already worktree-aware.
Changes:
- Replace custom findBeadsDB() with beads.FindDatabasePath()
- Remove duplicate getMainRepoRoot() (git.GetMainRepoRoot() exists)
- Remove unused imports (exec, strings, filepath)
- Clean up debug logging in tests
---------
Co-authored-by: Charles P. Cross <cpdata@users.noreply.github.com>
When git merge replaces the .beads/beads.db file, the daemon's
SQLite connection becomes stale (still reading deleted inode).
This adds FreshnessChecker that detects file replacement via
inode/mtime comparison and triggers automatic reconnection.
Implementation:
- freshness.go: monitors db file for replacement
- store.go: adds EnableFreshnessChecking() and reconnect()
- queries.go: calls checkFreshness() on GetIssue/SearchIssues
- daemon.go: enables freshness checking at startup
- freshness_test.go: comprehensive tests including merge scenario
Code quality (per review):
- Extract configureConnectionPool() helper to reduce duplication
- Handle Close() error in reconnect() (log but continue)
- Use t.Cleanup() pattern in tests per project conventions
- Rename setupFreshnessTest() per naming conventions
Overhead: ~2.6μs per read op (~0.8% of total query time)
Signed-off-by: Alessandro De Blasis <alex@deblasis.net>
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* bd-ckej: fix orphan skip count mismatch on fresh import
When OrphanSkip mode is used during import and a child issue's parent doesn't
exist, the issue ID was cleared to '' but then regenerated anyway in
GenerateBatchIssueIDs, causing it to be created in the database. This resulted
in a count mismatch: JSONL had 824 issues but only 823 were in the database (one
orphan was counted but not created).
Fix: Filter out orphaned issues with empty IDs before batch creation and track
them in result.Skipped so the count stays accurate.
* test: add TestImportOrphanSkip_CountMismatch for bd-ckej
Adds comprehensive test that verifies orphaned issues are properly skipped
during import when orphan_handling=OrphanSkip and parent doesn't exist.
Also improves the fix to pre-filter orphaned issues before batch creation,
ensuring they're not inserted then have IDs cleared (preventing count
mismatches).
---------
Co-authored-by: Amp <amp@example.com>
Add auto-commit, auto-push, local mode, sync interval, and daemon mode
to the status output when querying a running daemon.
This helps users understand the current daemon configuration without
having to check logs or remember what flags were used at startup.
Changes:
- Add config fields to StatusResponse in protocol.go
- Add SetConfig() method to Server for daemon to set its config
- Update handleStatus() to include config in response
- Update showDaemonStatus() to query and display config via RPC
- Add comprehensive test coverage for new functionality
Co-authored-by: Christian Catalan <crcatala@gmail.com>
GH#464: Add safety guards to prevent deletion of open/in_progress issues during sync:
- Safety guard in git-history-backfill (importer.go)
- Safety guard in deletions manifest processing
- Warning when uncommitted changes detected before pull (daemon_sync.go)
- Enhanced repo ID mismatch error message
GH#545: Fix bd blocked to show status=blocked issues (sqlite/ready.go):
- Changed from INNER JOIN to LEFT JOIN to include issues without dependencies
- Added WHERE clause to include both status=blocked AND dependency-blocked issues
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Mark unused ctx parameter with underscore in getRepoRootForWorktree
- Replace exec.Command("test", "-d") with os.Stat for directory check
- Handle file.Close() errors properly in compact.go and migrate_tombstones.go
- Explicitly ignore cleanup errors with _ assignment
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
