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
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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.
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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>
- 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
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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>
Modern git (2.28+) uses 'main' as default branch, not 'master'.
Tests were failing because they assumed 'master' branch exists.
Changes:
- Use 'git init --initial-branch=main' instead of bare 'git init'
- Change 'git checkout master' to 'git checkout main'
- Add git.ResetCaches() after os.Chdir() to clear cached git state
- Ensures test isolation when changing directories
Adds automatic database recovery when bd doctor --fix detects corruption:
- Detects SQLite corruption (malformed database, SQLITE_CORRUPT errors)
- Backs up corrupted database before recovery attempt
- Rebuilds from JSONL if available (issues.jsonl, deletions.jsonl)
- Falls back to fresh database if JSONL unavailable
- Reports recovery results (issues imported, success/failure)
Recovery is triggered automatically by --fix when corruption is detected.
No manual intervention required.
The CheckChildParentDependencies detection and ChildParentDependencies fix
were flagging ALL child→parent dependencies, including legitimate
'parent-child' type structural hierarchy relationships.
Now only blocking types (blocks, conditional-blocks, waits-for) are
detected as anti-patterns. The 'parent-child' type is a legitimate
hierarchy marker used for:
- Tracking parent-child relationships
- Transitive block propagation (if parent blocked, children blocked)
- Hierarchy visualization in external tools
Changes:
- Add type filter to SELECT queries (only blocking types)
- Add type filter to DELETE statement (preserve parent-child)
- Add regression test TestChildParentDependencies_PreservesParentChildType
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Claude Code's installed_plugins.json changed from v1 (plugins as structs)
to v2 (plugins as arrays). Update GetClaudePluginVersion() to handle both.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
GH#740: bd doctor --fix was auto-removing child→parent dependencies,
calling them an 'anti-pattern'. While these often indicate modeling
mistakes (deadlock), they may be intentional in some workflows.
Changes:
- Add --fix-child-parent flag (required to remove child→parent deps)
- Remove ChildParentDependencies from default --fix set
- Update warning message to reference new flag
- Update comments to reflect more nuanced understanding
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Extends bd doctor to detect complete-but-unclosed molecules (epics where
all children are closed but root is still open).
- Added CheckStaleMolecules() to doctor/maintenance.go
- Added resolveBeadsDir() helper to follow Gas Town redirect files
- Check appears in Maintenance category with warning severity
- Shows example IDs and suggests 'bd mol stale' for review
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The fix for GH#709 updated FindJSONLInDir to skip interactions.jsonl,
but the doctor check in CheckLegacyJSONLFilename was not updated.
This caused `bd doctor` to warn about multiple JSONL files when
both issues.jsonl and interactions.jsonl exist (which is normal
after `bd init`).
Also skip molecules.jsonl which is another system file that shouldn't
be counted as a duplicate issue database.
This prevents a common mistake where users add dependencies from child
issues to their parent epics. This creates a deadlock:
- Child can't start (blocked by open parent)
- Parent can't close (children not done)
Changes:
- dep.go: Reject child→parent deps at creation time with clear error
- server_labels_deps_comments.go: Same check for daemon RPC
- doctor/validation.go: New check detects existing bad deps
- doctor/fix/validation.go: Auto-fix removes bad deps
- doctor.go: Wire up check and fix handler
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
When 'bd doctor --fix' detects DB has more issues than JSONL, it runs
'bd export' to sync them. However, 'bd export' without -o flag outputs
to stdout instead of writing to .beads/issues.jsonl, making the fix a
no-op.
Add -o .beads/issues.jsonl --force to the export command to ensure the
JSONL file is actually updated.
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
- 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
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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.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.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>
* 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 CheckOrphanedIssues to detect issues referenced in commits but still open
- Pattern matches (prefix-xxx) in git log against open issues in database
- Reports warning with issue IDs and commit hashes
- Add 8 comprehensive tests for the new check
Also:
- Add tests for mol spawn --attach functionality (bd-f7p1)
- Document commit message convention in AGENT_INSTRUCTIONS.md
- Fix CheckpointWAL to use wrapDBError for consistency
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Modified fix.DBJSONLSync() to detect which direction to sync:
- If DB > JSONL: run 'bd export' to sync JSONL (DB has newer data)
- If JSONL > DB: run 'bd sync --import-only' to import (JSONL is source of truth)
- If equal but different timestamps: use file mtime to decide direction
- Updated CheckDatabaseJSONLSync() error messages to recommend correct fix direction:
- Shows different guidance based on whether DB or JSONL has more issues
- Added helper functions:
- countDatabaseIssues() to count issues in SQLite
- countJSONLIssues() to count issues in JSONL (local, avoids circular import)
- Added tests for countJSONLIssues() with edge cases
Fixes issue where 'bd doctor --fix' would recommend 'bd sync --import-only'
when DB > JSONL, which would be a no-op since JSONL hasn't changed.
The doctor's version tracking check was looking at metadata.json:LastBdVersion,
but version tracking was moved to .local_version file (gitignored). This caused
the "LastBdVersion field is empty" warning to persist even after running bd
commands, because those commands update .local_version but not metadata.json.
- Update CheckMetadataVersionTracking to read from .local_version
- Rename check from "Metadata Version Tracking" to "Version Tracking"
- Update tests to use .local_version instead of metadata.json
- Remove unused configfile import
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Adds configuration options for beads git commits:
- git.author: Override commit author (e.g., "beads-bot <beads@example.com>")
- git.no-gpg-sign: Disable GPG signing for beads commits
This is useful for users with Touch ID commit signing (like Secretive)
who get prompted for every beads auto-commit.
Config example:
```yaml
git:
author: "beads-bot <beads@example.com>"
no-gpg-sign: true
```
Environment variables: BD_GIT_AUTHOR, BD_GIT_NO_GPG_SIGN
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* test(doctor): add comprehensive tests for fix and check functions
Add edge case tests, e2e tests, and improve test coverage for:
- database_test.go: database integrity and sync checks
- git_test.go: git hooks, merge driver, sync branch tests
- gitignore_test.go: gitignore validation
- prefix_test.go: ID prefix handling
- fix/fix_test.go: fix operations
- fix/e2e_test.go: end-to-end fix scenarios
- fix/fix_edge_cases_test.go: edge case handling
* docs: add testing philosophy and anti-patterns guide
- Create TESTING_PHILOSOPHY.md covering test pyramid, priority matrix,
what NOT to test, and 5 anti-patterns with code examples
- Add cross-reference from README_TESTING.md
- Document beads-specific guidance (well-covered areas vs gaps)
- Include target metrics (test-to-code ratio, execution time targets)
* chore: revert .beads/ to upstream/main state
* refactor(doctor): add category grouping and Ayu theme colors
- Add Category field to DoctorCheck for organizing checks by type
- Define category constants: Core, Git, Runtime, Data, Integration, Metadata
- Update thanks command to use shared Ayu color palette from internal/ui
- Simplify test fixtures by removing redundant test cases
* fix(doctor): prevent test fork bomb and fix test failures
- Add ErrTestBinary guard in getBdBinary() to prevent tests from
recursively executing the test binary when calling bd subcommands
- Update claude_test.go to use new check names (CLI Availability,
Prime Documentation)
- Fix syncbranch test path comparison by resolving symlinks
(/var vs /private/var on macOS)
- Fix permissions check to use exact comparison instead of bitmask
- Fix UntrackedJSONL to use git commit --only to preserve staged changes
- Fix MergeDriver edge case test by making both .git dir and config
read-only
- Add skipIfTestBinary helper for E2E tests that need real bd binary
* test(doctor): skip read-only config test in CI environments
GitHub Actions containers may have CAP_DAC_OVERRIDE or similar
capabilities that allow writing to read-only files, causing
the test to fail. Skip the test when CI=true or GITHUB_ACTIONS=true.
The bd doctor command was pointing to a non-existent README anchor
(#claude-code-plugin). Updated to point to docs/PLUGIN.md which
contains the actual plugin installation instructions.
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The schema_probe.go and doctor/database.go had different column lists
for validating database schemas. Neither included the pinned column
added in migration 023, causing:
- Doctor to report "All required tables and columns present" on
databases missing the pinned column
- Potential failures when using `gt mail send` on databases without
the pinned column
Changes:
- Add pinned, sender, ephemeral to doctor's criticalChecks
- Add metadata, thread_id to dependencies check
- Add all missing columns to schema_probe.go's expectedSchema:
source_repo, close_reason, deleted_at, deleted_by, delete_reason,
original_type, sender, ephemeral, pinned
Fixes: beads-9yc
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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* refactor(doctor): split doctor.go into modular package files
Split the 3,171-line doctor.go into logical sub-files within the
cmd/bd/doctor/ package, reducing the main file to 834 lines (74% reduction).
New package structure:
- types.go: DoctorCheck struct and status constants
- installation.go: CheckInstallation, CheckMultipleDatabases, CheckPermissions
- git.go: CheckGitHooks, CheckMergeDriver, CheckSyncBranch* checks
- database.go: CheckDatabaseVersion, CheckSchemaCompatibility, CheckDatabaseJSONLSync
- version.go: CheckCLIVersion, CheckMetadataVersionTracking, CompareVersions
- integrity.go: CheckIDFormat, CheckDependencyCycles, CheckTombstones
- daemon.go: CheckDaemonStatus, CheckVersionMismatch
- quick.go: Quick checks for sync-branch and hooks
Updated tests to use exported doctor.CheckXxx() functions and
doctor.StatusXxx constants.
* fix(doctor): suppress gosec G204 false positives
Add #nosec G204 comments to exec.Command calls in CheckSyncBranchHealth
where variables come from trusted sources (config files or hardcoded
values like "main"/"master"/"origin"), not untrusted user input.
