The negation patterns (!issues.jsonl, !interactions.jsonl, etc.) in
.beads/.gitignore had higher precedence than the fork protection
exclusion in .git/info/exclude, effectively defeating fork protection.
Contributors could accidentally stage and commit upstream issue
databases because:
1. Fork protection added .beads/issues.jsonl to .git/info/exclude
2. .beads/.gitignore had !issues.jsonl which overrode the exclusion
3. .gitignore files have higher precedence than .git/info/exclude
The negation patterns were unnecessary anyway since no pattern in
.beads/.gitignore matches those files. Added a comment explaining
why negations should not be added.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.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>
The deletions.jsonl file contained merge conflicts and was causing
bd init/reset failures on fresh clones. Since we've migrated to
tombstones, these files are no longer needed.
Fixes GH#590
Co-Authored-By: Matt Wilkie <maphew@gmail.com>
🤖 Generated with Claude Code
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Tombstones are now stored inline in issues.jsonl.
Added deletions.jsonl to .gitignore to prevent re-tracking.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Root cause: bd doctor hydrate was re-adding migrated tombstones to the
deletions manifest because getCurrentJSONLIDs() included all issues,
including tombstones. When compared against git history, tombstones
appeared as 'deleted' and were incorrectly added to the manifest as new
deletions, corrupting the database on next sync.
Fix: Skip tombstone-status issues in getCurrentJSONLIDs() so they don't
participate in deletion detection. Tombstones represent already-recorded
deletions/migrations and shouldn't be treated as active issues.
Changes:
- cmd/bd/doctor/fix/deletions.go: Skip tombstones in getCurrentJSONLIDs()
- cmd/bd/doctor/fix/deletions_test.go: New tests for tombstone skipping
- cmd/bd/migrate_tombstones_test.go: Test that tombstones are valid
This fixes the bug where 'bd migrate-tombstones' followed by 'bd sync'
would add thousands of deletion records with author 'bd-doctor-hydrate'
The .beads/.gitignore now ignores everything by default and explicitly
whitelists tracked files. This fixes confusion about which files to
commit when using protected branches workflow.
Changes:
- Use `*` to ignore all by default, then `!file` to whitelist
- Fix config.json -> config.yaml (wrong filename in negation)
- Update doctor check to validate new patterns
- Update PROTECTED_BRANCHES.md documentation
- Simplify git add instructions to just `git add .beads/`
Fixes#473🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Root cause: metadata.json is tracked in git and contains last_bd_version.
When git operations (pull, checkout, merge) reset metadata.json to the
committed version, the upgrade notification would fire repeatedly.
Fix: Store the last used bd version in .beads/.local_version which is
gitignored, so git operations don't affect version tracking.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Removes noisy version mismatch warnings on every bd upgrade
- Version field in metadata.json was redundant with daemon version checking via RPC
- Daemon version mismatches still detected via HealthResponse
- Removes checkVersionMismatch() function and related test file
- Updates .beads/.gitignore to properly ignore merge artifacts
Amp-Thread-ID: https://ampcode.com/threads/T-7ba8aff2-97a0-4d0c-9008-e858bdfadd61
Co-authored-by: Amp <amp@ampcode.com>
When 'bd sync --import-only' completes, it imports JSONL changes into
the database but doesn't update the database file's modification time.
This causes 'bd doctor' to incorrectly warn that 'JSONL is newer than
database' even when they're in sync.
Root cause: SQLite in WAL mode writes to beads.db-wal; the main beads.db
mtime often doesn't change until a checkpoint. bd doctor compares JSONL
mtime to beads.db mtime, so it can misfire without an mtime bump.
The fix adds touchDatabaseFile() that:
- Only runs when import actually made changes (not dry-run, not unchanged)
- Sets DB mtime to max(JSONL mtime, now) + 1ns to handle clock skew
- Is best-effort (logs warning on failure, doesn't fail import)
- Includes tests for basic touch and clock skew scenarios
Fixes: bd-g3ey
