* fix(autoimport): auto-correct deleted status to tombstone for JSONL compatibility (GH#1223)
This fix addresses the 'Stuck in sync diversion loop' issue where v0.48.0
encountered validation errors during JSONL import. The issue occurs when
JSONL files from older versions have issues with status='deleted' but the
current code expects status='tombstone' for deleted issues.
Changes:
- Add migration logic in parseJSONL to auto-correct 'deleted' status to 'tombstone'
- Ensure tombstones always have deleted_at timestamp set
- Add debug logging for both migration operations
- Prevents users from being stuck in sync divergence when upgrading
Fixes GH#1223: Stuck in sync diversion loop
* fix(autoimport): comprehensively fix corrupted deleted_at on non-tombstone issues (GH#1223)
The initial fix for GH#1223 only caught issues with status='deleted', but the real
data in the wild had issues with status='closed' (or other statuses) but also
had deleted_at set, which violates the validation rule.
Changes:
- Add broader migration logic: any non-tombstone issue with deleted_at should become tombstone
- Apply fix in all three JSONL parsing locations:
- internal/autoimport/autoimport.go (parseJSONL for auto-import)
- cmd/bd/import.go (import command)
- cmd/bd/daemon_sync.go (daemon sync helper)
- Add comprehensive test case for corrupted closed issues with deleted_at
- Fixes the 'non-tombstone issues cannot have deleted_at timestamp' validation error
during fresh bd init or import
Fixes GH#1223: Stuck in sync diversion loop
* Add merge driver comment to .gitattributes
* fix: properly clean up .gitattributes during bd admin reset
Fixes GH#1223 - Stuck in sync diversion loop
The removeGitattributesEntry() function was not properly cleaning up
beads-related entries from .gitattributes. It only removed lines
containing "merge=beads" but left behind:
- The comment line "# Use bd merge for beads JSONL files"
- Empty lines following removed entries
This caused .gitattributes to remain in a modified state after
bd admin reset --force, triggering sync divergence warning loop.
The fix now:
- Skips lines containing "merge=beads" (existing behavior)
- Skips beads-related comment lines
- Skips empty lines that follow removed beads entries
- Properly cleans up file so it's either empty (and gets deleted)
or contains only non-beads content
---------
Co-authored-by: Amp <amp@example.com>
* fix: use os.Lstat for symlink-safe mtime and permission checks
On NixOS and other systems using symlinks heavily (e.g., home-manager),
os.Stat follows symlinks and returns the target's metadata. This causes:
1. False staleness detection when JSONL is symlinked - mtime of target
changes unpredictably when symlinks are recreated
2. os.Chmod failing or changing wrong file's permissions when target
is in read-only location (e.g., /nix/store)
3. os.Chtimes modifying target's times instead of the symlink itself
Changes:
- autoimport.go: Use Lstat for JSONL mtime in CheckStaleness()
- import.go: Use Lstat in TouchDatabaseFile() for JSONL mtime
- export.go: Skip chmod for symlinked files
- multirepo.go: Use Lstat for JSONL mtime cache
- multirepo_export.go: Use Lstat for mtime, skip chmod for symlinks
- doctor/fix/permissions.go: Skip permission fixes for symlinked paths
These changes are safe cross-platform:
- On systems without symlinks, Lstat behaves identically to Stat
- Symlink permission bits are ignored on Unix anyway
- The extra Lstat syscall overhead is negligible
Fixes symlink-related data loss on NixOS. See GitHub issue #379.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
* test: add symlink behavior tests for NixOS compatibility
Add tests that verify symlink handling behavior:
- TestCheckStaleness_SymlinkedJSONL: verifies mtime detection uses
symlink's own mtime (os.Lstat), not target's mtime (os.Stat)
- TestPermissions_SkipsSymlinkedBeadsDir: verifies chmod is skipped
for symlinked .beads directories
- TestPermissions_SkipsSymlinkedDatabase: verifies chmod is skipped
for symlinked database files while still fixing .beads dir perms
Also adds devShell to flake.nix for local development with go, gopls,
golangci-lint, and sqlite tools.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
---------
Co-authored-by: Claude <noreply@anthropic.com>
The metadata key 'last_import_hash' was misleading because it's updated on
both import AND export. Renamed to 'jsonl_content_hash' which more accurately
describes its purpose - tracking the content hash of the JSONL file.
Added migration support: read operations try new key first, then fall back
to old key for backwards compatibility with existing databases.
Files modified:
- cmd/bd/integrity.go: Update key name with migration support
- cmd/bd/import.go: Update key name
- cmd/bd/sync.go: Update key name
- cmd/bd/autoflush.go: Update key name with migration support
- cmd/bd/daemon_sync.go: Update key name
- cmd/bd/daemon_event_loop.go: Update key name with migration support
- internal/autoimport/autoimport.go: Update key name with migration support
- Updated all related tests
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Extract shared JSONL file discovery logic to internal/utils/path.go.
Both autoimport and beads packages now use this shared implementation.
Changes:
- Add utils.FindJSONLInDir with common logic
- Update autoimport.go to use utils.FindJSONLInDir
- Update beads.go to delegate to utils.FindJSONLInDir
- Update server_export_import_auto.go to use utils.FindJSONLInDir
- Move FindJSONLInDir test to utils/path_test.go
- Fix pre-existing duplicate countIssuesInJSONLFile in init.go
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
The staleness check compares last_import_time against JSONL file mtime.
File mtime has nanosecond precision, but last_import_time was stored with
only second precision (RFC3339). This caused a race condition where the
stored time could be slightly earlier than the file mtime, triggering
false "Database out of sync" errors - particularly in git worktrees.
Changed all 6 locations that set last_import_time to use RFC3339Nano.
The CheckStaleness parser already handles both formats, so this is
backward compatible.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Code review follow-up:
- Fix misleading docstring in FindJSONLInDir (does not return empty)
- Fix same bug in beads.FindJSONLPath (also fell back to matches[0])
- Add comprehensive tests for FindJSONLPath skipping deletions
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add FindJSONLInDir helper that correctly prefers issues.jsonl over other
.jsonl files. Previously, glob patterns could return deletions.jsonl or
merge artifacts (beads.base.jsonl, etc.) first alphabetically, causing
issue data to be written to the wrong file.
This fixes the root cause of deletions.jsonl corruption where full issue
objects were written instead of deletion records, leading to all issues
being purged during sync.
Changes:
- Add FindJSONLInDir() in internal/autoimport with proper file selection
- Update AutoImportIfNewer() to use FindJSONLInDir
- Update CheckStaleness() to use FindJSONLInDir
- Update triggerExport() in RPC server to use FindJSONLInDir
- Add comprehensive tests for FindJSONLInDir
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
After write operations in git worktrees, subsequent reads failed with
"Database out of sync with JSONL" even though the hash check passed.
Root cause: flushToJSONLWithState() updated last_import_hash but not
last_import_time after export. CheckStaleness() compares last_import_time
against JSONL mtime, so after export the JSONL appeared "newer" than the
last import.
Additional issue: RFC3339 only has second precision but file mtimes have
nanosecond precision, causing false positives when times were within the
same second.
Fix:
- Update last_import_time after export in flushToJSONLWithState()
- Use RFC3339Nano format for nanosecond precision
- Update CheckStaleness() to parse both formats for backward compatibility
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
When JSONL mtime changes without content change (e.g., git pull, touch),
the staleness check would repeatedly trigger but auto-import would skip
due to hash match, creating an infinite loop of "Database out of sync"
errors.
Now we update last_import_time even when skipping import due to hash
match, breaking the staleness loop.
Fixes#378🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Changes:
- CheckStaleness now returns errors for corrupted last_import_time metadata
instead of silently returning false (bd-o4qy)
- Added handling for empty string metadata (memory store behavior)
- Enhanced warning messages when staleness check fails to be more explicit
that operation continues with potentially stale data (bd-n4td)
- Added test coverage for corrupted metadata scenario
Closes bd-2q6d, bd-o4qy, bd-n4td
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Fix Windows binary path issues (bd.exe vs bd)
- Skip scripttest on Windows (requires Unix shell)
- Skip file lock tests on Windows (platform locking differences)
- Fix registry tests to use USERPROFILE on Windows
- Fix 8 unparam lint warnings by marking unused params with _
All changes are platform-aware and maintain functionality.
Amp-Thread-ID: https://ampcode.com/threads/T-bc27021a-65db-4b64-a3f3-4e8d7bc8aa0d
Co-authored-by: Amp <amp@ampcode.com>
- Extracted auto-import logic from cmd/bd/main.go to internal/autoimport
- Removed global dependencies (store, dbPath) by using parameters
- Uses callback pattern (ImportFunc) for flexible import implementation
- Both CLI and daemon can now call auto-import after detecting staleness
- Added detailed ID remapping output for collision resolution
- Improved error reporting for parse failures
- All tests passing
Amp-Thread-ID: https://ampcode.com/threads/T-b7faaa33-fc52-409f-82b3-28db143b335d
Co-authored-by: Amp <amp@ampcode.com>
