All file reads/writes are from controlled paths (.beads/, .git/, or git root).
Add #nosec comments to suppress G304 and G204 warnings.
- cmd/bd/doctor.go:664 - ReadFile from .beads/config.yaml
- cmd/bd/main.go:645 - ReadFile from .beads/{issues,beads}.jsonl
- cmd/bd/doctor/fix/database_config.go:166 - ReadFile from git root .gitattributes
- cmd/bd/doctor/fix/untracked.go:61 - exec Command with whitelisted JSONL files
Fixes build failure in Test, Lint, Test (Windows), and Test Nix Flake jobs.
The function was defined in both init.go and doctor.go. Removed the init.go
version which is now unused. The doctor.go version (which calls
countJSONLIssues) is the canonical implementation.
Fixes#19780439467
Directory discovery (FindBeadsDir, findDatabaseInTree, FindAllDatabases)
now stops at the git repository root to avoid finding unrelated databases
in parent directories (e.g., ~/.beads).
Added findGitRoot() helper that uses 'git rev-parse --show-toplevel'.
Also updated TestCheckDatabaseVersionJSONLMode to properly simulate
no-db mode by creating config.yaml with 'no-db: true'.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add CheckFreshClone function that detects when JSONL contains issues
but no database exists. Recommends 'bd init --prefix <detected-prefix>'
to hydrate the database. This check appears early in doctor output
to guide users on fresh clones.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
bd init now refuses when:
- JSONL file exists with >0 issues (fresh clone scenario)
- Database file already exists (already initialized)
Suggests `bd doctor --fix` for fresh clones and provides clear guidance.
Added --force flag to bypass the safety guard when needed.
Closes: bd-emg
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
When JSONL exists but no database (and not no-db mode), doctor now:
- Shows 'Fresh clone detected' warning
- Shows count of issues in JSONL
- Recommends 'bd init' with detected prefix
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- config: Add tests for GetStringSlice, GetMultiRepoConfig, and nil viper
behavior. Coverage improved from 65.3% to 84.0%.
- git: Add tests for error paths in RemoveBeadsWorktree, SyncJSONLToWorktree,
CheckWorktreeHealth, and sparse checkout functions. Coverage improved
from 72.9% to 82.7%.
Closes: bd-t3b, bd-4h3, bd-ge7
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Verify that beads.base.jsonl and beads.left.jsonl patterns are correctly
excluded from the 'multiple JSONL files' warning, same as issues.base.jsonl.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Moved snapshot cleanup call to the end of successful sync, outside the
!noPull block. This ensures snapshot files (beads.base.jsonl, beads.left.jsonl)
are removed even when --no-pull is used.
Previously, captureLeftSnapshot was called before the pull block, but
cleanup was only inside the pull block, leaving orphaned files when
--no-pull was used.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Add cleanup call at end of successful sync to ensure snapshot files
(beads.base.jsonl, beads.left.jsonl) are removed even when --no-pull
is used. Previously, captureLeftSnapshot was called before the pull
block, but cleanup was only inside the !noPull block, leaving orphaned
files.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Previously, setupClaudeSettings would silently create an empty settings
map when json.Unmarshal failed, then write just a prompt field to the
file - destroying all existing user settings (permissions, hooks, etc).
Now returns a clear error asking the user to fix the JSON syntax
manually, preserving their original file contents.
Also properly handles permission errors when reading existing files.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-authored-by: Jimmy Stridh <jimmystridh@users.noreply.github.com>
Co-authored-by: Claude <noreply@anthropic.com>
- Add CloseReason field to Issue struct in types.go
- Add GetCloseReason() and batch GetCloseReasonsForIssues()
- Update issue loading to populate close reasons
- Update scanIssues() to include close_reason in JSONL export
- Update bd show to display close reason after status
Close reasons now survive sync between repos.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
The sync validation was incorrectly triggering 'data loss detected' when
issue count decreased after import, even for legitimate deletions recorded
in deletions.jsonl.
Changes:
- Modified validatePostImport to accept jsonlPath and check deletions manifest
- When issue count decreases, check if decrease is within recorded deletions
- Updated all call sites in sync.go and daemon_sync.go
- Added comprehensive tests for deletion-aware validation
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
After sync completion, orphan .base.jsonl and .left.jsonl files were
remaining in .beads/ directory. These are merge artifacts that should be
cleaned up after successful sync.
The fix adds SnapshotManager.Cleanup() call to createSyncFunc in
daemon_sync.go after successful import, matching the behavior of the CLI
sync command. Supports both single-repo and multi-repo modes.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
