The root cause was isExternalBeadsDir() incorrectly identifying bare repo
worktrees as "external" repos. This caused bd sync to take the "external
beads dir" code path instead of the worktree-based sync branch path.
The bug: isExternalBeadsDir() compared syncbranch.GetRepoRoot() (which returns
incorrect values for bare repo worktrees) with getRepoRootFromPath() (which
uses --show-toplevel). These returned different values for bare repo
worktrees, causing local worktrees to be treated as external.
The fix: Use git rev-parse --git-common-dir for comparison instead of repo
root. This correctly identifies that worktrees of the same repo share the
same git directory, regardless of bare repo setup.
Also added:
- getGitCommonDir() helper function
- Tests for both getGitCommonDir and isExternalBeadsDir
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
gitCommit() was adding the JSONL file but then committing ALL staged
changes (no pathspec). If other files were staged (e.g., deletions from
git add -A), they would be swept into the bd sync commit.
Fixed by adding pathspec to both gitCommit() and commitToExternalBeadsRepo()
so they only commit what they explicitly staged.
This was the root cause of PR #722 files being deleted - they were staged
for deletion in the working tree and got committed by bd sync.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
