Summary

When running bd rename-prefix from a git worktree, the command updates the shared DB and the main worktree's issues.jsonl correctly, but leaves the current worktree's issues.jsonl with stale (old-prefix) IDs. Neither bd sync, bd sync --flush-only, nor bd export resolves the desync — they all write to the main worktree's path.

The same behavior occurs with or without --no-daemon.

Steps to Reproduce

# 1. Create test repo with issues
mkdir /tmp/test-rename && cd /tmp/test-rename
git init && git checkout -b main
export BEADS_NO_DAEMON=1
bd --no-daemon init --prefix=alpha
bd --no-daemon create --title="Issue one" --type=task --priority=2
bd --no-daemon create --title="Issue two" --type=bug --priority=3
bd --no-daemon export
git add -A && git commit -m "initial"

# 2. Create a worktree
git worktree add /tmp/test-worktree -b wt-branch
cd /tmp/test-worktree

# 3. Rename prefix from the worktree
bd --no-daemon rename-prefix beta

# 4. Observe the desync
cat .beads/issues.jsonl                    # Still alpha-* (stale!)
cat /tmp/test-rename/.beads/issues.jsonl   # beta-* (correct)
bd --no-daemon list                        # beta-* (reads from shared DB)

Expected Behavior

The current worktree's .beads/issues.jsonl should be updated with the new prefix, or the command should refuse to run in a worktree.

Actual Behavior

• Shared DB: updated correctly
• Main worktree JSONL: updated correctly
• Current worktree JSONL: stale, retains old prefix IDs
• bd sync, bd sync --flush-only, bd export: all write to main's JSONL, not worktree's
• bd list: shows correct IDs (reads from DB)

The worktree's JSONL becomes permanently diverged. On merge, git may auto-resolve (if changes don't conflict) or produce merge conflicts with stale IDs.

Root Cause

findJSONLPath() in cmd/bd/autoflush.go resolves the JSONL path via the database location. Since beads.db is gitignored and only exists in the main worktree, the path always resolves to the main worktree's .beads/issues.jsonl. The worktree redirect (getWorktreeJSONLPath) only activates when sync-branch is configured.

In a plain git worktree without sync-branch, all JSONL writes (rename, export, sync) go to the main worktree's file, leaving the worktree's git-checked-out copy untouched.

Suggested Fixes

Option A — Update all worktree JSONL files

• Enumerate all git worktrees after renaming in DB and main JSONL
• Update each worktree's .beads/issues.jsonl with renamed IDs
• Complete fix, but open questions:
  • Arbitrary count of worktrees — performance implications unknown
  • Other per-worktree state may also need updating (e.g., interactions.jsonl, cache tables per rename-prefix doesn't update blocked_issues_cache table #1016)
  • As external contributors we lack full visibility into these trade-offs

Option B — Block rename in worktrees

• Detect worktree at the start of rename-prefix
• Exit with error: "Cannot rename prefix from a worktree. Please run from the main worktree."
• Surfaces a silent desync as an explicit error
• Zero risk to existing behavior

Option C — Fix findJSONLPath() to resolve relative to cwd in worktrees

• Change findJSONLPath() in cmd/bd/autoflush.go to resolve JSONL path from the current working directory when in a worktree, instead of from the DB path
• Fixes the root cause — not just rename-prefix but also export and sync --flush-only
• Most architecturally correct, but largest blast radius — could affect other worktree behavior that depends on the current resolution logic

Environment

Related Issues

• rename-prefix doesn't update blocked_issues_cache table #1016 — rename-prefix doesn't update blocked_issues_cache table