Fixes#1103: bd sync --merge fails when sync-branch configured due to
skip-worktree/daemon write conflict.
Root cause: When sync-branch is configured, daemon/bd writes to main's
.beads/issues.jsonl which has skip-worktree set. This hides changes from
`git status` but `git merge` still detects them, causing merge failures.
Solution: When sync-branch is configured, redirect all JSONL writes to
the worktree's JSONL only. Main's JSONL is now read-only and only updated
via merges from the sync branch.
Changes:
- autoflush.go: findJSONLPath() now returns worktree JSONL path when
sync-branch configured, with safeguards for test isolation
- sync_branch.go: Remove incomplete skip-worktree manipulation code
that is no longer needed with this architectural fix
Data flow with sync-branch:
1. bd create -> SQLite
2. bd sync --flush-only -> worktree/.beads/issues.jsonl
3. bd sync --merge -> clean merge (main's JSONL unchanged)
4. auto-import -> SQLite updated from merged JSONL
6aa8ebd26f