John Zila 6aa8ebd26f fix(sync): write to worktree JSONL only when sync-branch configured (#1133) ...

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

2026-01-17 00:04:09 -08:00

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