When BEADS_DIR environment variable points to a separate git repository,
bd sync previously failed with "fatal: 'main' is already used by worktree"
because it computed repoRoot from cwd instead of the beads directory.
This fix detects when beads dir is in a different git repo than cwd and
uses direct git operations (add/commit/push/pull) instead of worktree-based
sync, bypassing the problematic worktree creation entirely.
Cherry-picked from PR #533 (cleaned up unrelated changes).
Co-Authored-By: dand-oss <dand-oss@users.noreply.github.com>
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