fix(hooks): pre-commit no longer blocks when .beads removed (GH#483)

Two fixes to make pre-commit hook more resilient:

1. Check if beads is actually initialized (has db, config, or jsonl)
   - Empty .beads directory no longer triggers sync attempt
   - Handles case where .beads was removed from git but dir lingers

2. Make sync failure a warning instead of blocking error
   - Beads issues shouldn't prevent code commits
   - User can still run 'bd sync --flush-only' manually

Also synced examples/git-hooks/pre-commit with template (worktree handling).

Closes #483

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.beads/.gitignore

@@ -30,3 +30,5 @@ beads.right.meta.json
 !issues.jsonl
 !metadata.json
 !config.json
+deletions.jsonl
+deletions.jsonl.migrated