fix: git hooks now stage deletions.jsonl for cross-clone propagation

The pre-commit and pre-push hooks were only staging beads.jsonl and
issues.jsonl, but not deletions.jsonl. This caused deletions.jsonl
to remain untracked after bd cleanup or bd delete operations.

Updated all hook locations:
- cmd/bd/templates/hooks/pre-commit
- cmd/bd/templates/hooks/pre-push
- examples/git-hooks/pre-commit
- examples/git-hooks/pre-push
- .beads-hooks/pre-commit
- .beads-hooks/pre-push

Users with existing hooks should run: bd hooks install

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

.beads-hooks/pre-commit

@@ -35,9 +35,9 @@ if ! bd sync --flush-only >/dev/null 2>&1; then
     exit 1
 fi
 
-# Stage both possible JSONL files (backward compatibility)
+# Stage all tracked JSONL files (beads.jsonl, issues.jsonl for backward compat, deletions.jsonl for deletion propagation)
 # git add is harmless if file doesn't exist
-for f in .beads/beads.jsonl .beads/issues.jsonl; do
+for f in .beads/beads.jsonl .beads/issues.jsonl .beads/deletions.jsonl; do
     [ -f "$f" ] && git add "$f" 2>/dev/null || true
 done