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>

examples/git-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
 

examples/git-hooks/pre-push

@@ -31,9 +31,9 @@ if command -v bd >/dev/null 2>&1; then
     bd sync --flush-only >/dev/null 2>&1 || true
 fi
 
-# Collect all tracked or existing JSONL files (supports both old and new names)
+# Collect all tracked or existing JSONL files (beads.jsonl, issues.jsonl for backward compat, deletions.jsonl for deletion propagation)
 FILES=""
-for f in .beads/beads.jsonl .beads/issues.jsonl; do
+for f in .beads/beads.jsonl .beads/issues.jsonl .beads/deletions.jsonl; do
     # Include file if it exists in working tree OR is tracked by git (even if deleted)
     if git ls-files --error-unmatch "$f" >/dev/null 2>&1 || [ -f "$f" ]; then
         FILES="$FILES $f"