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
 

.beads-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"

.beads/beads.jsonl

@@ -37,6 +37,7 @@
 {"id":"bd-mnap","title":"Investigate performance issues in VS Code Copilot (Windows)","description":"Beads unusable in Windows 11 VS Code Copilot chat with Sonnet 4.5.\nSummary event happens every 3-4 turns, taking 3 minutes.\nCopilot summarizes after ~125k tokens despite model supporting 1M.\nLarge context size of beads might be triggering aggressive summarization.\nNeed workaround or optimization for context size.\n","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T18:56:30.124918-05:00","updated_at":"2025-11-20T18:56:30.124918-05:00"}
 {"id":"bd-nq41","title":"Fix Homebrew warning about Ruby file location","description":"Homebrew warning: Found Ruby file outside steveyegge/beads tap formula directory.\nWarning points to: /opt/homebrew/Library/Taps/steveyegge/homebrew-beads/bd.rb\nIt should likely be inside a Formula/ directory or similar structure expected by Homebrew taps.\n","status":"open","priority":2,"issue_type":"chore","created_at":"2025-11-20T18:56:21.226579-05:00","updated_at":"2025-11-20T18:56:21.226579-05:00"}
 {"id":"bd-p6vp","title":"Clarify .beads/.gitattributes handling in Protected Branches docs","description":"Protected Branches docs quick start leaves untracked `.beads` directory and `.gitattributes`.\nQuestion: Are these changes meant to be checked into the protected branch?\nNeed to clarify if these should be ignored or committed, or if the instructions are missing a step.\n","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T18:56:25.79407-05:00","updated_at":"2025-11-20T18:56:25.79407-05:00"}
+{"id":"bd-pbj","title":"bd doctor --fix should run bd sync to commit untracked deletions.jsonl","description":"After running bd cleanup -f, the deletions.jsonl file is created but left untracked. bd doctor --fix should notice this and run bd sync to commit it.\n\nCurrent behavior:\n- bd cleanup -f creates/updates deletions.jsonl\n- git status shows deletions.jsonl as untracked\n- bd doctor --fix does not notice or fix this\n\nExpected behavior:\n- bd doctor --fix should detect untracked .beads/*.jsonl files\n- Should offer to run bd sync to commit them\n\nRelated: The git hooks were also missing deletions.jsonl from their staging loops - that's been fixed in this session.","status":"open","priority":2,"issue_type":"bug","created_at":"2025-11-26T20:29:33.901199-08:00","updated_at":"2025-11-26T20:29:33.901199-08:00"}
 {"id":"bd-qsm","title":"Auto-compact deletions during bd sync","description":"Parent: bd-imj\n\n## Task\nOptionally prune deletions manifest during sync when threshold exceeded.\n\n**Note: Opt-in feature** - disabled by default to avoid sync latency.\n\n## Implementation\n\nIn `bd sync`:\n```go\nfunc (s *Syncer) Sync() error {\n    // ... existing sync logic ...\n    \n    // Auto-compact only if enabled\n    if s.config.GetBool(\"deletions.auto_compact\", false) {\n        deletionCount := deletions.Count(\".beads/deletions.jsonl\")\n        threshold := s.config.GetInt(\"deletions.auto_compact_threshold\", 1000)\n        \n        if deletionCount \u003e threshold {\n            retentionDays := s.config.GetInt(\"deletions.retention_days\", 7)\n            if err := s.compactor.PruneDeletions(retentionDays); err != nil {\n                log.Warnf(\"Failed to auto-compact deletions: %v\", err)\n                // Non-fatal, continue sync\n            }\n        }\n    }\n    \n    // ... rest of sync ...\n}\n```\n\n## Configuration\n```yaml\ndeletions:\n  retention_days: 7\n  auto_compact: false              # Opt-in, disabled by default\n  auto_compact_threshold: 1000     # Trigger when \u003e N entries (if enabled)\n```\n\n## Acceptance Criteria\n- [ ] Auto-compact disabled by default\n- [ ] Enabled via config `deletions.auto_compact: true`\n- [ ] Sync checks deletion count only when enabled\n- [ ] Auto-prunes when threshold exceeded\n- [ ] Failure is non-fatal (logged warning)\n- [ ] Test: no compaction when disabled\n- [ ] Test: compaction triggers when enabled and threshold exceeded","status":"closed","priority":1,"issue_type":"task","created_at":"2025-11-25T09:57:04.522795-08:00","updated_at":"2025-11-25T15:03:01.469629-08:00","closed_at":"2025-11-25T15:03:01.469629-08:00"}
 {"id":"bd-s0z","title":"Consider extracting error handling helpers","description":"Evaluate creating FatalError() and WarnError() helpers as suggested in ERROR_HANDLING.md to reduce boilerplate and enforce consistency. Prototype in a few files first to validate the approach.","status":"open","priority":4,"issue_type":"task","created_at":"2025-11-24T00:28:57.248959-08:00","updated_at":"2025-11-24T00:28:57.248959-08:00"}
 {"id":"bd-t3b","title":"Add test coverage for internal/config package","description":"","design":"Config package has 1 test file. Need comprehensive tests. Target: 70% coverage","acceptance_criteria":"- At least 3 test files\n- Package coverage \u003e= 70%","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-20T21:21:22.91657-05:00","updated_at":"2025-11-20T21:21:22.91657-05:00","dependencies":[{"issue_id":"bd-t3b","depends_on_id":"bd-ge7","type":"blocks","created_at":"2025-11-20T21:21:31.201036-05:00","created_by":"daemon"}]}

cmd/bd/templates/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
 

cmd/bd/templates/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"

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"