Refactor rules_check.py git operations

.claude/skills/manual_tests.run_fire_tests/SKILL.md

@@ -86,6 +86,8 @@ For EACH test below, follow this cycle:
 
 **IMPORTANT**: Only launch ONE sub-agent at a time. Wait for it to complete and reset before launching the next.
 
+**IMPORTANT**: Always check the queue file before reverting to verify the rule was queued.
+
 ### Test Cases (run serially)
 
 **Test 1: Trigger/Safety**

.deepwork/jobs/manual_tests/steps/run_fire_tests.md

@@ -62,6 +62,8 @@ For EACH test below, follow this cycle:
 
 **IMPORTANT**: Only launch ONE sub-agent at a time. Wait for it to complete and reset before launching the next.
 
+**IMPORTANT**: Always check the queue file before reverting to verify the rule was queued.
+
 ### Test Cases (run serially)
 
 **Test 1: Trigger/Safety**

.gemini/skills/manual_tests/run_fire_tests.toml

@@ -86,6 +86,8 @@ For EACH test below, follow this cycle:
 
 **IMPORTANT**: Only launch ONE sub-agent at a time. Wait for it to complete and reset before launching the next.
 
+**IMPORTANT**: Always check the queue file before reverting to verify the rule was queued.
+
 ### Test Cases (run serially)
 
 **Test 1: Trigger/Safety**

src/deepwork/cli/install.py

@@ -115,6 +115,7 @@ def _create_deepwork_gitignore(deepwork_dir: Path) -> None:
     gitignore_path = deepwork_dir / ".gitignore"
     gitignore_content = """# DeepWork runtime artifacts
 # These files are generated during sessions and should not be committed
+.last_tree_hash
 .last_work_tree
 .last_head_ref