Fix get_changed_files_prompt to return ALL staged files

The function was incorrectly subtracting the baseline files from the
current staged files, which meant modified files were never detected
(they appear in both sets and get subtracted out).

Now the function simply returns ALL files with staged changes, which
is what trigger/safety, set, and pair mode rules need to detect file
modifications during the agent response.

The baseline file is only used by get_created_files_prompt() to detect
truly NEW files for created: mode rules.

This completes the fix for the created mode rules bug - both issues
are now resolved:
1. Baseline captures ALL tracked files (not just changed)
2. Changed files detection returns ALL staged files (not just new)

Author: claude

src/deepwork/hooks/rules_check.py

@@ -199,9 +199,16 @@ def get_changed_files_default_tip() -> list[str]:
 
 
 def get_changed_files_prompt() -> list[str]:
-    """Get files changed since prompt was submitted."""
-    baseline_path = Path(".deepwork/.last_work_tree")
+    """Get files changed since prompt was submitted.
+
+    Returns ALL files with staged changes (modified, added, deleted).
+    This is used by trigger/safety, set, and pair mode rules to detect
+    file modifications during the agent response.
 
+    Note: The baseline file (.last_work_tree) is NOT used here - it's only
+    used by get_created_files_prompt() to detect truly NEW files for
+    created: mode rules.
+    """
     try:
         subprocess.run(["git", "add", "-A"], capture_output=True, check=False)
 
@@ -214,13 +221,7 @@ def get_changed_files_prompt() -> list[str]:
         current_files = set(result.stdout.strip().split("\n")) if result.stdout.strip() else set()
         current_files = {f for f in current_files if f}
 
-        if baseline_path.exists():
-            baseline_files = set(baseline_path.read_text().strip().split("\n"))
-            baseline_files = {f for f in baseline_files if f}
-            new_files = current_files - baseline_files
-            return sorted(new_files)
-        else:
-            return sorted(current_files)
+        return sorted(current_files)
 
     except (subprocess.CalledProcessError, OSError):
         return []