diff --git a/.claude/scripts/generate_module_docs.sh b/.claude/scripts/generate_module_docs.sh
index 171a1c23..d439ea19 100644
--- a/.claude/scripts/generate_module_docs.sh
+++ b/.claude/scripts/generate_module_docs.sh
@@ -563,6 +563,12 @@ Instructions:
         # Store current output path for CLI context
         export DOC_OUTPUT_PATH="$output_path"
 
+        # Record git HEAD before CLI execution (to detect unwanted auto-commits)
+        local git_head_before=""
+        if git rev-parse --git-dir >/dev/null 2>&1; then
+            git_head_before=$(git rev-parse HEAD 2>/dev/null)
+        fi
+
         # Execute with selected tool
         case "$tool" in
             qwen)
@@ -647,6 +653,16 @@ Instructions:
             fi
         fi
 
+        # Check if CLI tool auto-committed (and revert if needed)
+        if [ -n "$git_head_before" ]; then
+            local git_head_after=$(git rev-parse HEAD 2>/dev/null)
+            if [ "$git_head_before" != "$git_head_after" ]; then
+                echo "   ⚠️  Detected unwanted auto-commit by CLI tool, reverting..."
+                git reset --soft "$git_head_before" 2>/dev/null
+                echo "   ✅ Auto-commit reverted (files remain staged)"
+            fi
+        fi
+
         if [ $docs_created -gt 0 ]; then
             local end_time=$(date +%s)
             local duration=$((end_time - start_time))