fix langgraph prebuilt dep; remove modification tools from research phase

pyproject.toml

@@ -27,7 +27,8 @@ dependencies = [
     "langchain-google-genai>=2.0.11",
     "langgraph>=0.2.74",
     "langgraph-checkpoint>=2.0.16",
-    "langchain-core>=0.3.39",
+    "langchain-core>=0.3.40",
+    "langgraph-prebuilt>=0.1.0",
     "langchain>=0.3.19",
     "rich>=13.0.0",
     "GitPython>=3.1",

ra_aid/tool_configs.py

@@ -152,7 +152,8 @@ def get_research_tools(
 
     # Add modification tools if not research_only
     if not research_only:
-        tools.extend(MODIFICATION_TOOLS)
+        # For now, we ONLY do modifications after planning.
+        # tools.extend(MODIFICATION_TOOLS)
         tools.append(request_implementation)
 
     # Add expert tools if enabled