diff --git a/agent/tool_use_cleanup_middleware.py b/agent/tool_use_cleanup_middleware.py
index 83fb733..5758f52 100644
--- a/agent/tool_use_cleanup_middleware.py
+++ b/agent/tool_use_cleanup_middleware.py
@@ -66,6 +66,45 @@ class ToolUseCleanupMiddleware(AgentMiddleware):
             # Other types, treat as having content if it's truthy
             return bool(content)
 
+    def _clean_content_blocks(self, content: Any, valid_tool_call_ids: set[str]) -> tuple[Any, bool]:
+        """
+        Clean up content blocks by removing orphaned tool_use blocks.
+
+        Args:
+            content: The content to clean (can be str, list, or other)
+            valid_tool_call_ids: Set of valid tool_call_ids to keep
+
+        Returns:
+            Tuple of (cleaned_content, has_meaningful_content)
+        """
+        if isinstance(content, str):
+            return content, bool(content.strip())
+        elif isinstance(content, list):
+            # Filter out tool_use blocks that don't have valid ids
+            cleaned_blocks = []
+            has_text_content = False
+
+            for block in content:
+                if isinstance(block, dict):
+                    block_type = block.get('type')
+                    if block_type == 'tool_use':
+                        # Only keep tool_use blocks with valid ids
+                        tool_id = block.get('id')
+                        if tool_id in valid_tool_call_ids:
+                            cleaned_blocks.append(block)
+                    elif block_type == 'text' and block.get('text', '').strip():
+                        cleaned_blocks.append(block)
+                        has_text_content = True
+                    else:
+                        # Keep other block types (images, etc.)
+                        cleaned_blocks.append(block)
+                else:
+                    cleaned_blocks.append(block)
+
+            return cleaned_blocks, has_text_content
+        else:
+            return content, bool(content)
+
     def _cleanup_tool_use_messages(self, messages: list[AnyMessage]) -> list[AnyMessage]:
         """
         Clean up messages by removing tool_use blocks that don't have corresponding tool_results.
@@ -98,21 +137,25 @@ class ToolUseCleanupMiddleware(AgentMiddleware):
                 ]
 
                 removed_count = len(current_msg.tool_calls) - len(filtered_tool_calls)
+                removed_ids = [tc.get('id') for tc in current_msg.tool_calls if tc.get('id') not in valid_tool_call_ids]
 
                 if removed_count > 0:
                     self.stats['removed_tool_calls'] += removed_count
                     logger.warning(
                         f"Removed {removed_count} orphaned tool_use(s) from AIMessage. "
-                        f"tool_call_ids: {[tc.get('id') for tc in current_msg.tool_calls]}, "
+                        f"tool_call_ids: {removed_ids}, "
                         f"valid_ids: {valid_tool_call_ids}"
                     )
 
-                has_content = self._has_meaningful_content(current_msg)
+                # Clean content blocks to remove orphaned tool_use blocks
+                cleaned_content, has_meaningful_content = self._clean_content_blocks(
+                    current_msg.content, valid_tool_call_ids
+                )
 
                 if filtered_tool_calls:
                     # Has valid tool_calls, keep the message
                     cleaned_msg = AIMessage(
-                        content=current_msg.content,
+                        content=cleaned_content,
                         tool_calls=filtered_tool_calls,
                         additional_kwargs=current_msg.additional_kwargs,
                         response_metadata=current_msg.response_metadata,
@@ -120,10 +163,10 @@ class ToolUseCleanupMiddleware(AgentMiddleware):
                         name=current_msg.name,
                     )
                     cleaned_messages.append(cleaned_msg)
-                elif has_content:
+                elif has_meaningful_content:
                     # No valid tool_calls but has meaningful content, keep without tool_calls
                     cleaned_msg = AIMessage(
-                        content=current_msg.content,
+                        content=cleaned_content,
                         tool_calls=[],
                         additional_kwargs=current_msg.additional_kwargs,
                         response_metadata=current_msg.response_metadata,
@@ -134,14 +177,14 @@ class ToolUseCleanupMiddleware(AgentMiddleware):
                     self.stats['cleaned_ai_messages'] += 1
                     logger.info(
                         f"Removed all tool_calls from AIMessage but kept content. "
-                        f"Content preview: {current_msg.content[:50]}..."
+                        f"Content preview: {str(cleaned_content)[:200]}..."
                     )
                 else:
                     # No valid tool_calls and no meaningful content, completely remove this message
                     self.stats['removed_ai_messages'] += 1
                     logger.info(
                         f"Removed entire AIMessage with orphaned tool_calls (no meaningful content). "
-                        f"Removed tool_call_ids: {[tc.get('id') for tc in current_msg.tool_calls]}"
+                        f"Removed tool_call_ids: {removed_ids}"
                     )
                     # Don't add to cleaned_messages - skip this message entirely
             else:
diff --git a/mcp/mcp_settings_deep_agent.json b/mcp/mcp_settings_deep_agent.json
new file mode 100644
index 0000000..ddf9962
--- /dev/null
+++ b/mcp/mcp_settings_deep_agent.json
@@ -0,0 +1,14 @@
+[
+  {
+    "mcpServers": {
+      "rag_retrieve": {
+        "transport": "stdio",
+        "command": "python",
+        "args": [
+          "./mcp/rag_retrieve_server.py",
+          "{bot_id}"
+        ]
+      }
+    }
+  }
+]