Move run_shell_command to READ_ONLY_TOOLS and update documentation

ra_aid/__main__.py

@@ -35,12 +35,12 @@ READ_ONLY_TOOLS = [
     delete_key_snippets,
     read_file_tool,
     fuzzy_find_project_files,
-    ripgrep_search
+    ripgrep_search,
+    run_shell_command # can modify files, but we still need it for read-only tasks.
 ]
 
 # Tools that can modify files or system state
 MODIFICATION_TOOLS = [
-    run_shell_command,
     run_programming_task
 ]
 

ra_aid/tools/shell.py

@@ -25,6 +25,7 @@ def run_shell_command(command: str) -> Dict[str, Union[str, int, bool]]:
        - Environment: .env, venv, env
        - IDE: .idea, .vscode
     3. Avoid doing recursive lists, finds, etc. that could be slow and have a ton of output. Likewise, avoid flags like '-l' that needlessly increase the output. But if you really need to, you can.
+    4. Add flags e.g. git --no-pager in order to reduce interaction required by the human.
     """
     # Check if we need approval
     cowboy_mode = _global_memory.get('config', {}).get('cowboy_mode', False)