Add skip_context_files option to AIAgent for batch processing

- Introduced a new parameter `skip_context_files` in the AIAgent class to control the inclusion of context files (SOUL.md, AGENTS.md, .cursorrules) in the system prompt.
- Updated the _process_single_prompt function to set `skip_context_files` to True, preventing pollution of trajectories during batch processing and data generation.

batch_runner.py

@@ -276,6 +276,7 @@ def _process_single_prompt(
             max_tokens=config.get("max_tokens"),
             reasoning_config=config.get("reasoning_config"),
             prefill_messages=config.get("prefill_messages"),
+            skip_context_files=True,  # Don't pollute trajectories with SOUL.md/AGENTS.md
         )
 
         # Run the agent with task_id to ensure each task gets its own isolated VM