[Feature Request]: .gitignore update

### Do you need to file a feature request?

- [x] I have searched the existing feature request and this feature request is not already filed.
- [x] I believe this is a legitimate feature request, not just a question or bug.

### Feature Request Description

I think .gitignore should have these extra lines:
/deepcode_lab/papers
mcp_agent.secrets.yaml
/logs

### Additional Context

_No response_