Update .gitignore: Add logs/, deepcode_lab/papers/, and mcp_agent.sec…

[VinodHatti7019]

Description

This PR addresses issue #43 by adding the following entries to .gitignore:

• logs/ directory for log files
• deepcode_lab/papers/ directory for paper storage
• mcp_agent.secrets.yaml for sensitive configuration

Related Issues

Fixes #43

Changes Made

• Added logs/ to the "Logs / Reports" section
• Added deepcode_lab/papers/ to the "Data & Storage" section
• Created new "Secrets & Config" section and added mcp_agent.secrets.yaml

Checklist

• [x] Changes tested locally
• [x] Code reviewed
• [x] Documentation updated (if necessary)
• [x] Unit tests added (if applicable)

Additional Notes

These additions help keep the repository clean and prevent accidentally committing sensitive data or generated files.