Merge configurable-permissions: add confirm_cpu_jobs, auto_file_upload, keep yolo mode

fixing logs

Add yolo mode for auto-approving tool calls

cleaned comments

Add auto_file_upload and confirm_cpu_jobs config settings

subprocess uploading

session logging

added the explore subagent, quality ok but not perf

prompt update and loading from file

a working mcp integration

intermediary commit

preliminary mcp

minimal impl. of the agent