Update pyrcmip tooling to work with the new phase of RCMIP (RCMIP3)

This PR is updating the pyrcmip tooling to support the new round of RCMIP (starting 2025). The changes include:

Enhanced features:
- The upload command now automatically converts the submission into scenario-specific netCDF files before uploading.
- Users can optionally point to a comments CSV file to include comments along with their submission.
- New command to convert netcdf files (as produced in this tooling) back to scenario-specific CSV files.

Other changes:

The tooling now points at a different endpoint to upload/download submission files. (NIRD, rather than AWS)
Fixed tests to work with updated dependencies, new functionality and new protocol.
Enhance testing suite to cover the new functionality
Update docs to reflect the new functionality and desired user workflow.