Add python 3.13 support and make it the default

[xylar]

This merge also updates mpas_tools to 0.36.0 and geometric_features to 1.6.0, the latest versions. Thus, it bumps compass to 1.6.0-alpha.2.

Some unused files are removed.

Checklist

• Developer's Guide has been updated
• Document (in a comment titled Testing in this PR) any testing that was used to verify the changes

[altheaden]

@xylar What you have now looks good to me. I think you also want to add 3.13 to the setup.py. There is also a mention of the latest python version in docs/developers_guide/quick_start.rst which you might want to update as well. I also see a mention of 3.12 in the conda/default.cfg but I'm not sure if that is something you'd want to update. I have these changes in a branch right now, so if you'd like I can push any or all of those here.

[altheaden]

@xylar just pushed those changes for you!

[altheaden]

Everything looks good to me now.

[xylar]

I feel like I should run the pr suite on Chrysalis to avoid any surprises now that python 3.13 has become the default.

[altheaden]

Let me know if you'd like me to do any testing as well.

[xylar]

Testing

I ran the pr suite on Chrysalis with Intel and OpenMPI. All tests passed successfully.

[xylar]

@altheaden, thanks for your help debugging and reviewing this!