Add steps and tasks for culling topography

[xylar]

This merge adds e3sm/init/<mesh>/topo/cull tasks for each supported base mesh, and associated steps for masking and then culling the base meshes to land and ocean regions (the latter with and without Antarctic ice-shelf cavities). A config option also allows a user to retain the grounded ice below Antarctica as part of the ocean domain (a need for future work on MALI coupling to MPAS-Ocean in the FAnSSIE project).

This work requires a bug fix in mpas_tools 1.2.2 (which requires updating polaris to v0.8.0-alpha.3) that fixes writing CDF5 format files with logging enabled.

The documentation has been reorganized to break out into separate documents the descriptions or combining and remapping topography, and then culling the base mesh based on this topography.

This merge also fixes a few issues discovered with e3sm/init/<mesh>/topo/remap tasks and steps discovered in this development.

Checklist

• Developer's Guide has been updated
• API documentation in the Developer's Guide (api.md) has any new or modified class, method and/or functions listed
• Documentation has been built locally and changes look as expected
• Testing comment in the PR documents testing used to verify the changes
• New tests have been added to a test suite

[xylar]

Testing

I successfully ran all the topo/cull tasks on Chrysalis:

/lcrc/group/e3sm/ac.xylar/polaris_0.8/chrysalis/test_20250616/cull-topo-all

I looked over the masks for the Icos30km mesh in detail to make sure things looked as expected (see the image in the documentation and shared again below showing the ocean with land cells culled out).

[xylar]

@sbrus89, is this something you would have time to review?

[xylar]

@sbrus89, let's chat about this one today if there's time. I'd ideally like to get it in soon.

[xylar]

I rebased and reran all tests successfully on Chrysalis. I wasn't able to get a review so I'm going to merge. I think that's fine, we can address any issues that turn up in future work.