feat/cubit: add controls for microstructure meshing

[gknapp1]

Summary

Final stacked PR from the feat/thesis/eol-temp split. This isolates the remaining Cubit-focused work: lower-memory orientation mapping, added meshing controls, and the associated example updates.

Related issues

• No related issues.

Details

This PR adds a serial orientation-mapping mode for vtk_to_exodus_region controlled by --orientation-segment-gb, allowing large cases to trade throughput for reduced peak memory during orientation transfer.

It also adds additional meshing control arguments for Cubit/SPN meshing workflows and extends the behavior tests and parser coverage for those options.

The example updates that depend on those Cubit options are carried here so the final stacked branch preserves the original feature branch behavior while keeping the Deer container support isolated to PR 1.

Included commits:

• 5904ea1 feat(cubit): serialize orientation mapping to reduce memory use
• b7b3e8b feat(cubit): add meshing control arguments

Impact

This changes Cubit workflow behavior by adding new execution-time controls and a lower-memory path for orientation mapping. It should improve operability for larger meshes while preserving the existing workflow for users who do not opt into the new arguments.

Risk level: Medium. The changes are concentrated in one Cubit app, but they affect meshing and orientation-transfer behavior and therefore deserve careful review of the new execution paths.

Architecture/docs: no update needed - this extends an existing Cubit application with additional execution controls without changing subsystem boundaries.

Testing strategy

Commit hooks passed during commit creation.

Covered by focused tests in CI-relevant areas:

• tests/test_cubit_vtk_to_exodus_region_behavior.py
• tests/test_app_argument_parsing.py

Stack context:

• Base branch: stack/thesis
• PR branch: stack/cubit
• Stack position: 3 of 3

Checklist

• Architecture/docs impact considered. Updated ARCHITECTURE.md and/or
  developer docs where needed, or explained why not.