toolchain: do not require (xyz)_domain extents on restarts

[sbryngelson]

Description

(xyz)_domain%beg and (xyz)_domain%end were required whenever m > 0, in every stage. That is wrong twice over:

1. The check ran in the wrong place. It lived in check_parameter_types(), which validate_common() calls, so it fired for simulation and post_process too. x_domain/y_domain/z_domain are pre-process-only parameters (_PRE in params/definitions.py); the other two executables never read them.
2. It ignored restarts. With old_grid = T, pre-process reads the mesh from the existing grid files and sets x_domain%beg/end itself from x_cb (src/pre_process/m_start_up.fpp). The case file must not supply them, which is exactly what the restart instructions in docs/documentation/running.md tell users to do.

The shipped examples/1D_vacuum_restart/restart_case.py fails validation for this reason as well. CI never caught it because the lint job globs examples/*/case.py only, and ./mfc.sh validate reports constraint violations as warnings rather than a nonzero exit.

The requirement moves into a pre-process-only check_domain_extents() that returns early on old_grid = T. It also now covers y and z: only x was checked before, though the grid generator needs the extents of every dimension that has cells.

Closes #1733.

Type of change

• Bug fix

Testing

• ./mfc.sh validate examples/1D_vacuum_restart/restart_case.py passes all three stages (it failed all three before).
• Ran every examples/*/*case*.py through all three stages before and after the change: the only difference is the restart case going from fail to pass. The new y/z requirements break no existing example.
• New unit tests in params_tests/test_integration.py fail before this change and pass after.
• ./mfc.sh format and ./mfc.sh precheck clean; toolchain pytest green.

Checklist

• I added or updated tests for new behavior
• I updated documentation if user-facing behavior changed

The docs already described the intended behavior; this makes the validator agree with them.

[Copilot]

Pull request overview

Updates the Python toolchain case validator so (xyz)_domain%beg/end are only required during pre_process grid generation, and are explicitly not required for restarts (old_grid = T) or for simulation/post_process, aligning validation behavior with restart workflows and parameter staging.

Changes:

• Removed the x_domain%beg/end requirement from check_parameter_types() (which runs for all stages).
• Added a new pre-process-only check_domain_extents() (skips when old_grid = T) and expanded coverage to y/z when n/p > 0.
• Added integration tests covering missing extents, restart behavior, and non-pre-process stages.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
toolchain/mfc/case_validator.py	Moves domain-extent requirements into a pre-process-only check, skips on restarts, and adds y/z coverage; updates physics-doc metadata.
toolchain/mfc/params_tests/test_integration.py	Adds integration tests to prevent regressions for restart and stage-specific domain-extent requirements.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 61.59%. Comparing base (55fb1b1) to head (310f4f2).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #1734   +/-   ##
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  Coverage   61.59%   61.59%           
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  Files          84       84           
  Lines       21493    21493           
  Branches     3176     3176           
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  Hits        13239    13239           
  Misses       6078     6078           
  Partials     2176     2176           

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