Prevent running models when input data is inside output dir

[AdrianDAlessandro]

Description

This PR adds a check to ensure the model input data directory is not inside the output directory. It is quite simple, I am unsure if it is addressing the issue properly.

Fixes #1299

Type of change

• Bug fix (non-breaking change to fix an issue)
• New feature (non-breaking change to add functionality)
• Refactoring (non-breaking, non-functional change to improve maintainability)
• Optimization (non-breaking change to speed up the code)
• Breaking change (whatever its nature)
• Documentation (improve or add documentation)

Key checklist

• All tests pass: $ cargo test
• The documentation builds and looks OK: $ cargo doc
• Update release notes for the latest release if this PR adds a new feature or fixes a bug
  present in the previous release

Further checks

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works

[codecov]

Codecov Report

❌ Patch coverage is 50.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 90.02%. Comparing base (121bad6) to head (55ffab4).

Files with missing lines	Patch %	Lines
src/cli.rs	50.00%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1482      +/-   ##
==========================================
+ Coverage   89.91%   90.02%   +0.10%     
==========================================
  Files          60       60              
  Lines        8556     8558       +2     
  Branches     8556     8558       +2     
==========================================
+ Hits         7693     7704      +11     
+ Misses        543      535       -8     
+ Partials      320      319       -1     

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[Copilot]

Pull request overview

This PR adds a guard to the run CLI flow to prevent running a model when the model input directory is located inside the chosen output directory, reducing the risk of accidentally deleting inputs when overwriting outputs (Issue #1299).

Changes:

• Add an ensure! check in handle_run_command to reject model_path values nested under output_path.
• Add an integration test intended to assert the new failure mode and a helper to capture CLI stderr.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 3 comments.

File	Description
tests/common.rs	Adds a get_muse2_stderr helper for integration tests to inspect failure output.
tests/cli.rs	Adds a new CLI integration test intended to verify run fails when the model directory is inside the output directory.
src/cli.rs	Adds a runtime guard in handle_run_command to prevent using an input directory nested within the output directory.

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[tsmbland]

Looks correct