Add config and cli option

[mjademitchell]

Description

Added a copy_input_files option to settings.toml and --no-copy-input-files CLI flag for the run command. When disabled, input files will not be copied to the output folder.

Also updated regenerate_test_data.sh to pass --no-copy-input-files so the test data folder doesn't get cluttered with duplicates of the example model input files.

Fixes #1298

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 37.50000% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.61%. Comparing base (97ffb30) to head (fa04515).

Files with missing lines	Patch %	Lines
src/cli.rs	28.57%	2 Missing and 3 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1303      +/-   ##
==========================================
- Coverage   89.65%   89.61%   -0.04%     
==========================================
  Files          57       57              
  Lines        8441     8447       +6     
  Branches     8441     8447       +6     
==========================================
+ Hits         7568     7570       +2     
- Misses        565      567       +2     
- Partials      308      310       +2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.