Refactor applications and update instructions

[gpauloski]

Description

This PR does a run through of all the applications to:

• Refactor and update docstrings for clarity and code health
• Validate dependency installation works
• Test data installation instructions are present and work
• Update the application guide
• Improve logging where needed

This is a breaking change because some application parameter names changed.

Fixes

• Fixes Revise application code and documentation #58

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Refactoring (internal implementation changes)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update (no changes to the code)
• CI change (changes to CI workflows, packages, templates, etc.)
• Version changes (changes to the package or dependency versions)

Testing

Tested all applications.

Pull Request Checklist

Please confirm the PR meets the following requirements.

• Relevant tags are added (breaking, bug, dependencies, documentation, enhancement, refactor).
• Code changes pass pre-commit (e.g., ruff, mypy, etc.).
• Tests have been added to show the fix is effective or that the new feature works.
• New and existing unit tests pass locally with the changes.
• Docs have been updated and reviewed if relevant.