feat: adding .xml extension to models

[Azzedde]

Summary

This PR ensures SBML model files are saved with .xml extension to clearly indicate their format and improve file type recognition.

Changes

• Modified _makeModelSource() in model.py to automatically add .xml extension for SBML model files (types: SBML_FILE, SBML_STR, SBML_URL)
• Maintained backward compatibility with existing model references
• Updated docstring to clearly document the new behavior

Motivation

Closes #6 - Model files should have the extension "xml". This change:

• Makes file types immediately recognizable
• Follows standard conventions for SBML/XML files
• Improves compatibility with tools that expect XML extensions

How to test

1. Create SBML models using different reference types (file, string, URL)
2. Verify saved files have .xml extension
3. Check that existing model loading still works
4. Test with both new and existing model files

Risks & considerations

• Any code that assumes model files don't have extensions may need updates
• The change only affects SBML files - Antimony files still use no extension
• Existing model files without extensions will still work due to backward compatibility

Additional information

The implementation preserves all existing functionality while adding the extension for better file type identification. The change is minimal and focused only on the file saving logic.