fix(init): 🥅 improve error handling

[djmaxus]

• replace rmdir with remove_directory wrapper function
• improve error handling for late template adoption cases

[Copilot]

Pull Request Overview

This PR improves error handling within the initialization routines and replaces direct calls to rmdir with a new remove_directory wrapper function.

• Replaces rmdir calls with a remove_directory function that wraps the removal process.
• Updates error conditions in functions (reset_file, set_license, reset_cff) to emit warnings instead of errors for better late template adoption handling.

Comments suppressed due to low confidence (2)

init.m:115

• Replacing a fatal error with a warning may lead to silent failures downstream. Consider returning an explicit error status or message so that calling functions can handle the failure appropriately.

warning(['Could not open ', name,' for writing: ',err_msg]); 

init.m:77

• [nitpick] There are TODO comments remaining in the diff. It would be beneficial to either address these comments or create corresponding issues to ensure they are not overlooked in the future.

remove_directory('.github/actions');