[Bug] Boilerplate is regenerated during updates if deleted

[lkubb]

Specifically, the following paths: src/**/*_mod.py and tests/**/test_*.py.

This is caused by this template abusing skip_if_exists to avoid updates to example code.

Cannot be fixed currently (unless we risk merge conflicts when updating the examples), need to wait for copier-org/copier#1733 (or its alternative) to be merged.

Remember to update the docs when fixing this becomes possible.