Don't overwrite existing files in `make_level.py`

If you start with `setup.spec` and `test.spec` but then want templates for the rest of the files and for `__init__.py`s and `setup.py`, right now `make_level.py` overwrites `setup.spec` and `test.spec`. We should avoid that and some other things.

This applies to
- `skills/skill/__init__.py`
- `skills/skill/_level/xyz`

Start by locating and reading make_level.py, then inspect the existing files under skills/skill/__init__.py and skills/skill/_level/xyz. Reproduce the case with existing setup.spec and test.spec files, and verify that generation leaves them unchanged while still creating the requested missing templates and files.

Written by the indexing model from the issue text.