Resolve "Create __init__ files"

Description

• Splits out Package wrapper generation and Module wrapper generation. Package wrappers will be run once per package while module wrappers will be run once per module per package.
• Adds the generation of init files if they don't already exist. If there is an existing init.py file, then this will never be overridden (even if force=True is set). The init file is empty except for a comment, but the purpose is to ensure that the python directory is always a valid package.

This relies on all python files for a package living in the same directory (the current assumption when running via the CLI). If this assumption changes then this requires some rework.

A bit of a sidetrack, but it was useful to play with the new templating engine.

Checklist

Please confirm that this pull request has done the following:

• Tests added
• Documentation added (where applicable)
• Changelog item added to changelog/

Closes #3 (closed)