Boilerplate management refactor

[oscarlevin]

We have been regenerating all boilerplate on every instance, and management of what files are generated is manual (the user must remove the magic comment).

With this PR:

• Boilerplate resources are only checked on pretext update or pretext new or pretext init
• The magic comments will still work, but the new files will contain a comment specifying which version of pretext was used to generate the file.
• For files with the version used to generate them listed in the comment, the file will be compared to the hash of the stock file. If they are different, we will assume the file is no longer managed.
• If a project is not a git repository, none of the git-specific boilerplate files will be generated or managed.

The PR also includes some refactoring of the entry main cli command. pretext upgrade no longer checks for a project, and pretext new runs without a warning that the default project.ptx is being used.