FIX: Respect exclude option in config file

[danielhollas]

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As explained in #110, the exclude option given via the config file did not work. Here's the fix, a bit of a refactor, and a bunch of new tests.

If this change looks good to you, I would do a bit more refactoring since right now we're needlessly re-parsing the config files for each FORTRAN file, instead of just parsing it once per directory. I didn't want to do it right away to make the initial review easier.

I build this PR on top of #98 since it touched the same code. I am happy to rebase if it gets merged first.

Closes #110.

CC @pseewald

sidenote: Instead of the exclude option, it would be nice to support something like the .gitignore file. For example, ESLint has .eslintignore.

[danielhollas]

@pseewald friendly ping. :blush: LMK if you want me to split this PR into smaller pieces to make it easier to review.

[danielhollas]

@gnikit @awvwgk I've merged in latest master. Would you mind approving the GHA workflow run? Thanks!

[gnikit]

I've approved the run but I won't have time until the end of the year to become familiar with this PR and review changes.