Finish migrating to `pathtype` library.

[patrickt]

The migration to pathtype has been overall a pleasant one—it makes functions much more indicative of their purpose, and it’s caught some bugs (though not serious ones). Right now we’re an uneasy hybrid of pathtype solutions and FilePath; we should move off of the latter completely. This involves overhauling Semantic.CLI to use pathtype; the documentation provides a recipe to make optparse-applicative parsers do the right thing (respecting the path semantics; i.e., if we tell a parser to expect an absolute path, the parser will fail unless said path is actually absolute.)