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I like the idea of having the config for a directory being able to provide "better defaults" for the tool, rather than always having that bound to the command-line invocation.
This allows for contextually "sensible" results when invoking glyptodont in a directory.
The changes here are bigger than I would have liked (extracting the Checker class) but I think that was neater than trying to graft the logic into the Glyptodont module directly (especially when trying to make the changes testable).