First of all it's a great tool and I wanted to integrate it into my project, though the use case of mine is a little bit different how you prefer to use it. Acutally I wanted to parse only a specific file list within the root directory so ignoring dirs doesn't help.

Reading the codebase I realised that I have another option, namely I can define parsers for patterns which is a cool a feature though it cannot be used for my use case, at least not for now.

Let's assume that we have two JS files within the src folder, and I want to use this pattern:
src/*.js

Currently it does not work as you get the basename from the absolute path of the file.
line 124 in check.js:
const basename = path.basename(filename);
This prevents to use a prefix pattern for the absolute path like mentioned before.

Can you please omit the basename call and pass the filename to the minimatch?

Thank you for fixing this.