Include Apex classes regardless of folder
In GitHub, Apex classes don't always have to be in a folder called "classes " to work with them. Some people using SFDX put test classes in their own folder (sometimes called "tests". Even Apex classes within the "classes" folder can be sub-grouped into folders. (Example at https://github.com/trailheadapps/apex-recipes/tree/main/force-app/main/default/classes)
I'd like Gearset to scan the entire repository and to group metadata by its actual type, not by the folder it is in.
I'm not talking about the sfdx-project.json saying where the metadata is located. This is within each of those locations, it should find all Apex (for example). The Apex Recipes repo is a great example of that.
David Schach commented
Following up: Many users put all test classes into a separate folder force-app/main/default/tests and SFDX still recognizes them as Apex for that project. New classes are still saved to the default folder, but can be moved.
Please find Apex wherever it is and include it in the comparison.