Files That Change Together Should Stick Together
I find it is easier to navigate, understand, and edit a codebase when the files that are edited together are closer together in the file system hierarchy. You have to keep less of the structure in your working memory, and it helps with discovery.
So, I propose this as more of a heuristic than a rule: the more likely files are to be edited together, the closer in the file system hierarchy they should be.
It is not possible to get this perfect.
I recommend grouping files by ‘component’ or ‘feature’ rather than ‘layer’ or ‘technology’. For example, in a model-view-controller style codebase:
Perhaps somebody could put together a tool that scores files based on how far apart they are from files that were changed in the same git commit!