This is true, but to be honest I was worried that abstracting over the true directory structure might still confuse things anyway.
There are a number of folders which shouldn't really be treated as languages: common, abstract, prelude, scandinavian, romance, etc. These could arguably be hidden and be made to appear only under each language, but I'm not convinced this is the best way forward.
As an alternative, I would rather leave things as they are and then offer a proper explanation of the directory structure. The tool could surely use from a brief user guide anyway.