Yea, it would be nice, but if you keep it organized on your end, just trust that C2 will keep it organized inside the application.
Or if you are really OCD, you can load the files via the "Request URL" AJAX instead of using the "Request Project File". Then you can put the files wherever you want on your webserver and load them from there manually.
Or if you don't want to do that, you could try organizing them by file name, like group1-data1.json, group1-data2.json, group1-data1.json, group2-data2.json, etc.