Configurable directory minification? (or, identify whether .min.js is from folder or file...)

[incredibleweirdo]

In my project - an AngularJS SPA - I have it structured like so:

app/
 -- controllers/
 -- directives/
 -- factories/
 -- app.module.js
 -- controllers.js
 -- directives.js
 -- factories.js
scripts/  -- angularjs, other libraries here

I am not minifying the directories, only the individual files - including the 4 .js files in the top of the app folder. The issue is when I add or modify a file within any of the three directories inside of app/, the directories get minified automatically and are overwriting the minified versions of the controllers.js, directives.js, and factories.js files.
I can work around this by renaming the files or folders so their names no longer match, but my preference would be to just disable directory minification. Or for the extension to be aware that the minified file was from either a directory or a file.