Looks like we cannot reproduce this. Please provide another test case to reproduce this issue.
Just do the full name of the object and it won't default to the app folder.
I've been doing this structure since 4.0. I did have to edit the path in 4.2 to go from the index.html location instead of my arch-app.js but that was it.
My directory structure is below:
For Sencha Dev's. My 4.0.7 file structure worked for 4.1 with no changes but in 4.2 I had to make a few changes to make it work correctly. Below is the other thread discussing it.