I am migrating an existing ExtJS 4 (4.1.3) app to use Sencha Cmd (GA).
The app is a single page app and uses a custom structure. I red all the guides for Sencha Cmd and
managed to migrate the app structure and produce a custom build for our app.
This is the test script we use to build all application files (excluding ext files).
sencha compile --classpath=lib/extjs/src,js ^
    --debug=true ^
    exclude -not -namespace Fms and ^
    save AppOnly and ^
    concat build/fms-all-debug.js and ^
    --debug=false ^
    restore AppOnly and ^
    concat -yui build/fms-all.js
This is the filder structure of the app JS folder

- js (folder)
  - app (folder)
    app.js (Ext.application();)
The build runs smoothly without errors, but the result is a bit strange. When I examine the debug build I see that the content of app.js is being placed somewhere in the middle of the build.

this is the result:
...class definitions...


...more class definitions
This causes the app to request all files defined after the 'Ext.application' (I have Ext.Loader turned on for test purposes ).
Is it possible to enforce the file app.js to be appended to the build after the build process ?
I tried excluding the file from the build but then I don't know how to append it afterwards.

Any help is appreciated.