I'm trying to follow your instruction and I've put ext-dev.js instead of ext-debug.js.

I get these errors:
$ sencha create jsb -a index-build.html -p app.jsb3 -v
[E] Failed loading 'src/app/Application.js', please verify that the file exists
[object Object]
Failed loading 'src/app/Application.js', please verify that the file exists
file:////media/Podaci/web/ks/lib/ext-4.0/ext-dev.js : 8712
file:////media/Podaci/web/ks/lib/ext-4.0/ext-dev.js : 8216
file:////media/Podaci/web/ks/lib/ext-4.0/ext-dev.js : 2454
file:////media/Podaci/web/ks/lib/ext-4.0/ext-dev.js : 7943
file:////media/Podaci/web/ks/lib/ext-4.0/ext-dev.js : 7892

This happens with original and with your phantom file so this is caused by ext-dev. Any idea why?

If I use ext-debug I don't see these errors.