you really should try to use Sencha Cmd, it reduces your app size and the number of files significantly.
However, If for some reason you don't want to use it, then it is safe to delete the build folder and the build.xml file.
If you are using ExtJS classic then you should keep the classic folder, otherwise delete it. The same goes for the modern folder.
You can also delete the cmd and examples folder.
You won't need the LICENSE file and the licenses folder, however, you should keep it for legal reasons.
Also, delete the Readme, release-notes, templates, sass and welcome files and folders.
You won't need those if you are not using Sencha Cmd, but then again, I advise you to use it, it does a lot better job at creating a nice and clean build of your app.