Files outside this directory are working (source) files.
There shouldn't be any. Neither directories nor files.
If you really need those files, then put them into a directory within your application root, and exclude them from being included in the app using a .pgbomit file.
Your PGB application (index.html and config.xml) should reside in the root of your uploaded package, or in a www/ subdirectory. Any other locations may cause unexpected behaviour.