AAPT2: Change how we generate Java classes

Previously we would be writing out the Manifest.java file as we
processed the AndroidManifest.xml. This would lead to empty
Manifest classes if there were no permissions or permission groups
defined in the AndroidManifest.xml.

This would pose problems for processes that checked for public classes
and considered them part of the API (support lib).

Now we collect the structure of the Java class in memory before deciding
if a file should be created.

Change-Id: I6b909f28d74356414c6ef5ad005180d6ea5e44ca