Running jarjar on Java resources.

Before this change, Java resources are added as a separate step
(add-java-resources-to-package) after dex is run, so jarjar isn't run on
the resource files.
With this change, we add Java resources immediately after we call javac,
so jarjar is run on the resource files (the module's own resource, as
well as resources carried by static Java libraries).
When we generate the final apk/jar, we use the jarjar'ed jar as the
inital pacakge file, with class files and empty folders removed.

(cherry-picked from commit 14027470)

Bug: 18837479
Change-Id: I15ecf282bfb65fd53dd03fbd03dd4c71927c186a