Re-enable filedeps - it was using a now-gone .expand_files() API.

This maintains a hack with special knowledge of the JvmApp target and
adds one more to deal with ScalaLibrary.java_sources.

Both of these hacks have unit-test coverage to help back up future
refactors away from these hacks.

Testing Done:
$ PANTS_DEV=1 ./pants goal test tests/python/pants_test/:all

CI went green here: https://travis-ci.org/pantsbuild/pants/builds/33652015

Bugs closed: 437, 522

Reviewed at https://rbcommons.com/s/twitter/r/939/