Allow javac to output resources.

As some annotation processors output resources.

This also updates various instant run components to properly detect if
there were changes rather than assuming that if transforms ran that the
changed inputs were interesting.

Test: AutoServiceTest.
Issue: https://issuetracker.google.com/37140464
Change-Id: I614f48cd52e65d35a5d1c188fce9357c37e1208e