Change-Id: Ib2bb5042deaabdf452d5be2ad1ce40d739ad8d1b

This includes all internal changes from around May 20 to now.

Java files are moved to un-do the hack in the prevous commit, which
moved the java files to the original position for integration.

Moving the files to their original location, so that opensource changes
can be picked during the internal merge. Those files will be moved into
the correct location after merging with internal code.

Note: do NOT merge this into master without the other internal
down-integration commit.

protobuf/java will become a parent pom that will contain two modules:

core - contains all of the code for the protobuf-java artifact
util - contains all of the code for the protobuf-java-util artifact

Also cleaned up various Maven warnings.