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* Uses build-helper-maven-plugin to add generated sources to the classpath
* Fixes an issue building with newer versions of the maven-compiler-plugin
(See https://issues.apache.org/jira/browse/MCOMPILER-240)
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Java files are moved to un-do the hack in the prevous commit, which
moved the java files to the original position for integration.
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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.
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