Remove some of the third party dependencies from the core build.

<!--<module>com.google.common</module>--><!-- Moved to third party repository -->
<!--<module>com.google.inject</module>--><!-- Available in Orbit repository  -->
<!--<module>com.google.inject.guice.v3</module>--><!-- Moved to third party repository -->
<!--<module>com.google.protobuf</module>--><!-- Available in Orbit repository  -->
<!--<module>com.mysql.jdbc</module>--><!-- Moved to third party repository -->
<!--<module>commons-beanutils.v1.8.0</module>--><!-- Moved to third party repository -->
<!--<module>edu.msu.nscl.olog.api</module>--><!-- Moved to third party repository -->
<!--<module>gov.bnl.channelfinder.api</module>--><!-- Moved to third party repository -->
<!--<module>gov.bnl.unitconversion</module>--><!-- Moved to third party repository -->
<!--<module>javax.annotation</module>--><!-- Moved to third party repository -->
<!--<module>net.coobird.thumbnailator</module>--><!-- Moved to third party repository -->
<!--<module>org.apache.jackrabbit</module>--><!-- Moved to third party repository -->
<!--<module>org.antlr.runtime</module>--><!-- Moved to third party repository  -->