fix JIRA TACHYON-2: Remove warning in mvn package

there are 4 types of warnings:
1. deprecated methods, which is solved by this patch
2. Some input files use unchecked or unsafe operations. I examined all these warnings by compiling with -Xlint:unchecked and find that all these warnings come from tachyon/thrift/*.java which are all auto-generated by thrift, so I didn't do anything to this class of warnings.
3. commons-beanutils-core-1.8.0.jar, commons-beanutils-1.7.0.jar, commons-collections-3.2.1.jar define some overlapping classes, maven has chosen the right class for each dependency, I didn't do anything.
4. "jar will be empty" in Tachyon Project Assemblies and Client. There is no harm that this is empty.