TACHYON-198 Move UserConf usage to use TachyonConf

This PR consist next steps to integrate new configuration work:
-) Remove usage of UserConf
-) Push TachyonConf to Tachyon Hadoop's file system (aka TFS class).
-) Remove UserConf.java from repo.
Not sure what do you mean by majority style? 
The usage of protected are common in the Tachyon code base and unless we have common style guide on not use protected I would say to punt the change to different PR.