Renaming, round 2

[ssalinas]

Been working on this one in the background, here is the WIP so far. All should be backwards compatible with deprecations marked. Still TODO:

• Fix all the findbugs issues
• Update endpoints to have an agents option, deprecating the old ones but keeping them active for compatibility
• Update UI request bodies to use agent everywhere now that the backend handles it

Once those are finished off that should cover most of the public facing portion of Singularity, now including the java client as well