Separated methods into compile and run phase

Hello @nicks,

Builder.js is pretty huge, and I think it'd be nice to eventually separate out some of the compiling and running code. This takes a step in that direction by separating things within the file and adding nice big headings.

Please review the following commits I made in branch 'kyle-code-reorg'.

1edbb72524494cbfdd6228d95c358cf5ea0a9b61 (2013-08-09 15:55:07 -0700)
Separated methods into compile and run phase


R=@nicks