Moves the source() stuff from .Rprofile to the analysis template.
Renames the variables.R file and packages.R file.

- Renames R/variables.R to config.R. Because it does not define a
  function, this file is not longer in the R folder.
- Renames R/packages.R to packages.R. This file does (now) define a
  function, but it is deleted as soon as it is run, so there's no
  reason to worry with it. The only file the use needs to source now
  is config.R. It will source and run packages.R AND automagically
  source all .R files in the R folder. How fun!
Alters README.md for the new structure.
Syncs to master.