Refactored the build inside Setup.hs and the various Makefiles.

* Refactored the Setup.hs script into a much simpler layout.
* Simplified the idris.cabal file, alphabetizing the modules,
  build dependencies, simplifying the indentation, standardizing the
  flags, and normalizing the formatting of lists.
* Fixed a bug in the generation of the executable_pom.xml file for
  the Java backend.
Reverting the change to the POM template and removing the templating/clenup logic for the Java backend.
Merge pull request #498 from gabemc/build-changes

Refactored the build inside Setup.hs and the various Makefiles.