Fix issues discovered during testing on Vanilla Ubuntu 14.04.

Some notes:
 - Not all distros ship with Skype and Sublime Text. Ignore errors
   installing those. Later, we'll pull the deb's appropriately from
   somewhere.
 - NetworkManager was an assumed dependency, but was not present
   on testing of Ubuntu 14.04 in a headless environment.
 - Create some directories that we already assumed existed.
 - Pull the submodules from the public GitHub, so authentication
   isn't needed by default.
 - Fix README to include submodule update.