renamed main Java class of Cooja from GUI to Cooja.

se.sics.cooja.GUI -> se.sics.cooja.Cooja

this commit does not contain any functional changes, but may require external scripts to be updated
such as Makefiles.
renamed getGUI() method to getCooja(), to better reflect its purpose
Renamed Java packages to match our contiki-os.org domain. Note that this commit does not affect external dependencies
like /tools/mspsim.

This is a very simple modification that affects a very large number of files in Contiki: Cooja,
/platform/cooja, Collect-view, Coffe-manager, and Cooja simulation files (.csc).

I've gone through Contiki to update all references I could find. Nevertheless, this commit will likely
break external dependencies, like saved Cooja simulation files.
Cooja backwards compatibility with simulation files that uses non-Contiki Java package names
Merge pull request #439 from fros4943/feature-contiki-org-refactoring

Cooja cleanup