TerasologyEngine.java refactoring - Work in Progress

**WARNING** - This PR is not intended for Merging. When the issues have all been worked out I'll produce a cleaned up Merge Candidate PR.

**CHANGES:**
- added a class-level javadoc
- rearranged methods in logical sections (see class-level javadoc)
- refactored init() by adding a number of support methods, to read more like a short index.
- added javadoc to constructor and a number of other non-trivial methods
- added a number of TODOs and questions
- renamed a few support methods and variables to improve readability
- moved a few variable declarations out of the main loop

I wonder if this is appropriate or I should perhaps remove it, leaving to any reference holder to check weather the engine is in a state compatible to the holder's workings.