TerasologyEngine.java refactoring - Work in Progress

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**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.
**WARNING** - This PR is intended to get some early feedback on the broader changes I've done while I work out the things I've broken. It currently generates a number of NullPointerExceptions most likely due to me shifting lines of code around. I'll work them out.

**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