TerasologyEngine, added javadocs and a few more minor changes

* added a number of class/method-level javadocs
* added a few comments
* renamed a few variables and one method
* moved three small instantiations to the head of the mainLoop() method and out of the main loop proper

This PR mostly salvages javadocs and a few additional minor changes from PR #1108. I left out javadocs for private methods (with a couple of exception) as they were recommended against by Immortius. 

I left out some reordering of methods that was done in PR #1108 as together with the suggested changes it would probably make the diff much harder to read . I plan to replicate that reordering (i.e. placing all state handling methods together and doing the same with life-cycle and accessor methods) in a reordering-specific PR.