Minor code and comment changes, focus on params

PVP_2.java:
- main: uncommented out parameters and prey/predator initialization
- main: added variable for counting which parameter is being read in,
so it is possible to pick and choose which parameters to use
- main: changed dir to be specified by parameter
- added filename:String as data member and parameter
- suppressed warning about serial
- start: fixed indentation
- start: took code for making clusters out to create its own method,
that is then called when clusters are wanted

Predator:
- step: commented out direction = deltaX + deltaY, and values for
deltaX and deltaY, because value not used
- updated some comments
- step: changed *first == true* to just *first*
- step: renamed Bag result to Bag neighbors
- step: removed the "else" in the last if, as it is unnecessary

Animal:
- initialize: new parameter of filename, with it used to create output
file; call to method in PVP_2 also updated
- removed dir and output file as data members, as they are only used in
initialize
-took some code out of reward method to make adjustRewardProbabilities
and calculateGoalIncrease methods
- commented out if(Math.abs(slope)>48) and added an assert