Change to version 1.3.  Add ability to calculate distances between trees.
Bug Fixes and crude functions to output in PAML acceptable fomrat
Commit before major change to try to fix memory issue
Major changes: Optimizers now only store node likelihoods on final run.  Added Conjugate Gradient search and test.

Minor Changes: Documentation (including missing GPL notices), parameter throws errow if an attempt is made to set it to an invalid parameter, various consequential throws additions.
Merge develop
1.3 commit (hopefully). Documentation and other minor changes ready for 1.3.
Start of an attempt to reorganise stuff so it's easier to write likelihood calculators that do slightly unusual stuff
Add support for BDIE - hopefully this really will be it for 1.3
Significant changes to allow very different likelihood calculations in the same framework.
Bgein code to deal with small partial likelihoods.
Bug fix found by Ryan (would result in infinite loop type behaviour although I don't think it ever was in one).
Completed changes for small double values
Testing use of small / normal doubles
Mainly small / normal double stuff
Remove Cosntarints stuff for Version 2.0, never been entirely happy with and not sure it's done in the best way
Lots of changes now done for v2.  Committing before trying to remove ArrayMap and seeing how much of a performance hit that causes.
ArrayMap successfully removed.  No noticable loss in speed.
And now all the old commented code associated with ArrayMap is also gone
And now remove ToRealHashMap - nice idea ut overly complicating things for little gain saying as how little it's now used
Changes to allow the use of the method of FitzJohn et al 2009 at the root
Some small tidy up missed previously
More sensibly allow different calculators and some consquential changes (not all of which are great but it's better than what was there).