Initial version of tree sampling code. Still some bugs to fix, mainly
relating to the initialisation of substition model variables.
Some refactoring of code.

Tree sampling and scoring of marginal likelihoods for inputted trees now
enabled.
Switched off caching of partial likelihoods since the caches were using
vast amounts of memory.
Merge remote-tracking branch 'origin/tree_sampling'
gradle settings and build file added and a test for CircularArray
Readme updated