Little tool that takes a set of taxa which are assumed to have the same value of a given discrete trait, and find the distribution (over a set of trees) of the value that trait had at the most recent node that is an ancestor of all the taxa and had a different value.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6592 ca793f91-a31e-0410-b540-2769d408b6a1
Reverts hack in OrderedLatentLiabilityLikelihood
BUTMP and TBUTMP now index for functions such as getParameter(int) with the same convention as other compound parameters
Implements a caching scheme in MatrixMatrixProduct

git-svn-id: http://beast-mcmc.googlecode.com/svn@6593 ca793f91-a31e-0410-b540-2769d408b6a1
Fixes indexing issue with MMP cache
TBUTMP now fires correct index for parameter changed event.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6594 ca793f91-a31e-0410-b540-2769d408b6a1