More bug fixes

git-svn-id: http://beast-mcmc.googlecode.com/svn@6578 ca793f91-a31e-0410-b540-2769d408b6a1
implement gibbs OP interface

git-svn-id: http://beast-mcmc.googlecode.com/svn@6579 ca793f91-a31e-0410-b540-2769d408b6a1
Fixed issue with different code needed to initialise spatial kernels in Java 6 vs 7.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6580 ca793f91-a31e-0410-b540-2769d408b6a1
Tool to convert a tree file with branches annotated with Markov jump timings to a file where each jump is a degree two node correctly annotated with the discrete trait.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6581 ca793f91-a31e-0410-b540-2769d408b6a1