Mean and standard deviation of times should be correctly reported now

git-svn-id: http://beast-mcmc.googlecode.com/svn@6582 ca793f91-a31e-0410-b540-2769d408b6a1
parser checks for lengths across partitions now

git-svn-id: http://beast-mcmc.googlecode.com/svn@6583 ca793f91-a31e-0410-b540-2769d408b6a1
Makes transposed parameter functional
Adds a mask to MatrixMatrixProduct and has it draw from a matrix parameter instead of an array.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6584 ca793f91-a31e-0410-b540-2769d408b6a1
print stack trace when catching errors in CLI

git-svn-id: http://beast-mcmc.googlecode.com/svn@6585 ca793f91-a31e-0410-b540-2769d408b6a1
added caching to MatrixMatrixProduct
BUTMP now is indexed in the same way as a matrix parameter: needed to have Compound Parameter send parameters and pindex to lower classes to make that work

git-svn-id: http://beast-mcmc.googlecode.com/svn@6586 ca793f91-a31e-0410-b540-2769d408b6a1
Fixed some bugs with BUTMP and TBUTMP
started chaching LFM
Removed caching from MMP because of errors.

git-svn-id: http://beast-mcmc.googlecode.com/svn@6587 ca793f91-a31e-0410-b540-2769d408b6a1
Added an 2 epoch exponential model

git-svn-id: http://beast-mcmc.googlecode.com/svn@6588 ca793f91-a31e-0410-b540-2769d408b6a1
Removed a problematic import

git-svn-id: http://beast-mcmc.googlecode.com/svn@6589 ca793f91-a31e-0410-b540-2769d408b6a1