add .p and .t test files to examine LnL and trees

this allows us to plot LnL and treespace on the same plot.
option for p.file to mds.single

now we can send a .p file from MrBayes, loaded as a table, to the
mds.single function.

This is only used for making the plot, in which case we can plot the
LnL and the mcmc.sample number on the same plot.

Need to add in a bunch of exceptions for when the .p file isn't there.
Right now there will be issues.
updated mds.plot function to include .p file

we should probably split this function so that we have one for analyses
with .p files, and one without.
add new test
deal with zero distances for MDS

MDS doesn't like zero distances. For RF the smallest non-zero distance
is 1, so it seems sensible to set this to a very small value instead of
zero.