[BioPython] kMeans.py -> Bio.Cluster

[Brad Chapman]

Hi Michiel;

> 1. I have added a Deprecation Warning to the kMeans module and the xkMeans 
> module. Btw, it seems that the import statement in xkMeans.py is no longer 
> valid (from Bio.Clustering import kMeans).
> 2. Below is my attempt at the DEPRECATED doc. Jeff, could you have a look 
> at this to see if there are any mistakes? Thanks!

Thanks for doing this! The deprecated documentation is excellent and
I definitely support the deprecation of xkMeans.py as well. From the
invalid import statement it is likely not it use much and if it
doesn't fit with the new system we might as well let it fall to the
side.

Glad to have things coming together nicely. I think I am going to
push for another release soonish (probably the week after next), so
if there is more work you want to do before then on the clustering
stuff please feel free to go ahead.

Thanks again.
Brad