reinstated warning on pthreads

don't know why this was removed.
added --kmeans-opt commandline option

which will specify how the kmeans algo actually works
error checking for --kmeans-opt

only '1' works with --raxml (though this might change) in future.
better user output for starting tree
added kmeans_opt to config object

with some basic checking for compatibility with RAxML
pass kmeans_opt to config
error checking on --kmeans-opt

that it's between 1 and 4
pass cfg to get_likelihood_list() in phyml

NB RAxML will now fail, needs to be updated
implement kmeans_opt in phyml.get_likelihood_list()

so we now return different things depending on the user input.
made the small_warning a debug statement

rather than an info statement.