added a c function to permute alleles at a locus.

This function will replace the old permutation scheme, which only
worked for diploids and haploids. This will now work for polyploids and
it now almost matches in speed with the mutlilocus style sampler.
changed internal .permut.shuff
Merge branch 'master' into devel
added ploidy argument [ci skip]
Merge branch 'master' into devel