scantwopermhk: implement stratified permutations
scantwopermhk: fixed major problem

 - previously, was using totally independent permutations for each
   chromosome pair. That gave high thresholds

 - now use a common set of permutations, but it means I need to pass
   a copy of a n_ind x n_perm matrix of permutation indices (and then I
   create a third matrix of this size, of the actual permuted phenotypes.

 - BUT it works and it's still considerably faster.