adonis: use permute package
anosim: use permute package
CCorA: use permute package
mantel, mantel.partial: use permute package
mrpp: use permute package
env/factor/vectorfit use permute package
nesteddisc uses permute package

nesteddisc is not a permutation routine at user level, but it tries
to iterate to better solution using permutatios of tied values.
Deprecate permuted index, document GetPermuteMatrix
R CMD check found some real problems

File man/permutations.Rd is outdated: it describes the ancient
vegan permutation scheme with permuted.index(n, strata). Needs to
be rewritten (@gavinsimpson).