Use permute pkg

Closes most of the issues (but not all) raised in #31: this issue discusses details and remaining issues. There really are some remaining issues, but the branch was growing too big: it is now 20 commits long and changes 33 files.
This one doesn't seem to check the ncols of permutations matches nrows of data. `anosim()` and `CCorA()` do for example, or at least they replicate this code for a check. Thinking on this, could this check not be folded into `GetPermuteMatrix()`?