permutest.betadisper: no. of permutations counted without observed stat

Although we put the observed value among permutations, the number
of permutations should be given without that observed statistic
(like done in all other vegan functions).
remove scoverage()

If this function is resurrected, it should be documented independently
and not with the decostand.
Merge pull request #50 from jarioksa/revert-scoverage

remove scoverage()
update tests/Examples
downplay scores.hclust: combine help into reorder.hclust

I considered dropping scores.hclust as it is pretty complicated
to use: you need to know how the internal nodes are ordered. However,
I have some uses for this small function and still let it be here
(but it still at vulnerable status).
update tests/Examples
Merge pull request #45 from jarioksa/fix-no-of-permutations-in-permutest.beadisper

@jarioksa has convinced me of the benefits of treating permutations following Phipson, B. & Smyth, G. K. Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. Stat. Appl. Genet. Mol. Biol. 9, Article39 (2010). permutest.betadisper: no. of permutations counted without observed stat
Update test example output
allow missing 'strata' in permutations

getPermuteMatrix used 'strata=NULL' to define there are no
strata. Vegan functions were adopted to this, but this broke
CRAN packages cocorresp and mpmcorrelogram. The fix was so simple
and obvious that it is almost annoying.
Do not yet warn on commsimulator deprecation

We do not yet warn on commsimulator deprecation in vegan 2.2-0
but only in the next release to give other packages time to
adapt. There were thousands of warnings in CRAN packages
bipartite and metacom.
Merge pull request #51 from jarioksa/remove-u.eig-etc

Remove u.eig etc