Update docs

This PR update documents in `vignettes/`directory for the current changes:
- update for the new **permute** package interface: remove references to `strata` and explain `permute::how()` instead, remove discussion on adaptive no. of permutations in `anova.cca`, and update `anova.cca()` arguments. This is partial solution to issue #31.
- update document for the move from R-Forge to GitHub.
- update for the split of **vegan3d** package (issue #29).
- remove **svn** specific code `$Date$` and `$Id$`(but something similar would be nice in GitHub).