Deprecated defunct

This PR will deprecate, make defunct or remove defunct functions:

*  `commismulator` is deprecated. It is still functional (but issues a warning), although it is replaced with the new `nullmodel` & `commsim`.
*  `metaMDSrotate` is made defunct. It was replaced with `MDSrotate` in **vegan** 2.0-0 and been deprecated since then.
*  `getNumObs` is removed completely. It was first moved to **permute** and deprecated then in **vegan** (2.0-0), and probably gone from **permute** , too.
*  `permuted.index2` was gone with the **permute** package, too. Now it is removed completely.

The PR will change `NAMESPACE` and this may cause conflicts with other open branches which change `NAMESPACE`  (jarioksa/vegan:parallel, guiblanchet/vegan:master). However, the changes are not physically close to each other so that these may pass.