Stage 1 of fixing R CMD check warnings with current R

Removes tens of  warnings of "no visible definition" for
external packages, but still leaves this one warning:

* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  ‘MASS’ ‘cluster’ ‘rgl’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.

Wording is not clear, but I assume require(MASS) should *not*
be used (like it is done now), but we need MASS::isoMDS().
vegan Depends on R >= 2.15.0: remove hack for R < 2.13.0
forgot to import mgcv::gam
passes more anal tests in modern R

Tested with
R Under development (unstable) (2014-09-01 r66505) -- "Unsuffered Consequences"
explicit mgcv::plot.gam needed in example

-- or perhaps require(mgcv)
change mgcv::plot.gam to library(mgcv);plot.gam
use selective importFrom(MASS, ...)
remove commented out ##require()
missed one ##require and fixed a bug introduced with adding ##
Merge pull request #28 from jarioksa/R-CMD-check-import-fix

R cmd check import fix
update tests/Examples
version up to 2.1-42 after December 2013: prepare for release of 2.2-0
make metaMDSrotate defunct
remove getNumObs (depraceted/defunct from 2.0-0)
add alias to metaMDSrotate (missed in a40f06498a)
remove permuted.index2 (defunct/deprecated for long
deprecate commsimulator
edit NAMESPACE for deprecated & defunct functions

This is a potential source of merge conflicts, because some other
new things can also touch NAMESPACE (ordiconsensus comes first to
my mind).
Merge pull request #30 from jarioksa/deprecated-defunct

Deprecated defunct
Explicit import of s() is needed in not-so-old mgcv

NAMESPACE upgrade (3dc3111, PR #28 in github) broke mgcv < 1.8-0:

Error in eval(expr, envir, enclos) : could not find function "s"
Execution halted

This can be fixed in two ways: adding dependence on mgcv (>= 1.8-0)
in DESCRIPTION, or with explicit import of s in NAMESPACE. mgcv
1.8-0 was released on 25-Jun-2014 so that it is pretty young, and
therefore this fix suggests editing NAMESPACE.