Fixed arbitrary phase in MDS

I added a few lines to set to a predictably value the
arbitrary phase in the eigenvectors used for MDS.
This should make the runs more reproducible.
Fixed error in gyration manual
Fixed error in gyration manual

(cherry picked from commit 650bc4f0c5b69ee7054cea263f7cd9edd50ef924)
Merge branch 'v2.0' into v2.1
patch: gmx466
Merge branch 'v2.1' of github.com:plumed/plumed2 into v2.1
Removed patch for gmx 4.6.6

(will be reintroduced with next commit)
GMX 4.6.6

Same as 55bc92d23815396bf612c5b8087528a37ec655bb
(written by Carlo), but in such a way that it results as a git mv
Forgot to remove this
changelog
WHOLEMOL: fix example
WHOLEMOL: fix example

(cherry picked from commit 30ff9e3cf4fc2f60b846e6dc4e78182885e6fb3b)

Conflicts:
	src/generic/WholeMolecules.cpp
Merge branch 'v2.0' into v2.1

Conflicts:
	src/generic/WholeMolecules.cpp
Fix arbitrary phase in eigenvectors in diagMat

As suggested by Gareth, I moved the fix in arbitrary phase from
ClassicalMDS to diagMat
Fixed regtest after last commit
Merge branch 'fix-mds' into v2.1
Merge branch 'v2.1'