Added PLMD::molfile namespace

Now all the types and functions declared in the
local version of molfile plugins are properly wrapped
in a namespace.

Possibly fixes #110
Renamed some global function

added "plumed_" prefix to some global functions.
Hopefully fixes #110

I would like @tonigi to have a look at it before merging!
Revert "Renamed some global function"

This reverts commit 69728b725778a2511ca4570b66ea816dba07aca2.
molfile plugins should now be only in their PLMD::molfile namespace
(no C linkage).
voodoo attempt to remove extern from stuff which is not extern
Fixed bug in replica exchange

I fixed a bug occurring when using replicas with different
Hamiltonians (either lamdba dynamics or plumed -hrex branch).
The acceptance was wrong when using a CV that depends on charges
or masses (if charges or masses were changed in the Hamiltonian,
respectively).
changelog
Merge branch 'v2.0' into v2.1
Merge pull request #111 from tonigi/fix-110-tg

No "extern C" in molfile plugins
Merge branch 'fix-110' into v2.1

internal molfile plugins are now contained in PLMD namespace
Merge branch 'v2.1'
NOE and RDC: parallelised
ensemble
ensemble: fix of the fix
Fixed a bug in calculation of MahalanobisDistance
Added new method for constructing functions of multicolvars

Also fixed bug in KernelFunctions
Added version number to manual "Home" button

Fixes #70
Readded a few tabs

I added a few tabs to the html manual:
Getting Started
Tutorials
Index of Actions
Added note on #115
Merge branch 'v2.0' into v2.1