(backported from v2.5)

no actual change

It should prepend the libplumed.so library with prefix -Wl,
so as not to disturb NAMD makefile. (suggested by @jcphill)

see #227

Thanks @hanatok!

it includes an additional modification to keep multisim in sync when using plumed

When doing plumed patch -e gromacs2016.5 a match with e.g. gromacs2016.4
will be accepted (and issue a WARNING). Useful for automatized patching
procedures.

For instance, in gromacs-plumed package of MacPorts it won't be necessary
to synchronize the Portfile with the exact plumed version.

Fixes #330

Plumed.cmake is now treated as Plumed.inc

cc: @ralf-meyer

When a single replica is present, do not add replica suffix

When using extra arguments after the name of the log file,
the former could have been overwritten by reeplica suffix.

Bug reported by Marco De La Pierre.