Changed the internal enum in switching function (for clarity)

This addresses #43

This is to avoid false errors in regtest

Coordination is now faster by approx 15% when using even
NN, even MM and d0=0

Closes #43.

Conflicts:
	src/core/CLToolMain.cpp

This allows them to be automatically skipped when molfile has
not been linked

This minimizes the difference between code with __HAS_MOLFILE
and code without it

Conflicts:
	patches/patch.sh

(cherry picked from commit e1d01e84)

Allows to avoid verbose logging. The option is now used in user-doc/extract
to simplify the generation of code-specific notes

(cherry picked from commit 7152d46f)

Conflicts:
	patches/patch.sh

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual

(cherry picked from commit a273bb84)

Allows to avoid verbose logging. The option is now used in user-doc/extract
to simplify the generation of code-specific notes

@ sign is now used within plumed to specify special groups of
atoms or special colvars whose labels are created by plumed and
not by a user

This allows one to create information on the differences in
the various patching procedures by executing:

plumed patch -i

This information is also put into the online manual