Merge remote-tracking branch 'origin/master'

regtest/basic/rt-make-extracv/COLVARX.reference

regtest/basic/rt-make-extracv/Makefile

regtest/basic/rt-make-extracv/config

regtest/basic/rt-make-extracv/main.cpp

regtest/basic/rt-make-extracv/output.reference

regtest/basic/rt-make-extracv/plumed.dat

src/colvar/ExtraCV.cpp

src/core/ActionAtomistic.cpp

src/core/ActionAtomistic.h

src/core/Atoms.cpp

src/core/Atoms.h

src/core/Colvar.cpp

src/core/Colvar.h

src/core/MDAtoms.cpp

src/core/MDAtoms.h

src/core/PlumedMain.cpp

user-doc/Miscelaneous.md