(backported from 2.1)

(cherry picked from commit d523213f)

(cherry picked from commit ab117d79)

Conflicts:
	src/vesselbase/ActionWithVessel.cpp

A component called "bias" is needed for replica exchange to work properly

(cherry picked from commit 15823407)

Conflicts:
	src/tools/BiasRepresentation.cpp

(cherry picked from commit 0f81aac6)

(cherry picked from commit 3f296491)

This will allow me to simplify the update of online manual
(before I needed to remove with a scripts the timestamps
a posteriori to avoid too many differences at every update)

(cherry picked from commit 30ff9e3c)

Conflicts:
	src/generic/WholeMolecules.cpp

(cherry picked from commit 650bc4f0)

The Doxyfile was appended instead of being replaced at any
new generation of the doc

(cherry picked from commit 5102dc33)

(cherry picked from commit e5679dad)

If "plumed" executable is not available, sourceme.sh file is sourced

fixed the examples

The example given for continuation line was wrong.

Fixed DUMPATOMS gro file with > 100k atoms.
I do not add any regtest because it would need a very large
trajectory file.

Closes #93

Linux is case sensitive

description of the components

Fix for #91, there were problems when using the keyword SUM
(components were still defined and derivatives were not allocated)
I have also added a keyword CMDIST to calculate the square
distance with respect to a reference map.
This close #90 #91.

Two bugs where there:
1. It was only working with double precision MD codes
2. It was returning energy in PLUMED units and not in MD ones

Both are fixed now