Fixed automatic backbone detection for secondary structure variables

The nature of the backbone is now specified by a class called MolDataClass.
A warning is given about GLY residues
Added functionality to read torsions for proteins using psi-4 or phi-6
METAD: added the possibility to calculate on the fly the acceleration
factor as proposed in Tiwary and Parrinello, PRL (in press)
Modified manual so that the online version is clearer
Reference to published paper

Plumed paper has now a volume and page
Merge branch 'v2.0'
Moved mpi gather of taskList from prepare to calculate.

This addresses bug #51.  I think there can potentially be problems
if you call mpi functions from prepare I don't fully understand why
perhaps @GiovanniBussi has some understanding.
Merge branch 'master' of github.com:plumed/plumed2
Changed Dependencies from set to vector

This makes it such the order in which dependencies are activated
is deterministic. It is related to a bug (#51) which was already fixed
by changing the way prepare() works in multicolvar. Anyway, I commit
this change because I think it is clearer if, in a multiple proc simulation,
all the procs prepare all the actions in the very same order.
Merge branch 'checking-51'
changelog
Improved doc

I removed one page (WhatsNew) and merged it in the changelog page for
2.0
Improved doc for DISTANCE
Improved doc for ANGLE
Merge branch 'v2.0'

Conflicts:
	user-doc/Intro.txt
Merge remote-tracking branch 'origin/master'
Added source code from crystallization to main trunk of plumed

The source code from crystallization allows you to calculate
Q4 and Q6 parameters.  You can also calculate local Q4 and local
Q6 parameters and you create compound collective variables based
on the relative orientations of internal vectors in adjacent molecules.

Regtests for this functionality are reasonably thorough.  Manual is
not so great as yet
Merge branch 'master' into fix-molinfo
Added colvar that measures dihedral correlation
Added regtests for dihedral correlation