There are now fewer warnings when Doxygen runs

I split up the section on the input syntax and rewrote the introductions
to plumed and to collective variables in general

Array elements weren't necessarily assigned when this is
run in parallel

This commit resolves issue #97  However, I also changed the layout of
the colvar page on the manual so I thought I would push it on a branch
before merging it into master.  Let me know if there are any objections
to the changes I have made.

It is possible to use
DISTANCE SCALED_COMPONENTS
to get components with the correct (-0.5,+0.5) periodicity

Fixed #63

I added the possibility to pass kbT from gromacs to plumed.
To allow compatibility between old and new versions, I used the API
number. Namely: gromacs checks that plumed API>1; if so, pass the
temperature.

KbT is only used in METAD so far (not in HISTOGRAM)

Addresses #35

this solution should be more general