Same as 55bc92d2
(written by Carlo), but in such a way that it results as a git mv

(will be reintroduced with next commit)

(cherry picked from commit 650bc4f0)

I am not 100% sure this will make it reproducible on different machines
(maybe we are trying to fight Lyapunov). Anyway, for sure this
test was not reset after commit 77aa3cd9
and this was a mistake

Conflicts:
	VERSION

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.