Added PDF manual. I had to reorganize a bit the documentation to make
it more linear. In particular, I assigned each of the previously
"dangling" pages as subpage of another one (e.g. DEBUG keyword).
Additionally, I changed a bit the way MD-specific instructions are linked
and added some comment about the PDF manual in the introduction.

The most important change is that I am not using the Layout anymore since
it was difficult to keep it in sync. Now, in the html version, only
the left-side tree is visible, and the tabs disappeared. I don't think
this is a big issue but we might try to solve it.

PDF manual is still a bit buggy: some links are not properly resolved
and images are not shown. I think we can solve these issues later.

Addresses #101

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

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.

Changes to the code are there so that I can reference the atoms
page in the descriptions of keywords that read atom numbers.  I also
changed the input to multicolvar functions.  I stopped using the ARG
keyword in these actions and used DATA instead because you are refering
to the data calculated in a multicolvar as opposed to a scalar quantity
calculated by a particular action.

One can e.g. specify ATOMS=10-1:-3

Closes #45

To be consistent with the paper, plumed is always capital letters.
I also changed 2.0 -> 2 and 1.0 -> 1 for sake of generality

ATOMS=1,4,7,10
can be replaced with
ATOMS=1-10:3

(suggested by Paolo Raieri)

Webpage with modules is not generated if no modules have been installed

having

DISTANCE
ANGLE
etc

which each one being a link you have

DISTANCE    calculate the distance between a pair of atoms
ANGLE       calculate the angle between three atoms
etc

each one of DISTANCE, ANGLE and so on is still a link to the more detailed description

the parts that are contained in the code

I also upgraded the doxygen configuration files to 1.7.4 version