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

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

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.

@maxbonomi check if I did the right thing!

The example given for continuation line was wrong.

@ sign is now used within plumed to specify special groups of
atoms or special colvars whose labels are created by plumed and
not by a user

I removed one page (WhatsNew) and merged it in the changelog page for
2.0

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

Here you can use regex to refer to argument in a list
For example in
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1.[xy]|t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f

(suggested by candrewn@gmail.com)

I added a directory CHANGES where we can add short description
of changes among versions. I use a separate file for each branch
(v2.0.txt now, then we can add v2.1.txt in the master branch)
so that it will allow merging from old branches to new branches
as usual.

This funcitonality allows you to add tutorials written in Doxygen
and links to external websites.  They are called How Tos though

This allows proper documentation to be written.

I added a regtest for INCLUDE but not one for LOAD,
as dynamic loading could not be available

For otherwise uncategorized actions

keyword registering is provided together with a description of how
to create the manual. Also fixed an error in the introduction to the
manual

the parts that are contained in the code

Added full documentation for all directives.
I also made some small fix to manuals

I also upgraded the doxygen configuration files to 1.7.4 version