I renamed all files from .txt to .md so that they can be
visualized on github.

In addition, I renamed all files to have a name consistent with the content.
This makes manual portions easier to find.

Notice that I left the original labels (e.g. "Syntax" instead of "Getting Started")
not to break direct links to manual, though I think we should rationalize these names
as well.

[makedoc]

I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile

in (hopefully) all the places where it was appropriate.

(backported from 2.1)

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.

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