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.

[makedoc]

[makedoc]

[makedoc]

[makedoc]

[makedoc]

[makedoc]

[makedoc]

I moved there from miscellaneus
- multiple time steps
- openmp

I also added some possible topics
I think in this way it will be easier for users to find what
they want and avoid basic performance regressions