addresses #228

Allow passing a single trajectory to driver --multi.
The same logic is implemented as in IFile tool, that is:
- look for file.##.ext
- if it does not exist, look for file.ext

Here ## is the replica index and .ext the extension of the file

Fixed #228

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I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile

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

I added a primitive syntax highlighter for plumed examples.
It links to manual as well.

Addresses #226

Addresses #226

[ci no]

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MOLTYPE is actually not needed in practice.

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