I added several examples with plumedfile, so I only
push this on master branch.

I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile

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

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

clang -Wextra-semi

If you want to but a plumed_assert in a loop you should now use
plumed_dbg_assert / plumed_dbg_massert.  This will not be included
in the code if you compile with -DNDEBUG

To do this I needed a small fix on Atoms so as to
allow external actions to modify atom positions