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

addresses #213

[makedoc]

Notice that as of now it is not fully integrated in the plumed
reference/ module. However, it is possible to compute
ERMSD from a given structure and to use it as a CV