See #678

I add back a single change that was in d38b951a
and that, based on an exchange of mail with @gtribello, should be the
relevant one

Revert "Fixed bug in manual building that meant parallel plumed inputs were not being processed correctly."

This reverts commit d38b951a.

@gtribello it looks that parallel tests are not correct now.
I try to revert this to see if this is the problem

(cherry picked from commit 66363a3f)