flags are either read from environment or from file

@christi Is there a reason to block ${COMMAND}_FLAGS to pass through the options file? I would like that, but perhaps I am missing some problem that may arise while doing so (related issue copasi/dune-copasi#64 (closed)).

This is so long ago... I guess the reason was that we wanted to avoid bad surprises when an entry in the opts file suddenly overwrites an environment variable.