clones should not share an env dict

This is similar to #2, but I think more correct.

Previously, cloned commands were sharing a single ._env attribute.
Classes' _clone methods should ensure that there's a copy made of any mutable attributes, and Operation wasn't doing this for its _env dict.

Your conftest.py simply didn't work for me. I think it was written for an old verision of pytest?
The bits of conftest that I deleted didn't seem to have any use.

Let me know if you hate the ancillary changes (Makefile, etc), and I'll take them out, but they made it easier for me to run the tests.