FIX: Run reset and clean after checkout (#500)

FIX: Run reset and clean after checkout (#500)

shallow fetching and resetting may result in a dirty working tree.
Ensure we have a clean working tree by running the reset and clean after the
fetch.

Previously, we needed the clean and reset before the PULL, to ensure a clean
pull, but since we are using fetch + checkout (which does not result in a
merge if dirty) we might end up with a dirty repo after the checkout, such
as if a clone remote has a different master branch than core.