Moved runs into their own dirs to correspond with changes in qe-test.py

As of maxhutch/qe-tools@93e5d43e07150c3ad1dfb2e2f8f16896c9c4b733,
runs are expected to be in their own dirs.  They can share the
same pseudo directory to reduce PP storage costs.

Also removed differences from Gr-hex.test and Gr-hex.ref