How to run calculations?

Performing calculation;
$ cli.py geometries_energies *.xyz **.xyz
$ . commands.sh
$ cli.py geometries_energies

If we would like to use HF instead of CCSD, after implementing the first command and editing apdft.conf,
$ rm -rf QM/
$ cli.py geometries_energies *.xyz **.xyz
$ . commands.sh
$ cli.py geometries_energies