Update naming for clarity

[streeve]

I would suggest a few name changes:

1. uq_workflow -> AM-Bench_2018/UQ_workflow (could also add a single small case in AM-Bench_2018/example/
2. Stage1/3 -> 1_Process/2_Structure/3_Properties (or similar - mostly I don't think it's useful to keep the ExaAM nomenclature)

Potentially others..