Moved xml simulation scripts into single file in root pyQCD directory
Updated readme to reflect changes in run.py script.
Added clauses to prevent saving of configs and propagators in test run.
Removed error catching in run script to allow for verbose xml exceptions.
Reverted to very basic xml file.
Fixed bug in indexing of new links when doing stout smearing.
Fixed bug in saving of configurations and propagators.
Updated smearing operator generation to bring inline with Dirac matrix generation.
Added more simulation examples.