When using multiple configuration files the work directory isn't initialize correctly

[rosswhitfield]

If you do something like ips.py -config=sim1.cfg,sim2.cfg ... the working directory is created for each config according to their SIM_ROOT but input files for both configurations are always copied to the first working directory only.

This test shows the bug, as these lines should be able to be removed

IPS-framework/tests/multirun/test_basic_serial.py

Lines 137 to 139 in 119dafa

	# This should also work for 2
	if no == "2":
	continue

[elwasif]

@rosswhitfield should this issue be closed now?