Cleaning
Cleaning deprecated code

Merge remote-tracking branch 'origin' into PDP

Conflicts:
	DeprecatedToolBox/CatalystProjector.py
	DeprecatedToolBox/GraphHandler.py
	DeprecatedToolBox/MetricHandler.py
	DeprecatedToolBox/SubstrateProjector.py
	DeprecatedToolBox/tulipDumpsJSON.py