Changed SheetRef to SheetSpec
Changed ProjectionRef to ProjectionSpec
Created superclass Specification
Make SheetSpec and ProjectionSpec callable
Cleaned up __str__ of SheetSpec
Various smaller renames
Changed setup() and init() to accept setup_options as a list
Changed call() to accept initialise_options as a list
Use self.message() instead of print()
Use dict specification to set parameters/matchconditions
Use new __init__ method
Use helper function specified in topo/misc/commandline.py