I've found myself in the need at work to be able to get all the references a shot had. What you can get with file(q = True, r = True) are only the top level references leaving behind the nested ones.
I've read somewhere that is a good practice trying to avoid such levels of depth, but in this case we were in a closet.
So after a while searching the web and the official Maya python documentation i hit with referenceQuery and the "children" flag.
Finally i developed this simple method that fills a python list with reference filenames:
def add_nested_references(self,parent_ref_list):
for parent_ref in parent_ref_list:
child_list = mc.referenceQuery(parent_ref, f = True, ch = True)
if child_list != None:
self.add_nested_references(child_list)
parent_ref_list.extend(child_list)
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