fixes for running muon algorithms on upgrade MC

Olli Luptonrequested to merge
olupton_muonreco into master

Changes mentioned in https://indico.cern.ch/event/653430/contributions/2794978/attachments/1560809/2457009/Muons-171117.pdf cc: @rvazquez @pgriffit so these changes don't get forgotten.

Edited by Marco Cattaneo

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