Fix pile-up modules reconfiguration (CMSSW_7_4_X)

The following issues discussed in https://indico.cern.ch/event/344151/session/4/contribution/10/material/slides/0.pdf are addressed:

- clone pile-up modules rather then re-configure them for use after RECO;
- clone isolation modules rather than re-configure them in miniAOD;
- resolve naming circle around top tagger in miniAOD.

Forward port of #6522 to CMSSW_7_4_X. Merging directly since the former is fully approved.