I re-ran EG-MON-1 Step 1 just now, with results at http://groups.geni.net/geni/wiki/GENIRacksHome/ExogeniRacks/AcceptanceTestStatus/EG-MON-1#ResultsofStep1from2012-12-18. Search down for "here are the files that aren't from an RPM" and you'll find a list of files that aren't part of RPMs.
I can't easily tell from Luisa's recent update whether she thinks that a site admin could easily tell where each of those files came from. I couldn't at a glance, although it's possible I could track them down with more research.
Luisa, what do you think? Is the existing documentation adequate here, or is more needed?