[MERGE, 162931, 165071] Fix check to not report spurious unreferenced ancestors.

[John Arbash Meinel]

John Arbash Meinel has voted approve.
Status is now: Approved
Comment:
Is Repository.check meant to check all versions of all files? (I'm 
guessing it is) in which case this is the correct fix.
Some of the code looks like it might check just a subset of the 
revisions.

For details, see: 
http://bundlebuggy.aaronbentley.com/request/%3C1196200820.32300.274.camel%40lifeless-64%3E