Ok, I had a look. A few comments/questions -

First, it's making me seriously consider using sourceforge cvs to manage
the Refactoring Browser code.

Second, something a bit funny - I filed out the RB, compared, and while
it was processing, I remembered I hadn't changed anything. Then when I
came back, it had found differences. Interesting...

Third, your two rules of when to filein/out sound very simple to enforce
in code, using OSProcess.

Fourth, I didn't understand the critical scene, where Alice integrates
her change with Bobs fix. Alice tries to commit her code, get notified.
She updates. At this point -
* does cvs replace her file with Bobs? does it create a merged version? 
* What happens if she updates before filing out her changes?
* Why would she want to reconcile differences with a text editor - isn't
that what DVS is good at? (show the difference, user edits, file in a
hand picked modified change set)

Daniel Vainsencher