According to a joint press release by the Cubs and Red Sox Friday night, Theo Epstein has resigned as Boston's general manager and will be introduced as the new President of Baseball Operations in Chicago on Tuesday. The Red Sox' new GM--by all accounts Ben Cherington--will be introduced at the same time in Boston.
The upshot of all this is simply that a deadline and process for agreement has been set. There is still no deal on compensation, and the Cubs and Sox will be left to hash out the details, likely with Theo and Cherington at opposite ends of the bargaining table as it should be.
If no agreement can be reached by Tuesday, presumably there's an agreement on what will happen then. It's quite possible that this will mean Bud Selig's intervention as an arbitrator, but one would hope that's as a result of an invitation from the team. There's dangerous precedent, after all, in the commissioner of baseball forcing himself into the middle of what is essentially a trade negotiation.
One way or another, this long, convoluted process is finally nearing its end.