Hmm, do we need a document somewhere (on bitcoin.org?) that clears this up? The Foundation pays Gavin, but that doesn't mean it controls development or tells him what to do. His mission from the Foundation can be summed up as, "carry on doing that thing you do".
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I don't doubt that what Gavin does is NOT directed by the BF. But I also don't doubt that the BF pays Gavin because he does pretty much what they desire.
Put another way, it would be a bit naive to believe that the goals of the BF's higher paying members and the work that Gavin performs in shaping the direction of the project are not somewhat aligned. It seems foolish to believe that the relationship would persist if that were not the case.
To this end, we can expect that Bitcoin evolves in some approximation of the direction that the higher tier members of the Bitcoin Foundation desire.