I've been trying to figure this out with no luck too. Apparently Tekkub found a way to extract
build 12694, which uses the same patch format. I couldn't find any mention of what tools he used though. The actual patch files look like bsdiff binary diffs with a proprietary blizzard header prepended to them. I had trouble applying any of the patches though, even with the extra header trimmed out.
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Edit: On second look at what Tekkub committed, he didn't extract patch 12694 properly. He has the changes between builds 12644 (pre-streaming client) and 12635 (base streaming client); None of the changes from wow-update-12694.mpq are included though.