In earlier versions of SPSource, I seem to remember associated content types being linked in schema.xml as a simple ContentTypeRef element. Now it looks like the whole content type is defined again in the ContentType element. This may or may not be an issue, but I've come across a couple things when dealing with lookup columns. I'll end up getting errors when trying to activate the feature (usually an internal one trying to update a field), or the document library's site columns won't be associated with the content type.
Like I said this may not be an issue for most people since I'm doing some crazy stuff with lookup columns, but it's something to look out for.
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