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I agree that links to files (whether embedded or referenced) needs some work. I've always liked OmniOutliner's metal lozenges, but if we can't get to that point by 1.0, I guess I'd vote for just displaying them as text links. As others have mentioned, I don't care much for icons disrupting text flow, although a 16x16 icon with proper vertical alignment might be good.

As for embedding vs. referencing files, I think it is best to give the user the option, with referencing being the default (opposite of OmniOutliner). I almost always link my files in, but there are circumstances where being able to just store the file in my OmniFocus database (usually temporarily) would be really helpful.

I use the term "database" loosely here, as I believe files embedded in OmniFocus are not actually stored in any kind of a database but rather as a file in the folder that comprises the OmniFocus data bundle in your home directory (just like OmniOutliner). So there's no more chance for file corruption when embedded than when stored elsewhere on your drive.