It sounds a lot like an idea I've had, which I call the programmer's note book or HyperInterWebNut. The HyperInterWebNut would be a thick client wiki with auto-linking features (beyond wiki words, using analysis), visual diff, infinite versions (and maybe branching) and server side publishing and editing. The programmer features would include documentation editing and diagramming.
But basically, it would be a thick client wiki. Which is what Pepys is. I wish I had more time to work on these stupid ideas I have...other people keep inventing them first! :)