I've believed for a long time that files were archaic and agree completely - and we should extend that idea to version control. If we version functions (and classes, stored procs, etc...) then you can create a type of failover to a last known good version down to that logical function.

As for the rest of the ideas - the table, organize and layout related code, the documentation and the interface are all terrific ideas and I can't wait to see where it goes. Imagine laying out all that code on a nice huge touch tablet with multi-touch support ... drool....