As far as I'm concerned, that the source code is divided into files of linear streams of characters is a technical detail. My navigation isn't linear and my editing often isn't, and the editor I use goes through great lengths to enable just that.

Having used node-based programming environments extensively (Max, Reaktor) I am not convinced that that there is a ergonomically sound alternative to just writing the code in linear text files, but admit that there are probably domains where it is more suitable. I found it tedious and straining, particularly when you have to use both mouse and keyboard.