The framework would be modular. Sure, no two projects are actually exactly the same but there is a whole lot of overlapping, repetitive, unnecessary, tasks.
I'm not saying you lock into forever using whatever name convention you're using.
It's my first time ever proposing to work with strangers on the internet. I don't have a whole lot of experience with it so I can't really come out with every angle of the final product before anyone asks. (You might think you're asking but you're not, you're saying "You are an incompetent "idea man" who just came up with something you assume is unique and now you want a developer as your pet slave". Instead of saying things like "Nor have you outlined...", you could say "But how do you plan to deal with...").
I imagine folder structure being defined in Finder, the whole concept of the framework is based on the idea that all apps are great at their own thing, so Finder being the core of navigating through folders and finding files it would be logical. While the framework running in the background, Finder could get some extra toggle buttons or drop down menu in the toolbar to let you select what the folder should have of attributes "Like this should be where the XX of the project goes". Could use color labels to make it faster to distinguis between the different folders if one didn't find them hideous. Depending on what'd you were developing cache flushing would obviously be handled different, who ever developed the scheme for that workflow would decide how it should be done. Someone likes to do it with changing filenames of the files you've edited. The workflow application would handle this, make sure where ever those files where included in the rest of your project their reference would be updated, and the browser you were using would be redirected to the new url. This would mean that your source files would have to be copied into a the deployment folder.
People are creative and resourceful and if you let them taste something great you should expect some of them to crave for more. I'm not saying the framework should have schemes (one computer is not limited to having a single scheme either) that fit perfectly for everyone but if you'd provide a few and show how smooth it can be I don't doubt that some people will want to roll their own.