How is ~/Library/Safari/ any different to ~/.mozilla/ and in any case if you aren't that application you really have no business poking around in there.
As for the ~/Library/Fonts & ~/Library/Fonts examples we already have ~/.fonts/ and ~/.icons. If there are generic places like that for other data files then thats an issue for the application/framework that first delivers them. What you are asking for is in my opinion really far out of scope for the tools that put bits onto disk which is what this project is about. -- Darren J Moffat
