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So what you're actually talking about has nothing to do with directory structure but a given distribution failing to properly setup the default applications to which Firefox points to.

Call me a luddite, but I prefer to manually download and save my files, then manually load the application I want to use to view the file with - too many times I have found that either applications hijack the file associations or the automatic assumption by the desktop that I want to open it with a particular application even though 5 minutes before I had installed the viewer that I preferred.

This is where the "Always ask" option in Firefox comes in handy ... as it will popup a dialog asking you what to do with a download. Want to save it to disk? Check that box. Want to open it with an app? Select the app from the list.

I also tend to dislike "automation" when it comes to web downloads. Like you said, too often, a random app/plugin update will hijack the mime-types/app-registration and cause all kinds of weird things to happen.

I think the main problem a lot of people have with computers is that they don't think they can take control. They think the computer should just know what to do, automagically. But all a computer knows how to do is what you tell it ... if you don't tell it to do something specific, then you really can't be mad when it screws it up.

Take control of your computer. Configure it to work the way *you* want it to. Don't become a slave to a hunk of metal.