Apple solve the first of these with libraries: your music library, your photo library, your film library. Any program can talk to these through the published API, so that solves this, for most people, for photo editing, music making.
The second is advanced-user stuff, and you make it hard to access and developers-only.
I want to create a presentation using Powerpoint or Keynote.
I then want to zip it up and mail it to someone.
Ok, we can skip the zipping step and assume that your mail client has a provision for compressing attachments before sending - where does the mail client pick up your presentation slides from?
You have to solve this problem by keeping an expandable list of libraries.
I suppose that's not a bad idea actually.
But then what happens when I want to copy my presentation, some associated video clips, my notes, the directions to the venue and the meeting agenda onto my USB drive? Suddenly all of the information relating to my presentation is scattered across multiple locations, which just gives me exactly the opposite problem to the one created by the file/folder heirarchy (i.e. now my data is grouped by type (e.g. in my photo library) instead of by subject (e.g. in a folder).
There are really only, I think, two use cases:
a) media b) source code.
Apple solve the first of these with libraries: your music library, your photo library, your film library. Any program can talk to these through the published API, so that solves this, for most people, for photo editing, music making.
The second is advanced-user stuff, and you make it hard to access and developers-only.