The best filesystem abstraction is GMail, because you can tag things and search them. Instead of saving my photos to /home/user/Christmas/2009/DecoratingTree/ I should be able to label a group of photos with those tags and filter by them later.
For the novice, the operation would go like this: Show me all things related to "Christmas..." wow, that's a lot of stuff, now limit those results to "2009"...and just show me photos. Ah yeah, there's the one of the kids chewing on the tree light wires.
"Tagging" files in this manner would require no more effort than organizing them in directories, and it's a lot more intuitive.
I've been meaning to write an application that works like this for years, but something else has always taken the priority away. If you want to work on it send me an email and I can dig up the code.
If I save to /home/user/Photos/Christmas/2009, then treat each one of those as a "tag."
If later I navigate to /home/user/2009/Christmas, I should see everything "under" that directory.
The point is that the hierarchical system filters too early. I want to see everything under a directory without having to drill down and filter from there.
Well, more or less. No file system, just databaselets and indexes and search.
Ironically, it's harder to reflect actual heirarchies when you have a set of flat, easily searchable records like this. What you probably /really/ need is a multi-edge graph with queries.
The Preferences argument made by the author is the same in my opinion. ~/Library/Preferences should be hidden by default. The user should be able to clear preferences from within Photoshop itself, or some sort of general preferences manager.
None of this needs a new abstraction layer, just some incremental UX work within individual applications.
Also it is relatively simple for application on either system (including generic unices) to find suitable place for their data. Making some OS-agnostic abstraction has fundamental problem in fact that different systems offer different types of standard locations (Unix has $HOME and dot-files, while in windows you have My Documents and three distinct Application Data directories and lot of specialized directories like Pictures, Saved Games etc.).
What we need is storage atom/fabric APIs that provide individual namespace (tagging, hierarchical or whatever) and storage (dedup/sync/versioning/replication or whatever) components to enable applications to innovate UX for each domain.
In the next a few years, we shall see the passing of traditional Filesystem APIs and blossoming of new storage APIs.
