If you're planning on doing all of the work required to implement a
virtual-folder system, you might consider implementing it using
fuse<http://fuse.sourceforge.net/>.
 Fuse let's you create a new file system that is run as application run by
the user.  For example, people have used fuse to create file systems that
mount over FTP and SSH and even git. To the user the new file system looks
like any other, so files and folders are accessible in any application,
including finder/explorer.

There are python bindings for fuse here:
https://github.com/terencehonles/fusepy.

The API will probably have a steep learning curve, but on the other hand,
you won't have to write any UI code.

chad.

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