So I have just check the Notebooks (notebooksapp) and it is so close to what I would love to have, I could cry.
Sadly it has no symbolic links.
There is no visible difference between an hdd file and the app note that is kept aside. IMHO there should be a different icon for the app-based note.
It does not work with my old wacom mouse, but that is just my fight with time.
And most of all it feels, well, sluggish. There is a slight delay before everything happens.

Still, it is a beautiful concept. So close, but not just there yet :-(

Thanks for pointing it out to me!

:)
k