After some hacking, I've been able to modify the wonderful Deft mode by Jason R. Blevins to support several directories. I had my notes divided in several directories, including my TO-DO entries, and I thought it would be nice to give Deft the possibility to support several directories, and at the same time, an exercise for my Emacs Lisp.
I tried to make the least modifications as possible to the original source, so that the change can be made with a patch, if the original author considers it (this is also why I didn't change the name of the mode either.) You can download it, and read instructions of installation and usage here:
As always, feedback is highly appreciated.