I've created a modified version of Joplin based on 2.13.2. Among the main features added is having all notebooks and notes automatically saved as folders and markdown files onto the local file system, and the files and folders are kept up-to-date with the database of Joplin.
So far, this feature works only with the desktop application. The default directory where the notebooks and notes are saved to are under "JoplinFiles" under "Documents" of the user's home directory, in Linux notion: "/home/yourname/Documents/JoplinFiles/" (it can not be customized now). Under there, there are sub-directories based on Joplin's profile ID. If the user hasn't added additional profiles when using Joplin, all the notebooks and notes are saved under the "default" directory. Notebooks are organized as directory trees and note files are under the associated notebook folders. (Note, if you are running a dev version from source, the directory would be "/home/yourname/Documents/JoplinDevFiles/").
Upon the start of Joplin when the said directories don't exist, Joplin will create them and populate them with sub-directories and files. Directories are named with the titles of the notebooks. Files are named with the titles of the notes, as: "the note title.md". If the note is a to-do note, it is named as "X | note title.md" (if the to-do is not completed), or "V | note title.md" (if the to-do has been completed).
You can create, update, move, delete notes or notebooks in Joplin and the files and directories are promptly updated.
One efficiency improvement is on the frequency of saving notes during editing. Originally, Joplin saves the note to DB on every key stroke, which appears quite inefficient. Now, note is saved upon receiving the addition or extraction of a return character, or upon change of focus (like pointer changed to title from body, or vice versa), or starting a new note.
Rich text editor is currently not supported.
The Linux application appears to work well. And an AppImage file is included in the release. I don't have versions for Mac or Windows and welcome anyone willing to build and test them.
Currently, modifications of directories or files outside of Joplin are not updated back into Joplin, but this is being worked on.
This feature is also being ported to mobile apps (specifically the Android app).
I appreciate comments, critics and suggestions.