Joplin is really nice feature-wise but the last time I looked at it a few years back I absolutely HATED the way that it structured your notes.

The way it worked was that they stored new/existing notes in an SQLite table with UUIDs. This of course makes it very difficult to use bash tools, other IDEs, etc. to work with your notes after Joplin has ingested them.

Further the related media was renamed "UUID.<related extension>" which were stored in `~/.config/joplin-desktop/resources`.

Compare this to apps like VS Code / Obsidian / Logseq (also open source) which don't mess with your markdown file organization. You can just point them to a root folder and they'll work natively with your markdown files. No syncing required.

Trilium.

https://github.com/zadam/trilium