For me currently, when trying to open a `text/markdown` file, there's a disassociation between what my file manager (Caja) runs (own bin/emacs script; was under the impression it was auto-creating a .desktop file), what mimeapps.list have (emacs.desktop), and what `xdg-open` runs (Firefox for some reason).

Older desktops don’t follow the specs and xdg-open does different things based on the desktop, so they indeed can get out of sync.

I’d have to look into your specific case but `gio mime` and `gio open` do the right things.