Go to system/file explorer
Find a .md file
Right-click → Properties
Select “Open With” tab
Set a custom text editor and click “Set as default”
In Obsidian, try to right click any md file and click “Open in default app”
I don’t think this answers the issue. The problem isn’t setting Obsidian as the default app for opening md files, its that Obsidian doesn’t open files using the app that IS set as the default app for md files.
I’m having a similar issue when selecting “Show in system explorer” from the menu. The default system explorer (Nemo) isn’t selected. Instead, Obsidian shows the file in Thunar. All other application seem to be honoring the default system explorer. (Ubuntu 22.04)
we have no control over this, we get what electron provides.
I think there maybe multiple places where to set the default on linux and the method electron uses may result in another program being opened that the one you expect.