When I right click on files/directories and click on “Open with another application”, I get a lot of duplicate entries and unwanted applications (like Wine applications I don’t have anymore, Minefield browser which I removed a long time ago, duplicate entries for Geany etc.). To remove them, I opened up my ~/.local/share/applications/ by pressing Alt+F2 and typing in
Then, I just removed the files with names like “wine-extension-X.desktop” and all wine entries were gone. You can choose to keep some if you have Wine installed and want then to appear in “Open With”. I also removed Minefield and Geany duplicate entries that I did not need. I also removed other files with “userapp” and “usercustom” in the names which I did not need anymore. That removed all the unwanted entries and my “Open With” box is clutter free again.