Intellij Idea not showing up in apps and cannot add it to Favorites
Solution 1:
Thanks to @Kulfy I found the problem: there was an old .desktop file for IntelliJ IDEA in ~/.local/share/applications which contained invalid path (pointing to old version).
After deleting it and restarting GNOME shell using Alt+F2 and ruuning restart, I was able to add it to Favorites.