I have several applications, for example "Joe", that litters entries in the Applications menu. I cannot see how to customize this menu. How does one remove entries without actually deleting shared resources in /usr/share/applications? What is the OS method for customizing this menu? I can see how to add applictions, but how does one move, or re-categorize existing ones?
Yes! There are multiple methods to do this.
You could try the AppEditor application from the AppCenter, and this will allow you to edit local .desktop entries that show up in your menu. By hiding these in AppEditor, they should become invisible in your Applications menu. http://appcenter.elementary.io/com.github.donadigo.appeditor/
There is also the option of manually copying the .desktop files, or creating new ones, of the applications you don't want to see, and adding the
NoDisplay=true criteria to it.