How to remove/edit program in gnome applications list?

Solution 1:

If an application is (still) in the application list, it means that there is still a representing .desktop file of the application in either:

/usr/share/applications

or

~/.local/share/applications

The "orphan" .desktop file should be removed, to remove the application from the application list (or from Dash if you use Unity)

I suspect it is the last mentioned, since you mention wine, and wine sometimes installs (a lot of) .desktop files locally. Normally, when you uninstall an application (not wine applications), the corresponding .desktop files in /usr/share/applications is removed automatically.

Finding the right .desktop file

It can sometimes be a bit difficult to identify the right desktop file, since the file's name does not necessarily match the application's name. By making the (local) desktop file executable, it should be easier to identify, since the displayed name is then the same as the application's name, and the file also shows the application's icon once it is made executable.

Solution 2:

If there is an icon remaining in the GNOME Application Menu, that means that there is a '.desktop' file linking that to the Applications Menu. The location of this file is different depending on where you got it from (apt, wine, pacman, snap, etc) and probably your distro (this is for Ubuntu).

If it's from the apt the files will be located in either

/usr/share/applications

or

~/.local/share/applications

For wine applications:

~/.local/share/applications

or

~/.local/share/applications/wine/Programs

For snap applications:

/var/lib/snapd/desktop/applications

Sometimes the name of the .desktop file will not match the name of the program - watch out for that.