I run gnome shell 3.6 and Eclipse 4.2. I installed Eclipse manually, in my /opt directory, because the Ubuntu package for Eclipse is very outdated.
I've created a .desktop file for it, and placed in in ~/.local/share/applications. It looks like this:
[Desktop Entry] Type=Application Name=Eclipse Comment=Eclipse Integrated Development Environment Icon=/opt/eclipse-4.2.1/icon.xpm Exec=/opt/eclipse-4.2.1/eclipse Terminal=false Categories=Development;IDE;Java;
I can run Eclipse from the Activities menu; if I hit the super menu and type in "Eclipse" and run it, it starts just fine, and shows up in my launcher/sidebar/dock/whatever it's called.
But if I right-click on its icon, there is no "Add to favorites" option.
(I notice this is also the case if I run some very old programs, like xeyes and xcalc. it's amazing these are still distributed!)
So what is it about a program that determines whether or not the "Add to favorites" option is available? if I knew and understood that, maybe it'd set me on the right path to fixing this Eclipse problem.