I think there might be an issue on El Capitan with Java applications force quitting, because I've seen multiple people talk about similar problems to this with no actual solutions presented.
I've been writing applications in eclipse, and one application of mine occasionally has an issue where the program ends, yet the java icon stays in the dock.
I can right-click the icon and tell it to Force Quit, but this has no effect. If I open the force quit window with command-option-escape, the application shows up, but again, force quitting does nothing. The application does not show up in Activity Monitor, so I can't end the process.
Shut-down is impossible while this application remains open. I have to force shutdown and reboot in order to get rid of this program.
I can run "killall Dock" from Terminal, which makes the application disappear from the dock... BUT, the application still shows up in the force quit window, and it still cannot be force quit from there. Furthermore, a terminal-looking window labeled "java" appears after running this command. This new application cannot be force quit through right-click, does NOT show up in the force quit window, and doesn't show up in Activity Monitor either. Shutting down normally is still impossible.
I've seen various other topics where people had this issue with certain java programs under El Capitan, but most had very little detail, and none had a true fix to the issue.
Does anyone know why this happens? How to prevent it from happening in my programs? How to truly force quit applications like these?