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I can start up IntelliJ Idea using the commandline, which is a shell script that starts up a java process. It then appears in the launcher, as normal. I can select "Keep in Launcher", but it only remains there until I reboot, then it disapears again.

This is the only application I've seen that does this - Stuff already in the applications menu stocks around fine if I tell it to stay in the launcher.

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Related:… – Jorge Castro Mar 6 '11 at 17:32

Also reported as a bug for IntelliJ: Giving a name to WM_CLASS to enable better desktop integration . A WM_NAME is not enough, because, e.g chromium-browser, or any other application could also have "IntelliJ Idea" in the titlebar.

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Docky has the same problem with Java applications and their entries in the dock. Following this advice should help in Unity: How to Customize Window Matching .

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