I have a similar problem with IntelliJ IDEA. I cannot get it to be kept
in Launcher at all.

If you download and install a cross-platform Java application, not
specifically packaged for Ubuntu, then you will obviously not get any
.desktop file. Are you, as a user, supposed to write a .desktop file for
it in order for Unity to handle it properly?

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https://bugs.launchpad.net/bugs/757991

Title:
  java applications a double icon appears

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