I was able to fix this for SQLDeveloper:

Using xprop, I found the following line

WM_CLASS(STRING) = "sun-awt-X11-XFramePeer", "oracle-ide-boot-Launcher"

Based on the comments above, I added the following line to my local
sqldeveloper.desktop file.

StartupWMClass=oracle-ide-boot-Launcher

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

Title:
  java applications a double icon appears

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