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In general, the right solution to this is to source your workspace's setup.bash file and then start your IDE directly from that shell, rather than trying to launch it from the GUI.

If that works well, you can usually create a custom launcher icon which sources your workspace's setup.bash file and then runs your IDE; the QtCreator instructions describe how to do this, and it shouldn't be hard to adapt it to another IDE. See the IDEs Page and the QtCreator Section. Note that the instructions there assume that your bashrc sources the setup file for your workspace by default.