Modelio is RCP-based so a specific target configuration is required to debug a Modelio module. This target configuration will then be used in the debug configuration. The procedure is as follows:
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Open the preferences window (Window –> Preferences)
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Select Plug-in Development / Target Platform. (1)
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Click on the "Add…" button. (2)
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Select "Nothing" in the ‘Target definition’ box. (3)
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Type in the target definition name: (4)
modelio-by-modeliosoft4.1 - 
Click on "Add…" (5)
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In the ‘Add Content’ dialog box, select "Directory" and click on "Next >"
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Enter the Modelio installation directory path
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Click on "Finish"
 
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Click on the "Finish" button (6)
 
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Select the
modelio-by-modeliosoft4.1target platform. (1) - 
Click on the "Apply" button (2)