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In Version 3.0.0 of STS Gradle tooling you should be able to configure commandline options like -debug in the preferences page.
This is via menu "Widows >> Preferences >> Gradle >> Arguments".
STS 3.0.0 is not officially released yet... and unfortunately this is recently added feature, it is not available in STS 2.9.2.
In STS 2.9.2 there is no way to set commandline options to the Gradle process.
One thing I should warn is that many bundles and packages have been renamed between 2.9 and 3.0 so the 3.0 version isn't really compatible with 2.9. However, it should be possible I think, to uninstall the Gradle 2.9 support and then install Gradle 3.0 support if you make sure not to install the optional Dashboard and UAA features from the update site.
The gradle tooling themselves are quite separate from the rest of the tools and only depend on core eclipse functionality. So in theory this ought to work.
Let me know if you need more help than this.
If this seems like too much hassle then I'd suggest waiting for 3.0.0 to be officially released probably in about a week or so.