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In our "org.eclipse.cdt.managedbuilder.core.buildDefinitions" extension we have defined an abstract toolchain that is subclassed in several configurations at which point it is filled with the necessary tools. So the 'abstract' toolchain superclass itselve has no tools in it, but currently the extension point schema requires at least one tool in it, hence a warning is issued.
Created attachment 82527 [details] Patch proposal
Your patch is applied.
Fixed.