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The MBS allows specification of a ManagedCommandLineGenerator to process tool flags into a command line. The same class however is not called to process the flags shown in the C/C++ build dialog when a Tool is selected (ToolSettingsBlock).
Reassigning to Build.
*** Bug 112790 has been marked as a duplicate of this bug. ***
Created attachment 32405 [details] Patch proposal
Problem fixed: org.eclipse.cdt.managedbuilder.ui.newui.ToolSettingsPrefStore.java: - applied Wieant's patch org.eclipse.cdt.managedbuilder.internal.core.ManagedCommandLineGenerator.java: - added check for empty inputResources.
Oleg, Checked it in 4.0, and the patch seems to do the trick. Thanks!