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Scan the "Outputs" field of custom build steps and add .o object files to "OBJECTFILES" in respective Makefile-${CONF}.mk files. When using NetBeans for CUDA development the .cu files can be compile to .o with a custom build step but must be manually added as "Library Files" in the Link options. You might want to add an option check-box to indicate if the user wants this actions to be performed.