We should have a new boolean property "cpp.prependSysroot", which is enabled by default. If cpp.sysroot is set, this would result in all paths sourced from cpp.includePaths, cpp.systemIncludePaths, cpp.frameworkPaths, cpp.systemFrameworkPaths, cpp.libraryPaths, etc., to be prepended with the value of cpp.sysroot when they are passed to the compiler and linker (unless of course these paths are children of the project's sourceDirectory or buildDirectory).

This will help prevent host contamination when cross compiling.