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Navid also mentioned that ROOT libraries are setup similarly to how they are handled now with a standard set of RootLibs, and a set of GUI libs.
Issues
By default, SCons searchs for tools in the site_tools directory, or the user can provide a list of tool paths. This mechanism is working except in the case of a container package such as celestialSources. Navid is trying to avoid hard-coding anything into the SConscript files and external tools. The worst case scenario is that a container will have to announce itself as such.
Private includes should remain in the src directory as suggested currently. Actually, there were some public includes in some of the ST package, such as optimizers. Jim will look into that.
Navid is working on overriding package, aka multiple CMTPATHs.