In my build I am required to copy header files in a flat structure while source code files are copied in a hierachical structure. 
By default when specifying duplicate = 1 (my build is a variant dir build) in SCons all header files and .c/.cpp files are duplicated in a hierarchical structure.
Is there a way to deactivate duplication of header files ?
What I tried until now:
To provide an empty list to CPPPATH. 
To remove source scanners from my builders.
I want to install them by myself in a separate folder. I don't want to turn off duplication since I need that for .c/.cpp files.
You can't turn off the duplicate method for only a subset of files (based on their extension for example).
Installing a subset of source and target files to a specific directory is usually handled by calling the Install() method. Independent of whether you plan to use duplicate=0 or duplicate=1 for your actual builds, I'd suggest to not interfere with what happens in the variant dirs...and just letting SCons do its thing.
How to deactivate header files duplication in SCons?