In most cases and with most tool sets, SCons can place its target files in a build subdirectory without duplicating the source files and everything will work just fine. You can disable the default SCons behavior by specifying duplicate=False when you call the SConscript function:

SConscript('src/SConscript', variant_dir='build', duplicate=False)
    

When this flag is specified, SCons uses the variant directory like most people expect--that is, the output files are placed in the variant directory while the source files stay in the source directory:

% ls src
SConscript
hello.c
% scons -Q
cc -c src/hello.c -o build/hello.o
cc -o build/hello build/hello.o
% ls build
hello
hello.o