SCons: List `.gen.cpp` sources explicitly to avoid globbing errors

Whenever we change the name (or remove) generated cpp files with the `.gen.cpp`
extension, users run into build issues when switching between branches (i.e.
switching before and after the name change/removal). This is because we glob
`*.cpp` so if a now-obsolete file from a previous build is present, we'll
include it too, potentially leading to bugs or compilation failure (due to
missing headers or invalid code).

So globbing patterns in `add_source_files` will now skip files ending with
`.gen.cpp`, which should instead be passed explicitly where they're used.

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