build: ensure `make clean` doesn't remove source files

Adding a file to `OUTPUT` in `add_custom_command` marks that file as
`GENERATED` in cmake, and will thus be removed when running the `clean`
target. As cmake doesn't have a good way to mark that certain files
should not be removed, we instead "lie" to it by omitting the files we
want to keep from `OUTPUT`. This hack only works as long as there aren't
any other files that depend on the generated files we want to keep,
which currently seems to be the case. If this assumption changes in the
future, then we need to separate the parts that are generated and the
parts that are not as to prevent an infinite dependency chain.

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