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The rust-src component contains some files that are marked executable, e.g. src/jemalloc/include/jemalloc/internal/private_namespace.sh. When I download the component manually from https://static.rust-lang.org/dist/rust-src-nightly.tar.xz, I can see that the permissions are correct in that file (same for the .gz). However, ~/.rustup/toolchains/nightly-x86_64-unknown-linux-gnu/lib/rustlib/src/rust/src/jemalloc/include/jemalloc/internal/private_namespace.sh is not executable, so permissions get lost somewhere on the way.
I am trying to figure out how rustup goes about extracting the tarball, but the code is so abstract I couldn't find the right place yet...