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Both (line-buffered stdout, raw stderr) date to the initial implementation 10 years ago: https://github.com/rust-lang/rust/commit/94d71f8836b3bfac337... . The commit message mentions that stderr is no longer buffered (probably as a result of the RFC 899 discussion, which I cannot seem to locate).
I did some more digging. By RFC 899, I believe Alex Crichton meant PR 899 in this repo:
https://github.com/rust-lang/rfcs/pull/899
Still, no real discussion of why unbuffered stderr.
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