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As it stands, the Clippy configuration variable avoid-breaking-exported-api defaults to true for binary crates. This probably doesn't make a lot of sense: binaries don't have an API, and it is not uncommon to have pub symbols in them for various reasons: most notably to temporarily suppress "unused" warnings during development.
I would suggest the default for binary crates should be false.
It is worth considering whether there should be a lint for exported API in binary crates. This would catch some unused code cases, as noted above. Let me know if I should file a separate issue for that.