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Currently Cargo doesn't allow the metadata to be separately updated. This doesn't seem right (as the semantic versioning only concerns about the public API and the metadata is not a part of the public API).
In order to fix this issue, the publish endpoint (/api/v1/crates/new) should be adjusted to accept the metadata without the tarball (well, or have a new endpoint for that), and the server will check if the name, version, dependencies and features match to those stored before updating that. In the CLI the cargo publish command should ask for the metadata update when the version hasn't been changed.
azerupi, Storyyeller, gyscos, tmccombs, vbfox and 12 more