While this is noisy and hides other deprecations, I figured deprecations would
make it easier for people to discover what tasks remain and allow us to
divide and conquer this work rather than doing a heroic PR.
In theory, this will be short lived and we'll go back to seeing
deprecations in our tests.
In 12914 we stabilized pkgid spec as unique package identifier for
`cargo metadata`. However, we forgot to make the same change to
JSON message format[^1]. This PR does so.
Note that the `package_id` field in JSON message is not clearly stated
as "opaque", so it might be considered as a breaking change to some extent.
[^1]: https://doc.rust-lang.org/nightly/cargo/reference/external-tools.html#compiler-messages
