Fix deduplication in cargo tree (fixes #9599)

[Nutomic]

What does this PR try to resolve?

cargo tree --duplicates wrongly shows the same crate version multiple times if it is used with different features, or as both normal dependency and dev dependency. #9599 has more details.

How to test and review this PR?

Ran the code as cargo run -- tree --manifest-path /path/to/Cargo.toml -d and compared the output to stable cargo.

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The reviewer was selected based on:

• Owners of files modified in this PR: @ehuss, @epage, @weihanglo
• @ehuss, @epage, @weihanglo expanded to ehuss, epage, weihanglo
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[weihanglo]

FWIW, for bugfixes, we usually follow a variant of atomic commit pattern:

1. Commit a test that asserts the current buggy behavior (passes).
2. In the next commit, fix the bug and update the test/snapshot.

Every commit passes, and the test/snapshot diff shows the behavior change.

[Nutomic]

Not sure I understand. The test in this file already asserts the current behaviour and passes. Do you simply want me to squash the two commits in this PR into one?

[arlosi]

Any changes to the test (like adding optdep 2.0.0), should be made in the first commit.

The 2nd commit should then only show the impact caused by the bug fix to the test (only the stdout_data should change).

[Nutomic]

Updated, I hope its right now.