Rust: fix crate_graph.rs

[aibaars]

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[Copilot]

Pull Request Overview

This PR refactors the crate graph extraction logic by removing the direct dependency on the old CrateGraph type and using updated database interfaces instead.

• Replace usage of "CrateGraph" with methods on "db" and updated iteration over crates.
• Update function signatures and invocations to remove the extra "crate_graph" parameter.
• Adjust helper functions (e.g. make_path, emit_visibility) accordingly.

Comments suppressed due to low confidence (1)

rust/extractor/src/crate_graph.rs:62

• [nitpick] The variable 'krate_id' now appears to represent a Crate instance rather than an identifier; consider renaming it (e.g., to 'krate') to reflect its meaning more clearly.

crate_id_map.insert(*krate_id, (root_module_file, hash));

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