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One test runs extract with the cargo flag against a repo that has no Cargo.toml at all and confirms it still succeeds and still writes the graph built from the code already indexed, with a note explaining the crate edges were skipped. A companion test confirms a repo that does have a valid manifest still gets its crate node, so the fix only changes the missing manifest path. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_017qfdzgbA5KedGEjD1AayNh