Autofix detection and potential ghost crate issue in unlinked_file

Description:
While addressing a FIXME related to autofix detection in unlinked_file, I noticed that some files are incorrectly marked as unlinked due to what seems to be a ghost crate detection issue. This occurs when a file appears to belong to a crate but isn’t properly linked to a valid root (main.rs or lib.rs).

Key Observations:

• is_in_crate = true, is_crate_root = false, but is_unlinked = false, yet autofix suggestions still appear.
• Some files seem to be falsely classified as part of a crate even if they lack a proper root.
• Modifying crate detection logic affects multiple tests, suggesting intentional behavior (e.g., for VS Code extension).

Current Status & Next Steps:

• My attempted fix in [PR #19398](https://github.com/rust-lang/rust-analyzer/pull/19398) refines crate detection logic but breaks existing tests.
• Seeking feedback on whether this behavior is intentional or if an alternative approach is needed to handle indexing issues without regressions.

Logs & Test Output:
(See PR for details)

Would appreciate any insights on how best to resolve this while maintaining expected behavior. Thanks !

Start with the unlinked_file logic and the crate-root cases involving main.rs and lib.rs. Read PR #19398 and its reported test regressions, then inspect the affected existing tests to determine which behavior is intentional. Done means the crate and autofix classifications are agreed on and the full affected test set passes without regressions.