Autofix detection and potential ghost crate issue in unlinked_file

[ljahier]

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](draft: fix: unlinked-file diagnostic handling #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 !