Stale SemanticDb files

[vovapolu]

For some reason metals doesn't update SemanticDb files when the source file is changed (or it does update but doesn't write the updated file on disk and give access to it). The message is stale SemanticDB <path to file>. Not sure how it can determine staleness without updating the DB, needs to be investigated.

We should try to force metals to update Semantic DB files or, if we can't, we shouldn't show diagnostics on stale files because they are displayed shifted in updated file making it worse.