Duplicate entries when receiving a `textDocument/didOpen` before indexing is complete

[vinistock]

If the user opens the editor with files already opened, the editor might be able to get some didOpen notifications sent before indexing is complete. In this case, opening the documents will also index them, but we have no way to tell the indexing process to drop the URI.

We need to ensure that that indexing the same file twice without any modifications never results in duplicates because there are some scenarios that risk it:

• open a document before indexing is finished
• a file is modified on disk before indexing is finished
• a file is modified on disk and then immediately opened