[ty] Add virtual files to the only project database

[dhruvmanila]

Summary

Previously, the virtual files were being added to the default database that's present on the session. This is wrong because the default database is for any files that don't belong to any project i.e., they're outside of any projects managed by the server. Virtual files are neither part of the project nor it is outside the projects. This was not the intention as in the initial version, virtual files were being added to the only project database managed by the server.

This PR fixes this by reverting back to the original behavior where virtual files will be added to the only project database present. When support for multiple workspace and project is added, this will require updating (astral-sh/ty#794).

This is required for #19264 because workspace diagnostics doesn't check the default project database yet. Ideally, the default db should be checked as well.

The implementation of this PR means that virtual files are now being included for workspace diagnostics but it doesn't work completely e.g., if I save an untitled file the diagnostics disappears but it doesn't appear back for the (now) saved file on disk as shown in the following video demonstration:

Screen.Recording.2025-07-14.at.14.00.18.mov

[github-actions]

mypy_primer results

No ecosystem changes detected ✅
No memory usage changes detected ✅

[dhruvmanila]

Actually, this is not an "internal" change as the server now starts checking virtual files in workspace diagnostic mode.

[dhruvmanila]

The implementation of this PR means that virtual files are now being included for workspace diagnostics but it doesn't work completely e.g., if I save an untitled file the diagnostics disappears but it doesn't appear back for the (now) saved file on disk as shown in the following video demonstration:

I think the reason the other case isn't working is that the file doesn't exists on disk and so the File's initial status is NotFound. This is based on the warning that I get in #19264:

2025-07-14 14:17:26.316681000  WARN notification{method="textDocument/didOpen"}: Failed to create a salsa file for /Users/dhruv/playground/ty-server/src/ty_server/other.py

Now, the linked PR does fix the issue here which I'm not exactly sure how.

[MichaReiser]

This is required for #19264 because workspace diagnostics doesn't check the default project database yet. Ideally, the default db should be checked as well.

I don't think this will be necessary. We only use the default database so that we can provide basic LSP features for those files. I don't think we have to provide diagnostics.

I think the reason the other case isn't working is that the file doesn't exists on disk and so the File's initial status is NotFound. This is based on the warning that I get in #19264:

I'm not sure where this message is logged which makes it difficult to help. It probably makes sense to add a log statement to system_path_to_file to see why it returns None and if it's because the status is NotFound, why apply_changes doesn't update the file status.

[dhruvmanila]

Somehow, this change is also initializing the default database when I open a virtual file and select the Python language for that virtual file.