Treat merged stub symbols as untyped in pyrefly coverage

[jorenham]

Summary

From the typing spec (src):

Type checkers should merge the stub package and runtime package directories. This can be thought of as the functional equivalent of copying the stub package into the same directory as the corresponding runtime package and type checking the combined directory structure. Thus type checkers MUST maintain the normal resolution order of checking *.pyi before *.py files.

So this ensures that annotated symbols in a .py are treated as untyped if those symbols are not annotated in the .pyi by pyrefly coverage {check, report}.

Fixes #3778

Test Plan

There are tests :)

[github-actions]

According to mypy_primer, this change doesn't affect type check results on a corpus of open source code. ✅

[meta-codesync]

@samwgoldman has imported this pull request. If you are a Meta employee, you can view this in D108648927.

[yangdanny97]

Review automatically exported from Phabricator review in Meta.

[meta-codesync]

@samwgoldman merged this pull request in 33a79bd.

[jorenham]

Thanks!