Pyrefly reports `missing-import` for workspace package exposed via `.pth` editable install

[DebanKsahu]

Describe the Bug

Pyrefly fails to resolve imports for a workspace package that is available at runtime via a .pth shim in the project's virtual environment. The project uses uv as the package manager/workspace tool. The import that triggered the error in my project was:

• from shared_core.config import Settings

Pyrefly's IDE diagnostic shows:

Cannot find module `shared_core.config`
Looked in these locations (from default config for project root marked by `packages/google-service/pyproject.toml`):
Import root (inferred from project layout): "packages/google-service/src"
Site package path queried from interpreter: [ ... ]

However, importing the same module in the configured venv succeeds:

$ d:/Projects/Python/Invoice_Intelligence/.venv/Scripts/python.exe -c "from shared_core.config import Settings; print(Settings.__name__)"
Settings

Steps to reproduce

1. Create a workspace with sibling packages: packages/google-service and packages/shared-core (source at packages/shared-core/src).
2. Use your workspace tooling or installer to expose shared-core in the venv via a .pth file (e.g., .venv/Lib/site-packages/shared_core.pth pointing to packages/shared-core/src).
3. Open packages/google-service/src/google_service/gmail/core_service.py which contains from shared_core.config import Settings in the editor using Pyrefly LSP.
4. Observe a missing-import diagnostic for shared_core.config in the editor even though the import succeeds at runtime in the same venv.

Actual behavior

Pyrefly's resolver does not follow the .pth shim used by the editable/workspace install, so imports provided only via that shim are reported as missing.

Expected behavior

Pyrefly should either:

• Respect .pth shims found under the configured site-package-path during environment autoconfiguration, or
• Clearly document that .pth shims are not followed and recommend configuration workarounds, or
• Improve heuristics to detect and include workspace source paths from editable/install wrappers.

Environment / diagnostics

• Project: monorepo with per-package pyproject.toml files and a repository .venv.
• Package manager / workspace tool: uv (workspace members configured in the root pyproject.toml).
• The venv contains shared_core.pth and shared_core-0.1.0.dist-info.
• Pyrefly initially searched packages/google-service/src and the interpreter site-packages; after adding a search-path override in packages/google-service/pyproject.toml (pointing to ../shared-core/src) the missing-import diagnostic for shared_core.config disappeared.

Workarounds

• Add search-path = ["src", "../shared-core/src"] to [tool.pyrefly] in packages/google-service/pyproject.toml (explicitly include sibling source trees).
• Install the package in the venv as an editable package where the source directory is discoverable without a .pth shim.

Sandbox Link

No response

(Only applicable for extension issues) IDE Information

No response