Unable to find references of code in multiple packages

### Describe the Bug

I'm using uv workspaces like this:
```toml
[tool.uv.workspace]
members = ["packages/*"]

[tool.uv.sources]
analytics = { workspace = true }
billing = { workspace = true }
identity = { workspace = true }
foo = { workspace = true }
shared = { workspace = true }
```

If I go to a file in the billing package with a method that is used in billing and foo and try to search for references of that method, I will only see the references in billing package. The expected behaviour is to see all references from all packages.

I don't have any pyrefly configuration, but I've tried this one in `pyproject.toml`, without success:
```toml
[tool.pyrefly]
search-paths = ["myproject", "packages/analytics/src/", "packages/billing/src/", "packages/identity/src/", "packages/foo/src/", "packages/shared/src/"]
```

If I disable the pyrefly extension and try to find the references, then I can see all the expected references.

### Sandbox Link

_No response_

### (Only applicable for extension issues) IDE Information

- pyreflix 1.0.0
- vscode (code - oss):
```
Version: 1.121.0
Commit: 987c9597516278c9fcf10d963a0592ce1384ab93
Date: 2026-05-19T23:32:58Z
Electron: 39.8.10
ElectronBuildId: undefined
Chromium: 142.0.7444.265
Node.js: 22.22.1
V8: 14.2.231.22-electron.0
OS: Linux x64 7.0.10-arch1-1
```