per-file-ignores have inconsistent behavior in symlinked directories

I am trying to ignore the `S101` rule in tests. I have a base `ruff.toml` which is used in `pyproject.toml`.

Adding this to `ruff.toml` doesn't work:

```toml
[per-file-ignores]
"**/test/**" = ["S101"] # <- still warnings in tests
```

However, adding the same in `pyproject.toml` works:
```toml
[tool.ruff]
extend = "/path/to/ruff.toml"

[tool.ruff.per-file-ignores]
"**/test/**" = ["S101"] # <- this works as expected
```

I tried without wildcards as well and `extend-per-file-ignores`. Nothing added to `ruff.toml` is considered.

Ruff version: `0.0.284`

Reproduce the behavior using the shown ruff.toml and pyproject.toml configurations, including a symlinked directory and the S101 rule. Then trace how Ruff loads per-file-ignores from each configuration and matches paths; done means equivalent ignore behavior in both locations, with coverage for symlinked directories.

Written by the indexing model from the issue text.