Update directory submodule to latest master

The primary reason for this bump is to fix the warning from `ghc-pkg
check`:

```
Warning: include-dirs: /data/home/ubuntu/.ghcup/ghc/9.6.2/lib/ghc-9.6.2/lib/../lib/aarch64-linux-ghc-9.6.2/directory-1.3.8.1/include doesn't exist or isn't a directory
```

This also requires adding the `file-io` package as a boot library (which
is discussed in #25145)

Fixes #23594 #25145