Custom skills from `chat.agentSkillsLocations` are not inherited by Git submodules (and potentially subfolders)

- Copilot Chat Extension Version: `0.48.1`
- VS Code Version: `1.136.1`
- OS Version: Ubuntu `22.04.5 LTS` (ARM64)
- Feature: Agent mode / custom agent skills
- Selected model: irrelevant
- Logs: None attached

## Steps to Reproduce

1. Open a Git repository containing a Git submodule in VS Code.
2. In the parent repository, enable:
```json
"chat.useCustomizationsInParentRepositories": true
```
3. Add the following to the parent repository’s `.vscode/settings.json`:
```json
"chat.agentSkillsLocations": {
".github/collections/mattpocock-skills/skills/engineering": true,
".github/collections/mattpocock-skills/skills/productivity": true
}
```
4. Add custom skills under those locations in the parent repository.
5. Open a file inside the Git submodule and start a Copilot Chat session.
6. Attempt to use one of the skills configured through `chat.agentSkillsLocations`.

## Expected Behavior

Skills configured through the parent repository’s `chat.agentSkillsLocations` setting should be discovered and available inside the submodule when `chat.useCustomizationsInParentRepositories` is enabled.

## Actual Behavior

Parent-repository customizations are available inside the submodule, but skills configured through `chat.agentSkillsLocations` are not discovered or available.