fix(skills): refresh user storage after config reload

[wutongyuonce]

Why

When the app config is hot-reloaded, the per-user skill storage could remain bound to paths from the previous config instance.

What changed

• Rebuild per-user skill storage when the app config instance changes.
• Keep reusing storage when the config instance is unchanged.
• Add a regression test covering both behaviors.

Validation

• git diff --check
• Added backend/tests/test_skill_storage_lifecycle.py::test_user_storage_is_rebuilt_when_app_config_changes

Fixes #4971