Function load_skill_roots 

pub fn load_skill_roots(
    shared_user_root: Option<&Path>,
    user_root: Option<&Path>,
    project_roots: &[PathBuf],
) -> Result<SkillRegistry, ConfigError>

Loads explicit skill roots in low-to-high project precedence order.

shared_user_root is the cross-client ~/.agents/skills convention and ranks below the cookie-agent-native user root. Each project directory contributes its .agents/skills root before its .cookie-agent/skills root, so native roots win same-scope name collisions.