Function compute_relative_install_path 

pub fn compute_relative_install_path(
    tool_root: &Path,
    dep_path: &Path,
    flatten: bool,
) -> PathBuf

Computes the relative install path by removing redundant directory prefixes.

Strips redundant prefixes to prevent duplication (e.g., .claude/agents/agents/example.md). Also strips prefixes that match any component in the tool root path to avoid .claude/skills/agpm/skills/skill-name when installing skills/skill-name.