feat: generate manifests from packages and polish cache tools

[RexWzh]

Summary

• streamline leanup setup for the mathlib-only workflow: flatten the mathlib project templates, validate interactive input, add clearer setup progress logs, and verify the result with import Mathlib.Init plus #eval Lean.versionString
• stop shipping version-specific bundled top-level manifests; instead generate lake-manifest.json from resolved .lake/packages when git metadata is available, while keeping the existing update/cache-get fallback path
• polish cache tooling with a single leanup mathlib cache pack command, correct symlink-root archive packing, and add an optional --pigz flag for parallel compression when pigz is installed
• bump LeanUp to 0.2.0 and refresh docs/tests to match the final setup and cache workflow

Testing

• pytest tests/test_setup.py -q
• pytest tests/test_mathlib_cache_cli.py tests/test_setup.py -q
• pytest tests -q