Add garbage collection design for layers and universes
- Layer GC: aggressive cleanup after each run, delete any layer
not referenced by current solutions
- Universe GC: store universe refs in each package's docs directory
(universes.json), derive live universes from blessed packages,
delete unreferenced universe directories
The universe refs move atomically with the docs via the same .new/.old
swap mechanism, so failed rebuilds keep old universes alive.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>