monopam: unify root-file generation in new Root module
Replace the two duplicate dune-project generators (Init.write_* and
Import.update_root_deps) with a single Monopam.Root module that
computes and regenerates the four monorepo root files — dune-project,
README.md, llms.txt, CLAUDE.md — with one git commit per run, only
when files actually change.
Identity-preserving dune-project: regenerated from scratch but the
top-level (name ...) and root package (maintainers ...) / (authors
...) are carried forward when set, guessed from the global git user
otherwise. Lang version bumps from 3.20 to 3.21. Root.opam is no
longer written explicitly — dune handles it via (generate_opam_files
true). Added Root.check for dry-run diffs, surfaced through Lint.