fix(docs): update all stale command paths and version refs for three-tier CLI (#106)

- Replace every old flat-namespace command (muse notes, muse harmony, muse hotspots, muse patch, muse query, muse reserve …) with the correct three-tier path (muse midi …, muse code …, muse coord …) across all 12 affected doc files. - Update docs/README.md: replace "15 commands" count with three-tier description; add cli-tiers.md to Quick Navigation and directory map. - Expand CLI Command Reference in muse-vcs.md into three explicit tier sections (Tier 1 plumbing, Tier 2 porcelain, Tier 3 semantic). - Fix module tree in muse-vcs.md: "14 commands + domains" → accurate Tier 1/2 description. - Bump version references from v0.1.1 → v0.1.2 across all docs. - Update test count from 691 → 1903 in muse-vcs.md.

Co-authored-by: Gabriel Cardona <gabriel@tellurstori.com>