docs: full sweep — domain-agnostic rewrite of all docs

README.md: fix repository structure tree, package install instructions, and CLI examples (remove legacy groove-check/emotion-diff, add revert/show).

docs/architecture/muse-vcs.md: complete rewrite from 8,751-line Maestro/ORM history to a clean 200-line domain-agnostic architecture reference covering the plugin protocol, core engine modules, commit data flow, merge/checkout algorithms, and command map.

docs/architecture/muse-e2e-demo.md: rewrite from Docker/HTTP/JWT walkthrough to a plain CLI walkthrough (init → commit → branch → merge → conflict → cherry-pick → revert → stash → tag).

docs/architecture/muse_vcs.md: deleted (exact duplicate of muse-vcs.md).

docs/protocol/muse-protocol.md: repurposed from Stori-specific variation UX to the language-agnostic MuseDomainPlugin protocol specification, covering all five method contracts, snapshot format, naming conventions, and invariants.

docs/protocol/muse-domain-concepts.md: new — answers the terminology question. Defines universal VCS terms, explains what "Variation" currently means and how it could generalize across domains, provides a cross-domain mapping table for music-specific terms (track, region, phrase, section, emotion), and gives guidance for new domain authors.

docs/protocol/muse-variation-spec.md: repurposed from full variation UX spec to a scoped music-domain reference, clearly noting it is not part of the core Muse VCS engine.

docs/reference/muse-attributes.md: generalized from music-specific examples (drums/*, keys/*) to a domain-agnostic format reference with a genomics example showing the format applies to any domain.