Align context and metadata-declared skills with Rust.

[samuel-williams-shopify]

agent:context:list, show, and install handle ordinary context and metadata-declared skills together. The list marks skill documents, show reads them by source filename, and install refreshes all definitions from the selected providers.

Package#definitions holds ordinary Definition instances and Skills::Definition instances in one collection. Installer#install resolves providers and loads their definitions once, then applies the appropriate destination and ownership rules. Skill front matter is updated through Markly's native front matter node; authored metadata and the original Markdown body are retained, with resolved ecosystem, package, and version recorded under metadata.

The shared design document maps the Ruby classes to the Rust implementation, and the shared specification defines the observable contract. Validation: bundle exec bake decode:index:coverage lib, bundle exec bake test (83 tests), and bundle exec rubocop pass.

Companion PRs: Rust implementation, Ruby conventions, and standalone gem deprecation.