Add shadow suspend and refresh commands

[sjquant]

Why

• add explicit tracked shadow suspend/refresh commands
• make tracked root-instruction shadows survive upstream HEAD changes without relying on mutable cache state

Changes

• add skul shadow --suspend and skul shadow --refresh CLI parsing and execution
• persist raw shadow overlay content in registry metadata so refresh recomposes from stored state
• materialize tracked AGENTS.md and CLAUDE.md as shadows during add/apply/update and retire them correctly during remove/reset
• add CLI coverage for tracked AGENTS.md and CLAUDE.md shadow creation, suspend/refresh, reset, and cache-independent refresh