fix: generate Claude runtime under the install root

[yasuhirofujii-medley]

Summary

• generate Claude skill docs into the install root instead of reading directly from the source checkout
• link top-level Claude slash commands from the generated runtime root
• add setup regression coverage for runtime-root linking and repo-root generation

Why

This keeps the Claude install self-contained under the chosen install root and makes the top-level skill links point at the runtime that setup actually generated.

Testing

• bun test ./test/gen-skill-docs.test.ts --test-name-pattern 'setup script validation'