Beta migration assistant workflow

• Adds staged migration flow: scan, plan, apply --global, apply --skills, validate
• Repositions cc2codex as an unofficial Codex migration assistant for fast migrations
• Improves safety with selective apply, backup fixes, warning/reporting, and stronger validator coverage
• Fixes MCP and plugin migration consistency, including real plugin writes for bundle-plugins --apply
• Adds test coverage for staged flows and real-world migration regressions