Centralize CLI command discovery

[rtcoder]

Summary

• add a shared CLI command registry for framework, application, and module commands
• use the registry in the main CLI dispatcher and help command
• normalize command names across colon, dash, underscore, and class-like forms
• document command discovery in README, developer docs, and refactoring notes

Tests

• composer validate --no-check-publish
• composer test
• ./shift help migrate-status
• DB_CONNECTION=sqlite DB_DATABASE=:memory: ./shift migrate-status