Add command metadata and request diagnostics

[rtcoder]

Summary

• add #[Command] attributes for CLI command names, aliases, and help groups
• extend CommandRegistry with command definitions and alias resolution
• group ./shift help output and show aliases in command-specific help
• add ./shift doctor project diagnostics for PHP version, extensions, composer config, lint, tests, environment, database config, and module cache
• add request id lifecycle with generated or preserved X-Request-Id response headers
• include request id in structured exception log context
• update module command stubs, README, developer docs, and refactoring notes

Tests

• composer validate --no-check-publish
• find src application tests -name '*.php' -print0 | xargs -0 -n1 php -l
• composer test
• DB_CONNECTION=sqlite DB_DATABASE=:memory: ./shift ms
• ./shift help ms
• ./shift help
• DB_CONNECTION=sqlite DB_DATABASE=:memory: ./shift doctor
• ./shift h ms