Update command reference documentation with new features and structure

This commit updates the command reference documentation to align with
recent changes to the Makefile and Docker configuration:

- Add environment variables section for easier manual command execution
- Update all commands to use APP_DIR instead of APP_DIRECTORY
- Add new commands: composer-script, apidocs-generate, apidocs-serve,
  php-connect, and mailhog
- Replace old clean/clean-all commands with env-clean/env-reset
- Improve manual alternative commands with better error handling and
  variable usage
- Add examples for commands that accept parameters
- Update framework installation instructions with new configuration approach
- Add detailed documentation for container shell access
- Improve explanations and examples throughout

This update ensures the documentation remains a valuable reference for
users who cannot use Make and need alternative command-line approaches.

Author: nanoninja