Enhance Docker PHP setup and Caddy configuration

- Updated the `docker-php-set-file-permissions` script to include `/config` and `/data` directories for permission settings.
- Simplified the Dockerfile by removing unnecessary comments and ensuring the correct environment variable is used for the health check command.
- Adjusted the SSL generation script to clarify the notice regarding Caddy Auto HTTPS.
- Improved the Caddyfile by adding clear section headers for global configuration, common snippets, and dynamic imports, enhancing readability and organization.

Author: arnaud-ritti