Compressing the entire archive
$phar->compress();
overrides your stub file.
Use compressFiles to have the the files compressed keeping your own stub in tact (which is not being compressed).
The compression is a little bit worth (since one file is left uncompressed), but enables you to have your own stub file executed with browser requests.
Don't get confused, compressing doesn't rise the security level of your code or obfuscating it strongly enough. The source code of your compressed phar is still easy to read.
