There is some more information about stubs here:
Creating Phar Archives: Introduction
To be written fully in the near future. Before reading this, be sure to read How to use Phar Archives.
A great place to start is by reading about Phar::buildFromIterator(), and the specifics of the file format choices available for archives. A healthy understanding of what a stub is and does is crucial to phar archive creation, and so Phar::setStub() and Phar::createDefaultStub() are good places to start as well. If you are distributing a web-based application, it is crucial to know about Phar::webPhar() and related method Phar::mungServer(). Any application that accesses its own files should also consider using Phar::interceptFileFuncs().