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.