The only layer is the PHP processor, which can be used by any web server as a handler for PHP pages. The global configuration file includes a list of libraries, which are available to all pages.
The server holds a dictionary of objects in memory for each session, accessible as the $_SESSION array.
All the source files are simply copied to the web server.
Some third party tools of varying quality exist, but PHP is typically developed with a text editor and an FTP client.