The beautify plugin allows for a customized Php beautifier based on jedit indenter.

As I wanted something more sophisticated, I installed PHP_Beautifier which comes as a package under PEAR. This beautifier is written in Php itself. The beautifier can be called from the command line assuming there is a PHP-CLI installed, which is the case if we have Apache installed. I detected a bug in the available options listed in the documentation of PHP_Beautifier though, but the basic command:

$PHP_Beautifier -s4 -f SourceFile -o TargetFile

for instance, where -s4 means indent with 4 spaces, works fine for me on Ubuntu 10.04.

To speed things up in Jedit, I integrated PHP_Beautifier as a commando in the console plugin through a simple .xml file which basically: 1) makes a backup of the current buffer 2) calls the Php beautifier as a system command line as described above, and 3) replaces the current buffer with the beautified result.

Hope this helps.