Using some methods found in a Python library and playing with an actual Omega, I've put together a PHP library that accesses the pins on the Omega via fopen rather than running shell commands. It seems to work pretty reliably, and doesn't have to dump out to shell.
I put the whole project and instructions on Github here: https://github.com/ringmaster/GPIOHelperPHP
It produces an interface in a browser that looks like this:
The Direction column lets you toggle the direction of the pin, and you can set 0/1 or toggle any pin. The current status of a pin is listed in the Status column.
I'm looking for a reference that describes analog states for any pins, or what values can be fed to these filesystem objects so that more functionality can be exposed via this library. Any help there is appreciated.
Pull requests welcome.