I know I can manually run it through PHP's exec() command but I was hoping if there was a ready to download and deploy PHP-based system that could act as a bridge and terminal and you can run commands on it like you were in the terminal itself.
Try PHPShell. I tried it and it works great. Although it can't use vim or any program that requires user input in the middle of execution but that's enough for me.
Kloxo has a command line interface, you can use it
PS: I don't think you can find a php script that acts like a terminal, i think you should go for java.
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