Chuck Burgess has posted a discovery he made while working with Eclipse PDT and a command line script that he needed to debug:
This week, I found a need to do this same kind of remote debugging, but for a command-line PHP script. This seems to be something that Eclipse is not already designed to do, as there is no "perpetual listener" available for its debug client. Instructions for remote CLI debugging are available, which showed me that environment variables might be the missing link to getting it working with Eclipse. It turned out to be one of two missing links. The other link was tricking Eclipse into keeping a debug session open (and therefore "listening").
He found that by loading up the PHP file in a shell script with the XDEBUG_CONFIG and XDEBUG_SESSION variables defined, it allows the Eclipse listener to connect and work through the file like a normal web page request.