Is there anyway to stop the debugger from halting on the auto_prepend_file with ?

I would like it to ignore the file. I cannot simply remove the file as a lot of legacy code relies on it to remap the DOCUMENT_ROOT environment variable as we are in a mass virtual hosting environment on Apache. https://issues.apache.org/bugzilla/show_bug.cgi?id=26052

Any ideas of how to get round this situation?

Thanks.

PhpED would not need to load this file if it wasn't going to show you its content with currently executed line.
There are two solutions:
1) uncheck "Stop on the first line after run" and rely on breakpoints and/or DebugBreak() calls.
2) have local copy of the file and add an extra mapping entry (Project Properties->Mapping tab) that will establish connection between /etc/php5/ and the local file's directory.