Well, this probably isn't exactly what you want, but maybe it'll spark some ideas:
http://www.cis.hut.fi/kaip/linkkuri-0.01.02.pl
Its Perl. The beauty about it is it uses RobotUA for bot handling and good behavior. It can be disabled though (see code comments). I believe you might use it with a command such as:
Find all files in your website:
linkkuri -c http://domain.example/ > mysite.txt
Which will find all site files and save the links to a file.
The only trick left to solve is formatting and viewing. One approach might be to use this Perl script as is and have PHP launch it and parse the output file...