I have used eclipse and pydev to do calibre development for some 3 years. A few times I have looked at what it would take to connect the debugger and have always given up. The many hours I would spend to probably in the end fail are better spent doing something else.
My take: calibre has a very complex startup structure, working through the OS and file systems it is running on, which host libraries are in use, whether or not it is running from source, loading its C helper libraries, and installing the zipfile module loader. As far as I can tell the debugger runtime can't handle all of that. Perhaps you can prove me wrong.