Yeah, that is the one major annoyance with CGI::Ajax, it kind of takes over completely. When you call build_html, it actually spits out a big mess of javascript into your page to make its magic work, and then, when you call one of its javascript helper functions, it intercepts that and takes over the back-end request handling, bypassing whatever your normal dispatch method might be. Towards the end of my time using CGI::Ajax, I delved into that and managed to at least partially unravel it and figure out how to bypass some of the magic, but I don't recall any of the details, only that I did it.
These days, I'm using Dancer and Dancer::Plugin::Ajax, which requires me to manually write a little bit of javascript to invoke the ajax functionality, but it's much more transparent and fits into the rest of the application's framework, so I feel it ends up being a lot easier to work with overall. But that might not be an option for you if you're already dealing with legacy CGI scripts and aren't in a position to migrate to Dancer.
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