Can I use Eclipse CDT to debug a PIC18 using PICkit3?
Theoretically, it's possible to build stuff. The XC toolchains are based around GCC, so if you could figure out all of the needed command-line arguments, they should work with any IDE. That being said, one of the nice things about using the IDE is it abstracts those command-line arguments away into nice menus and GUIs.

Where you may run into difficulty is flashing and debugging, as these are functions of the IDE itself (to the best of my understanding) and not the XC toolchains themselves.