The FGD-parsing code is pretty well integrated now. Given an FGD and a BSP, it's easy to find all the places that models/sounds/materials etc. are being used in the map entity data. There are some wrinkles for relationships not part of the FGD, such as skyboxes on the "worldspawn" entity.
Right now I'm experimenting with rewriting the GUI as a backward/forward style interface (similar to an installer) and using the JSR-296 project along with property listeners. The older GUI code didn't need any of this since it basically functioned as a convenient way to launch a command-line program. However, I'm ditching command-line support until end-users seems to want it.