Ok, it has been discussed in the past, but I couldn't figure out what is the current state (or I can't find a working state).
When in the new Jucer, I set a "header search path", I can't figure out how relative it is from the current project (or it doesn't work, since I don't see this path in the output XCode project).
Ideally, this should also be in the main project tab (not in the debug/release one, since for 99% of people, it'll be the same for both configuration), just don't remove the existing one and add a "+" button that pop up a file browser dialog to select the folder.
Similarly for the final libraries to link with. I've tried to put -L and -l in the GCC based specific linker line, but it's a bit counterintuitive, if you need to know the command line of the tool, why should we use a front end?
If you want to be high level, you'd add a "Dependencies" tab/dialog, where one would select the include paths + libraries to build with. The Jucer would then add a common include path for all exporters, but add a per-exporter library link command.
If you have additional resources, it could go there too.