Combining Hex Files For Bootloader Projects etc
In MPLAB you could export a specific memory areas only hex file from a bootloader project and then use this:
Menu > Configure > Settings > Program Loading > 'Clear program memory uploading a program'
to import it into the main project so the hex files became combined. You can't in MPLAB X. Firstly you can't export a hex file and specify specific memory areas you want it to contain and secondly the 'Clear program memory uploading a program' option is no longer provided. The solution is to use "Loadable projects". Look at the MPLAB X IDE User's guide (stored under $inst_dir_mplab_x/docs/MPLAB_X_IDE_Users_Guide_52027B.pdf) at section 5.5 "Loadable Projects and files". Basically you can add to your project another project that will be 'loaded' in memory (merged with).