I am slow to adopt Arduino IDE 1.6.13 just a few days ago as experimental. After it compiled a custom hardware (328PB), I inspected the results in its build folder. The build folder name has changed from build215309328509385.tmp into arduino_build_409850. Also there are two .HEX files, with the second one marked as with_bootloader. This is interesting. I used to manually combine them in a text editor when I need the code with bootloader. Is this a few feature of the IDE or maybe a feature of the particular hardware files?
New IDE feature. Been there since sometime in 1.6.x
I just tested with my trusted 1.6.5 r5. That feature has definitely NOT been there. It must have been added after 1.6.5 r5. I wonder what made Arduino LLC developers add this feature, not that I'm complaining.