After digging around on a separate problem, I found that
avr-gcc and some more tools can be found in two different locations:
(1): C:\Program Files\Arduino\hardware (2): C:\Users\<user>\AppData\Local\Arduino15\packages\arduino
These two folders also both contain similar copies of the
hardware directory where all the bootloader hex-files and source code is stored:
(3): C:\Program Files\Arduino\hardware\arduino\avr (4): C:\Users\<user>\AppData\Local\Arduino15\packages\arduino\hardware\avr\1.6.17
I say similar because the
bootloaders\caterina folder in (4) contains quite a few hex-files that are missing in (3).
When burning a bootloader, looking at verbose output from the Arduino IDE reveals that hex-file and executable of avrdude from (2) are used, not (1).
What is the reason for this? My guess would be that location (1) is deprecated, but why choose to put stuff like this into Appdata in the first place?