Not sure if this is the right place to log the issue, but the source kernel-headers package doesn't match the kernel for version 1.20161101-1 0

raspberrypi-kernel_1.20161101-1_armhf.deb installs in/as

./lib/modules/4.4.27-v7+/...

With a funny looking symlink

./lib/modules/4.4.27-v7+/source -> /kernel_repos/adafruit/adafruit-raspberrypi-linux/v2

But raspberrypi-kernel-headers_1.20161101-1_armhf.deb installs

./usr/src/linux-headers-4.4.26-v7+/...