[MojoDwarf]

currently the base userland is not controlled by the pkg system. You can use freebsd-update to do a binary upgrade, which will also sync your kernel sources if you have stuff in /usr/src, so you can simply rebuild kernel after running the update.

Should be noted in 11-CURRENT there is currently ongoing work to move userland and the generic kernel into pkg, so look forward to that as well.

[voltagex_]

I reverted to a generic kernel (it doesn't look like I ever had /boot/GENERIC - did I read out of date doco?), then ran freebsd-update as normal. Seems to be fine. I'll rebuild my custom kernel later.