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I figured out how to enable and change the pullup/puldown on the GPIO pins, including I2C, etc. It's actually very easy and straightforward.
If you look in /sys/kernel/debug/gpio_debug/gpio* you will see a whole slew of pseudo-files. Two of those are current_pullmode and current_pullstrength. To turn on e.g. a 2k pullup, you just do:
echo "pullup" > current_pullmode
echo "2k" > current_pullstrength
You can get a list of the values that are accepted by catting e.g. available_pullstrength.
I tested this with a volt meter (both the voltage for pullmode and current for pullstrength), and it appears to work as expected.