The wilderness permit reservation system within Yosemite National Park is operated by the good folks at the Yosemite Conservancy. They have been working hard to migrate to the internet the way hikers request permits, but I have it on good authority that, at least through the winter, the old fax system will remain in place. That means that it is likely that all 2016 John Muir Trail hikers, who begin in Yosemite, will get their permits the old way.
Last year the park service implemented changes to the wilderness permitting rules that made a huge difference to John Muir Trail hikers – particularly those who begin at Happy Isles. Among those changes were an exit quota over Donohue Pass and the complete elimination of walk-up permits for JMT hikers who want to begin at Happy Isles and exit the park. (Technically, you could still get a walk-up permit if someone cancels a reservation.)
I’ve been told that great progress has been made towards getting the reservation system online, but that the test site was just not working up to the standard they wanted. One can hardly fault them for wanting to do it right.