The issue:
When selecting a nav menu item that links to a differing html file, the nav panel 'auto-closes'. This is an awkward UI experience as you're eyes are fixed on a group of links and then POOF, they're gone when you click them. The behavior is shown at 0:13s in the first video below.

I would recommend an option to neither 'auto-scroll' nor 'collapse' the nav menu items as the links are expanded and clicked. If you expand a parent menu item to reveal say, 2 sub-items, then having the nav list "shift around" as you click sub-items is cognitively and visually confusing. Tree based 'explorer' navigation with expansion have been around forever and none of those trees 'auto-scroll' or move the contents about when you select items...so folks are used to that navigational paradigm. Ideally, you'd like the nav tree to stay put as you're clicking/expanding them as you're mind has registered them in a fixed location that your mouse needs to move to. Otherwise, you end up 'chasing links" around the nav menu as they jump around. Making it an option still would allow the current behaviors of course.