Just a quick update:
I gave up, and tried reinstalling the 2.4.1 pl advanced, which all worked fine, except now my resource tree is empty.
I don't want to upgrade until I can actually fix this because I don't want to risk this happening on the live site, and I need the versions to match.
I've tried the:
compress_css - 0 (off)
compress_js - 0 (off)
suggestion but it makes no difference.
The Elements tree now works fine, as does the Files tree, and the Resources is just completely empty.
You can see the arrow to expand the list appear very briefly when the page loads, then it vanishes.
The resources are all present, and visible in for example resource search, but the resource nav tree is empty.
The site itself loads and runs fine, so it's purely a manager problem.
Given how common this problem is (
https://frogabog.com/news/2015/modx-manager-empty,-blank,-resource-tree-missing,-menu-non-functional-%28menu-doesnt-work%29/ but note there the fallback: if this doesn't work, reinstall), it might be worth taking a much closer look at it I think, for example, if this happened on the live site, that would be a killer, unless there's a fix that's not too hard.
I'm now at the point where I'm going around in circles, that is:
Updating the db with the live db data, clearing cache, logging out, clearing browser cache, etc, and I can also of course reinstall again, but technically, there's a point where I have to stop because it takes too much time from paying client work.
It seems to me like there's a major weak spot in the design if data in the database, which is readily accessible in the manager via other routes, like search for id, or title, etc, and visible in the resource list in search, isn't just there in the tree. It's like something in the programming is thinking too much rather than just looking for what is actually there and printing it out.
The only real difference between live and local systems is php versions and mysql versions (PHP live: 5.3.39, local: 5.6.15; mysql local: 5.6.27; live: 5.6.23)