[masklinn]

> I heard people mentioning that (for 10.11 btw, not 10.10), but I never saw anyone give any reason for believing that that's what the installer was doing.

because that's exactly what the logs showed it doing: https://discussions.apple.com/message/26856483#26856483 and because the preemptive fix (if you hadn't started the update yet) was moving /usr/local's content elsewhere: https://jimlindley.com/blog/yosemite-upgrade-homebrew-tips/

And it was for 10.10. I'm sure people who'd been bitten (or had avoided it through the procedure above) repeated it for 10.11 reflexively or just in case, but the issue was the 10.10 upgrade.

[eridius]

Huh, I only ever heard people mentioning this issue for 10.11. Never heard about it at all when 10.10 came out. I bet that's why I never saw any explanation for this reason, because people who had heard about this with 10.10 were just assuming that's what was going on.

Incidentally, I had no idea about ⌘L to show logs during OS update.

In any case, even if the OS update takes a long time, the end result is you still have the same /usr/local you did before.

Also, FWIW, the discussion you linked to references TeXLive, as does the blog post you linked. I wonder if the issue here is not in fact having anything in /usr/local, but rather having used a package installer to install something into /usr/local (which I assume TeXLive does). It doesn't make much sense to me for the OS updater to move everything out of /usr/local and then back in one-by-one under normal conditions. But if you used a package installer to install into /usr/local, then it would make more sense for it to do something like that (which is to say, it may have special behavior around things covered by package receipts).

Edit: Well, under normal conditions, it might still move the folder away and back, but I'd expect it to just move all the top-level items from the folder back, instead of manually copying all of the nested files).