I think this is something to fix in pacman itself. The default hookdir should be assumed to be relative to the root, in the same way that the DBPath is. Otherwise, you risk Bad Things™ happening due to the two not being in sync.

Yes Dave, I was initially surprised first, indeed I first think opening a ticket for pacman, but later reading pacman manpages seems to be the desired bahavior. In any case, the documentation seems to be confused al least for options about paths.

In any case I opened a ticket for pacman and --hookdir parameter. FS#49349

Hrm... in terms of being relative to the root --hookdir is acting the same as --dbpath and --config.

I think it would be okay to default HookDir relative to RootDir. But, regarding "Bad Things", -r is already dangerous when (mis)used this way. -r is not equivalent to a chroot, as many people seem to assume. It is just a path prefix determining where package files are extracted. The host config is still used, including DBPath and LogFile if they have been set. So, Bad Things™ can easily still happen even with paths defaulting under RootDir; we just don't see that because most people don't set those options. What we probably need is something like a --chroot option that gets prepended to all configuration paths even if they are manually set.

Unassigning myself - I am assigned to the bug on the pacman end.

This would be fixed by using --sysroot instead, cf. FS#58778