configure_alpm() in alpm-utils/src/conf.rs:45 configures hook directories with:

alpm.set_hookdirs(conf.hook_dir.iter())?;

set_hookdirs wraps alpm_option_set_hookdirs, which replaces the entire hookdir list. alpm_initialize adds SYSHOOKDIR (/usr/share/libalpm/hooks/) to the list by default, but this call overwrites it with only the directories from pacman-conf output (typically just /etc/pacman.d/hooks/).

so any consumer using alpm_with_conf or configure_alpm to set up a handle will not find system hooks, and post-transaction hooks do not run.

pacman itself calls alpm_option_add_hookdir for each configured directory rather than alpm_option_set_hookdirs, which preserves the system directory that alpm_initialize already added.

is the current behavior intentional, or would it make sense to align with pacman and iterate with add_hookdir instead?