Don't load configuration files from /etc/suricata if Suricata is rooted at /opt/suricata.
If Suricata with bundled Suricata-Update is installed with a --sysconfdir of something like "/opt/suricata/etc", it will still load configuration files (ie. modify.conf) from /etc/suricata. This should not happen, it should stay within the bounds of --prefix, --sysconfdir, --localstatedir and --datarootdir for reading and writing.
Setting target to 1.3.0 as this could affect existing installations. So not planning to fix this issue in 1.2 or 1.1.