configure: fix secondary config file location when using --prefix=/usr #488

Job	Run time
build	1m 9s
build (--enable-snmp --enable-snmp-rfc --enable-json --enable-dbus --disable-checksum-compat --en...	56s
build (--enable-dbus --enable-dbus-create-instance --disable-dynamic-linking --disable-fwmark --d...	49s
build (--enable-dynamic-linking --disable-vrrp-auth --enable-snmp-rfc --disable-snmp-reply-v3-for...	51s
build (--disable-libnl --enable-snmp-checker --disable-vmac)	47s
build (--enable-conversion-checks --enable-stacktrace --enable-mem-check --enable-mem-check-log -...	46s
build (--disable-lvs --enable-snmp-vrrp --enable-snmp-rfc --enable-json --enable-dbus --disable-r...	47s
build (--disable-vrrp --enable-snmp-checker --enable-regex)	42s
build (--disable-hardening --enable-dump-threads --enable-epoll-debug --enable-snmp-rfcv3 --enabl...	50s
build (--enable-snmp-rfc --enable-snmp --enable-dbus --enable-json --enable-bfd --enable-regex --...	54s
	8m 31s

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