install-ldconfig-file target creates ${LOCALBASE}/${LDCONFIG_DIR} directory (which is usually /usr/local/libdata/ldconfig). It's in mtree for PREFIX == LOCALBASE case, but not for PREFIX != LOCALBASE, for which case it should be explicitly added to plist. This change fixes stage-qa for cad/brlcad and biology/emboss.
http://poudriere.amdmi3.ru/data/10-amd64-default/all_2015_08_11/logs/errors/emboss-6.6.0_2.log
http://poudriere.amdmi3.ru/data/10-amd64-default/all_2015_08_11/logs/errors/brlcad-7.24.0_3.log
While here, add indentation to make conditionals for more readability, end replace empty .if defined(USE_LINUX_PREFIX) ... .else block with .if !defined(USE_LINUX_PREFIX)