Make sure that the configuration file suffix is propagated to subdirs

This prevents alternate configuration files that aren't in the top-level
directory from being ignored.
merge develop -D org -I include -E exclude: PR 528 (Tile performance improvements for VMS and NDPI)
merge develop -D org -I include -E exclude: PR 836 (Update JPEGTurboServiceImpl.java)
merge develop -D org -I include -E exclude: PR 857 (Initial support for Zeiss .lms files)
merge develop -D org -I include -E exclude: PR 858 (Initial support for Veeco AFM data)
merge develop -D org -I include -E exclude: PR 859 (Assorted metadata/tile parsing fixes)
merge develop -D org -I include -E exclude: PR 865 (Remove docs/release section from the Bio-Formats repository (rebased onto develop))
merge develop -D org -I include -E exclude: PR 868 (Make sure that the configuration file suffix is propagated to subdirs (rebased onto develop))