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 529 (Still more bug fixes)
merge develop -D org -I include -E exclude: PR 548 (SEQ: do not automatically pick up files with the .seq suffix)
merge develop -D org -I include -E exclude: PR 556 (Add ``mkfake`` tool)
merge develop -D org -I include -E exclude: PR 559 (Complete revert of Image->Transform)
merge develop -D org -I include -E exclude: PR 561 (Update Bio-Formats 5 docs to 2013-06)
merge develop -D org -I include -E exclude: PR 562 (Zeiss CZI improvements)