fix Zeiss readers to include ROIs in metadata store

fillMetadataPass7 processes the ROIs noted by storeROIs
merge dev_4_4 -D org -I include -E exclude: PR 673 (Make configuration file suffix configurable)
merge dev_4_4 -D org -I include -E exclude: PR 683 (Avoid throwing exception when parsing URL in Location constructor)
merge dev_4_4 -D org -I include -E exclude: PR 690 (Bio-Formats downloads page (rebased onto dev_4_4))
merge dev_4_4 -D org -I include -E exclude: PR 691 (ND2 defensive parsing)
merge dev_4_4 -D org -I include -E exclude: PR 694 (Properly populate metadata with Zeiss ROIs)