fix Zeiss readers to include ROIs in metadata store

fillMetadataPass7 processes the ROIs noted by storeROIs
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 635 (Use jgit-buildnumber to set version information in Maven)
merge develop -D org -I include -E exclude: PR 642 (DateTools fixes)
merge develop -D org -I include -E exclude: PR 643 (Data test updates)
merge develop -D org -I include -E exclude: PR 644 (Add support for writing ModuloAlong* annotations)
merge develop -D org -I include -E exclude: PR 686 (CellWorx: do not assume that the first well/field file exists (rebased onto develop))
merge develop -D org -I include -E exclude: PR 689 (Initial C++ implementation)
merge develop -D org -I include -E exclude: PR 697 (Avoid throwing exception when parsing URL in Location constructor (rebased onto develop))
merge develop -D org -I include -E exclude: PR 700 (ND2Handler: parse numbers defensively)
merge develop -D org -I include -E exclude: PR 702 (Upgrade SLF4J to 1.7.2 (rebased onto develop))
merge develop -D org -I include -E exclude: PR 704 (Properly populate metadata with Zeiss ROIs (rebased onto develop))