Update ome_tools.jar to include almost everything that loci_tools.jar does

Only slfj4-log4j and log4j are removed.  See ticket #11955.
merge dev_5_0 -D org -I include -E exclude: PR 871 (Fix tiled TIFF reading and writing)
merge dev_5_0 -D org -I include -E exclude: PR 874 (SDT: read each data block into a separate series (rebased onto dev_5_0))
merge dev_5_0 -D org -I include -E exclude: PR 880 (Update ome_tools.jar to include almost everything that loci_tools.jar does)