Merge pull request #553 from hinerm/itk_dirs

Updated ITK build instructions
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 534 (Revert "MetadataTools: Remove deprecated and unused methods")
merge develop -D org -I include -E exclude: PR 537 (Consolidate OME-XML primitive type logging)
merge develop -D org -I include -E exclude: PR 541 (Adjust logging of setId)
merge develop -D org -I include -E exclude: PR 544 (Zeiss ZVI: ignore invalid plane coordinates)
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 550 (AFI: only initialize internal SVS readers once per file)