Complete revert of Image->Transform

Additional changes needed to fully revert:
https://github.com/qidane/bioformats/commit/d3c2ceb9b607c40411f89e1e67ee24aad0e06f95
As the changes were copied into released-schema/2013-06 between the original
commit and the revert, so the changes ended up still in released-schema/2013-06
version.
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 555 (Adding 2013-06 versions of the samples)
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)