Remaining renaming

This contains the following PRs in order, rebased onto develop:

http://github.com/openmicroscopy/bioformats/pull/911
http://github.com/openmicroscopy/bioformats/pull/918
http://github.com/openmicroscopy/bioformats/pull/922
http://github.com/openmicroscopy/bioformats/pull/924
http://github.com/openmicroscopy/bioformats/pull/920
http://github.com/openmicroscopy/bioformats/pull/929
http://github.com/openmicroscopy/bioformats/pull/927

Together with gh-935, that should be all of the renaming changes that were made prior to 5.0.0.