WIP Remove more compile errors
WIP: first pass of compiling code

Note that the scifio methods are commented out since they rely on earlier
ImgPlus definitions. We need to update scifio to use a newer beta of imglib2
and depend on the img-metadata definitions.

Also note that this version should not run. There are some compromises in
place that are a little questionable. They are makred in the code with an
all caps EVIL tag. They need to be revisited.