So far it has been necessary to rename diffusion images in .nii or .nii.gz formats to .fsl and .fslgz respectively.

This should be avoidable after the DiffusionImage replacement and the adaption of the new reader/writer concept.

A .nii/.nii.gz is a valid diffusion image if it is accompanied by bvals/bvecs files.

Possible scenarios are:

foo.nii(.gz)
foo.bvals
foo.bvecs

bar.nii(.gz)
bar.bval
bar.bvec

Those files should be read and written. For saving purposes the alternative appending the s should be the default.