RAIS: fix Kryo serialization and setLength behavior

This is critical for big image (and slow setId) support.  See #12001.
Fix small discrepancies in I/O introduced during component migration
merge dev_5_0 -D org -I include -E exclude: PR 920 (Fix hard-coded link in documentation)
merge dev_5_0 -D org -I include -E exclude: PR 921 (Final BF doc updates for 5 release)
merge dev_5_0 -D org -I include -E exclude: PR 922 (Remove bioformats_package.jar from the bftools.files)
merge dev_5_0 -D org -I include -E exclude: PR 924 (I/O fixes for ticket #12001)