Replace existing duplicate files on APFS with clones
As of June 2020, Jdupes can do this.
For example, this will find all duplicates in your Applications folder:
jdupes --recurse --dedupe /Applications/ 

WARNING: Versions before 1.19.0 will overwrite metadata (date, owner, permission), more recent versions preserve all metadata when using jdupes --dedupe on APFS filesystems.