Good to hear you're enjoying the software.
This issue was reported off-list by another user late last year, and users will be warned if it might happen in version 3.1. It is logged under
The workaround in that issue is to set your working directory under the File menu. That is where any temporary files are written, and for some reason the Mac version of Biodiverse sets it to be the system root directory.
The other alternative is to not write out any checkpoint files. They were originally added as a workaround for crashes caused by memory leaks, as then the system can be restarted from the most recent checkpoint. Those leaks were fixed for version 0.18, so
they are no longer needed for that purpose.
To disable the checkpoints, set the value to -1 (this is the default value).