Great tool, thank you for building it and sharing it. I especially like your configurability among what to clone or not, and your good handling of so many edge cases.

IMHO the concept of "deep clone" is a design pattern and a potential language improvement idea. An example is "How does this deep clone handle external items, or transient items, or circular items?" Your project shows (correctly IMHO) that there many be many choices, and also reasonable defaults.