When there are several encrypted scripts on the site, each one contains functions rc4(), base64(), md5().
If you added the disable include option for these functions in the CLI, I could add them only to the first script.

I found that function mod2pi is not implemented yet, but mod works. Is there any list of implemented functions? Minimal working example is:

using Zygote

# This is working
gradient(x -> mod(x, 2pi), 1.)

# This is not
gradient(x -> mod2pi(x), 1.)

It will be good to analyze var_dump leftovers in project, and to add support for other functions that cause same behavior.