> this appears to disagree with the software-engineering principle of avoiding 
> a mutating global state

I disagree.
In embedded systems engineering, for example, it's customary to use
global variables to represent ports.

Also, I note that the use of global variables, is similar to using pen
and paper, to do mathematics and statistics.
(Which is good).
Whether that's consistent with software engineering principles or not,
I don't know.

However, I partly agree with you.
Given that there's interest from various parties in running R in
various ways, it may be good to document some of the options
available.

"Running R" (in "R Installation and Administration") links to
"Appendix B Invoking R" (in "An Introduction to R").
However, these sections do not cover the topics in this thread.

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