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I usually pronounce it "clee." I have never really heard anyone say it out loud though.
Ha! That's where I was at. Looks like C-L-I is the way forward. I might secretly pronounce it "clee" when I'm alone though ;)
The appropriate pronunciation of CLI is "terminal".
Is it possible that they were saying see el eye with a strange accent?
Yeah. There was an accent (at least to me as an American). I definitely did a double take when I thought I heard "silly".
Have been working 20+ years (in the US) and never heard anyone say anything other than "C-L-I"
I say "command line" or "command prompt" when speaking to a Windows-based/minded audience. I drop the 'interface' part as there shouldn't be confusion over it.

I use "terminal" when speaking to a UNIX-based/minded audience.

I pronounce it "C-L-I" when thinking to myself.

I only say "C-L-I". It is an initialism (read the initials), not an acronym (read as a word).
I find that I generally pronounce 3 letter acronyms letter by letter but I pronounce four letter (or more) acronyms like words if I can, and only fall back to letter-by-letter if there's not an obvious word-like pronunciation. There are certainly exceptions ("SQL" being a notable one).
When people pronounce SQL as "sequel" and CLI as "clee", I insist on pronouncing PHP as "fap".