As titled state I’m looking for an example of the JavaScript agent being used with a cli.
?
Do you mean like a CLI command executing a node script that includes a call to the IC via the JS agent?
Not sure exactly neither what you are looking for neither.
In Juno got plenty of NodeJS scripts 
https://github.com/buildwithjuno/juno/tree/main/scripts
To load the identity from the pem file of dfx I use the solution of @ZenVoich https://forum.dfinity.org/t/using-dfinity-agent-in-node-js/6169/60?u=peterparker
Which I implemented in that script utils https://github.com/buildwithjuno/juno/blob/9bb589e98ba04997d734cacb94e47d5ea18c8b80/scripts/identity.utils.mjs#L32
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