Update CLI reference

[inteon]

Adds newly added flags and removes hidden flags.

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[inteon]

How was this generated? This doesn't match the changes from ./scripts/gendocs/generate-new-import-path-docs when run locally.

This is obviously an improvement, but my recollection was that this was done by a script!

Thanks for pointing me to that script, I did not realise it existed. I updated some issues that caused the script to fail for me & pointed the script to master, so it is up-to-date for release-next.

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