update internal CLI prune_pkgs

[Borda]

What does this PR do?

by default run prune package on all requirements files to reduce issue with setting wrong file

Does your PR introduce any breaking changes? If yes, please list them.

that was our issue in past #12318 (comment), we were removing horovod from a file where it was not
now it is from all require files unless you set a specific i=one

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Did you have fun?

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cc @carmocca @akihironitta @Borda

[tchaton]

LGTM !