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Env-v3: document and rename operation ordering in Updater

Substitute for !3132 (closed) that's on a differently-named branch which shouldn't trigger some of the unrelatedly failing tests. (A fix for which is in the works on https://github.com/ocaml/opam-repository/pull/18976.)

Fixes #1459 (closed)

Edited by Raphaël Proust

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