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The comment explains this in more detail, but basically one previously needed the `--from-git` option to `upgrade-zulip-stage-2` if one had last installed/upgraded from Git, and not that option otherwise, which would have forced us to make the OS upgrade documentation much more complicated than it needed to be.
This directory contains scripts that:
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Generally do not require access to Django or the database (those are "management commands"), and thus are suitable to run operationally.
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Are useful for managing a production deployment of Zulip (many are also used in a Zulip development environment, though development-only scripts live in
tools/).
For more details, see https://zulip.readthedocs.io/en/latest/overview/directory-structure.html.