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> Last year, postmarketOS core developer Pablo Correa Gomez and a few others started an effort to move the FHS work under the freedesktop.org banner and create 4.0 of the standard

No. freedesktop.org is the place where standards go to die and CADT development takes place.

A little surprised that the linked systemd file-hierarchy(7) manpage makes no mention of /opt
>there's far less emphasis on creating native distribution packages for third-party software in 2025. Flatpaks, Snaps, and AppImage packages seem more popular with desktop-application developers these days. A lot of server-side software is now expected to be deployed as a container—or a group of containers run in Kubernetes—rather than installed as a package.

Are CLI tools or low-level, privileged software (e.g. anything that requires root) also distributed using flatpak or snap these days?

There's an awful lot of back and forth in the comments there over whether it should be a specification that defines its requirements in terms of whatever systemd programs happen to do, or whether it should be a specification with its own concrete basis that systemd is held to like everything else.
Honestly? We need not a successor of FHS but of filesystems, who are intimately tied package managers and installers. Zfs timidly start the change, with IPS (Image Package System) and BE (Boot Environments, as zfs clones), and we need to go much beyond that instead of wasting resources keeping up an '80s model like some do from btrfs to stratis.

We need:

- query-able storage, because search&narrow is the current way of accessing information and collecting/transcluding data is the way to go;

- easy storage management, the "rampant layer violation" of zfs we really need;

- integration of such storage to the software stack, from the OS to single packages, it's a nonsense having to "spread" archives in a taxonomy to deploy them or downloading archives to be unpacked as well for updates when we have send-able filesystems (zfs send of snapthots) and binary diff (from a snapshot "tagged version" of a fs-package to another, sent over internet).

Unfortunately we need operation people together with devs and nowadays operation is nearly disappeared. Devs alone can't understand what we need, they can't go beyond their desktops in a mass large enough to avoid a positive evolution.