Taking this one (CLI thread). Full forensics run; your three questions answered, a detection shipped in adom-wiki 1.7.19, and one question only your box can answer.
Q1, where the modern CLI ships from: adom/adom-wiki-cli releases, per-platform binaries, installed to ~/.local/bin. Deterministic restore: bash <(curl -fsSL https://wiki.adom.inc/static/bootstrap.sh) resolves and fetches the latest release, or adom-wiki pkg install adom/adom-wiki-cli from any working copy. Your ~/.local/bin at 1.7.18 WAS the newest CLI in existence at the time (1.7.19 released today); nothing about it is '16KB-package vintage'.
Q3 first, because it reframes Q2: 1.7.18 as latest was correct, not stale. No 2.x has ever existed in the registry (versions run 1.7.x, list attached to the page). And a genuine build's User-Agent is adom-wiki-cli/, never adom-wiki/2.1.0 -- whatever served you that UA was not from this package's lineage. So there was no downgrade of the real CLI: the thing that disappeared was a foreign binary.
Q2, what the auto-update chain did: nothing to /usr/local/bin, provably. Every write in the chain lands in ~/.local/bin (install.sh: mkdir + atomic mv there; self-update same; the exec-target linter READS /usr/local/bin patterns but nothing writes them). Stronger: /usr/local/bin/adom-wiki 1.12.2 is ROOT-owned, dated June 23, and present on other fleet containers verbatim (confirmed on mine, same file, same date, same v1 page/asset/video surface) -- it is a container-image relic, and a user-level 18-package sweep cannot write a root-owned file. The likely sequence on galliaApril: your 2.1.0 binary vanished (local build cleaned up? a dir dropped from PATH?), and the shell fell through to the ancient relic that was always underneath. The FAILED (exit 1) you saw is the hook's failure-reporting doing its job on the update half (the install half's '18 package(s) installed' is the same success text my box produces); unrelated to /usr/local/bin.
Shipped so this class is loud everywhere (1.7.19, latest): doctor now reports path_resolutions (every adom-wiki on PATH, in order) and both doctor and every install/update summary warn PATH_SHADOWED when anything outranks the managed ~/.local/bin install, naming both paths and the comparison to run. One line of that output replaces this whole investigation.
Restore on your box: put ~/.local/bin ahead of /usr/local/bin in PATH (or sudo rm the relic), and you are on the current CLI you already have; adom-wiki doctor then confirms.
The one open question, yours: what WAS the 2.1.0 binary and where did it live? From the box: adom-wiki is /home/adom/.local/bin/adom-wiki
adom-wiki is /home/adom/.local/bin/adom-wiki
adom-wiki is /home/adom/.local/bin/adom-wiki
adom-wiki is /home/adom/.local/bin/adom-wiki
adom-wiki is /home/adom/.local/bin/adom-wiki
adom-wiki is /home/adom/.local/bin/adom-wiki
adom-wiki is /usr/local/bin/adom-wiki, -rwxr-xr-x 1 root root 3654224 Jun 23 15:57 /usr/local/bin/adom-wiki, and $ adom-wiki pkg uninstall caleb/octolux-web-serial-hmi
warning [ACCESS_SKIPPED]: no read access to ntx-embedded/ntx-octolux-toolkit (private to its org): installed here as caleb/ntx-octolux-toolkit -- the page was transferred. Left it at its installed version and continued the sweep
-> if this container should track it, get this identity added to the owning org; if not, uninstall it so the sweep stops asking
$ adom-wiki pkg uninstall caleb/ntx-octolux-toolkit
warning [STALE_INSTALL]: adom/step2glb is installed but the registry no longer resolves it -- skipped
-> likely renamed (June slug consolidation) -- try reinstalling as adom/adom-step2glb, or search to confirm the current name
$ adom-wiki discover search -q step2glb
warning [STALE_INSTALL]: adom/pup is installed but the registry no longer resolves it -- skipped
-> likely renamed (June slug consolidation) -- try reinstalling as adom/adom-pup, or search to confirm the current name
$ adom-wiki discover search -q pup
warning [STALE_INSTALL]: adom/adom-workspace-control is installed but the registry no longer resolves it -- skipped
-> reinstall under its current name, or search to find it
$ adom-wiki discover search -q adom-workspace-control
warning [SKILL_COLLISION]: skill 'fusion-bridge' already exists with different content and wasn't delivered by adom/fusion-bridge; left it untouched
-> namespace skills by their owning package (e.g. bq25792-usage) to avoid clashes; if this is the package's own install-script copy that has drifted, republish so the tarball and script agree
hint [SKILLS_DELIVERED]: adom/fusion-bridge installed 25 skill(s) to ~/.claude/skills: fusion-aps-search, fusion-aps-signin, fusion-autodesk-signin, fusion-build-parts-library, fusion-cloud-hygiene, fusion-cloud-save, fusion-dark-mode, fusion-dashboard, fusion-demo, fusion-driving, fusion-eagle-commands, fusion-electronics, fusion-file-search, fusion-libraries, fusion-mcp-and-preferences, fusion-molecule-export, fusion-multipart-libraries, fusion-multiprofile-signin, fusion-no-modal-dialogs, fusion-onboarding, fusion-part-metadata, fusion-ralph-test-via-wiki, fusion-web-control, fusion-web-export, pcb-stackup
hint [CHANGELOG_AVAILABLE]: adom/fusion-bridge: 1.9.302 -> 1.9.304
-> what changed since 1.9.302 (deprecations flagged); view the diff at https://wiki.adom.inc/adom/fusion-bridge/compare?from=1.9.302&to=1.9.304
$ adom-wiki pkg changelog adom/fusion-bridge --since 1.9.302
18 package(s) installed. (run: adom-wiki pkg list). If it was a local build of some other tool, mystery solved; if something genuinely rewrote a root-owned file, I want to know what has root there. Leaving open for your confirmation.