docs: prepare server Codex deployment handoff for ThothII and Omics

PROJECT_STATE.md

@@ -29,15 +29,15 @@ independent reviews, local browser checks and rollback details.
 
 Current rendering architecture is in `docs/architecture/application-shell.md`;
 the exact portal identity/proxy contract is in `docs/install/authentication-upstream.md`.
-`docs/operations/shell-and-localization.md` is the configuration and coordinated
-Omics delivery/deploy runbook, including server-side fetch GitHub → explicit push
-Gitea PSD from `/home/chirone/omics_portal`. The acceptance matrix is
+`docs/operations/server-codex-handoff.md` is the current server delivery/deploy
+runbook, including Omics source integration from GitHub, configuration, tests and
+rollback. It supersedes the earlier Omics repository-relay instructions. The acceptance matrix is
 `docs/testing/authentication-manual-acceptance.md`. README, documentation navigation,
 user/installation/authentication guides and descriptor examples point to these
 paths. Local examples explicitly use full/en; the projected server example is
 for standalone OIDC, not Omics upstream. No runtime configuration or deployment
-was changed by this documentation pass. Closing/merging the branch and actual
-PSD acceptance remain separate, unperformed steps.
+was changed by that documentation pass. The 2026-09-14 delivery is prepared for
+promotion to main; the actual merge is recorded in Git. PSD acceptance remains pending.
 
 ### Navigation readiness and session accordions — 2026-09-13
 
@@ -64,27 +64,23 @@ Core, catalog, Qdrant and embedding containers were not changed. The prior
 frontend image is retained as
 `thothii-frontend:before-single-session-accordion-20260914` for rollback.
 
-### Agreed Omics delivery route — 2026-09-13
+### Current Omics delivery and server handoff — 2026-09-14
 
-The owner approved GitHub as an intermediate transport for Omics: publish only
-`codex/thothii-embedded-shell` from the Mac to
-`https://github.com/Dallavilla-Tiziano/omics_portal.git`. The operator then works
-in `/home/chirone/omics_portal` on the PSD server, fetches that branch without
-changing the shared checkout, verifies the delivered SHA, and pushes only that
-branch to `ssh://git@localhost:2222/aritmolab/omics_portal.git` using existing
-server credentials. Do not require a PSD Gitea token on the Mac to continue.
-Do not use the server's dual-push `origin` or merge into its current branch as
-part of transport. Production integration/rebuild is a separate operator gate.
-ThothII still uses its canonical TYL Gitea; this exception is for Omics only.
-Exact commands and the handoff are linked from
-`docs/operations/shell-and-localization.md`; the full server procedure lives in
-Omics `docs/thothii-integration.md`. Never report the PSD push or production
-deployment as complete until the operator supplies confirmation.
+The owner corrected the delivery requirement: Omics is obtained from GitHub,
+not relayed to another repository as part of this deployment. Any optional
+server-side repository copy is solely the owner's separate concern. This
+supersedes the 2026-09-13 relay agreement, including historical delivery notes
+in the Omics branch. Do not make another remote publication a prerequisite.
 
-GitHub delivery verified on 2026-09-13 at
-`fca10901a73666ca257d8f4cc4b77066295c400a` (functional commit `95154e1` plus
-the server relay runbook). GitHub `master` remains `aff7581`. The operator's
-PSD Gitea push and production deployment are still pending.
+GitHub branch `codex/thothii-embedded-shell` at
+`https://github.com/Dallavilla-Tiziano/omics_portal.git` was reverified at
+`fca10901a73666ca257d8f4cc4b77066295c400a` (functional commit `95154e1`).
+The server operator integrates it with the current code in the confirmed Omics
+checkout, normally `/home/chirone/omics_portal`, preserving later server changes.
+`docs/operations/server-codex-handoff.md` is the authoritative ordered procedure:
+inventory, source verification, native CLI and installation projections,
+embedded/upstream auth, Omics templates/static assets/proxy, coordinated rollout,
+acceptance and rollback. Server deployment and real IdP acceptance remain pending.
 
 ## Current product shape