docs: fix plan/repo drift, retire dead Goose+Nomos and Caveman tooling

Documentation and repo-hygiene pass following the client/server split:

Plan drift (audited all other active plans against current code):
- oikos-gaps-and-improvements.md: mark Section C and D.5 resolved (both
  described cmd/hermes, renamed to cmd/nomos with a real LLM loop since);
  refresh ~10 stale file:line citations; fix tool-count (33, not 28).
- liveness-drift-and-ux-cohesion.md: fix stale default-model claim (now
  deepseek-v4-pro since 2026-07-10) and "not yet deployed" status.
- nomos-agent-code-review.md: fix C1's citation (one unauthenticated route
  to nomos now, not two, after the client/server split).
- wails-desktop-app.md: record the production deploy outcome.

Repo structure: added missing directories to README/CONTRIBUTING layout
tables (checks/, tools/, cmd/webhook/, docs/operations/), fixed a broken
link, added ADR 0015 documenting the auth/CORS/client-split model (there
wasn't one despite CONTRIBUTING's own process requiring it), normalized
ADR 0013/0014's format drift, added an Authentication section to
AGENTS.md/CLIENTS.md (every example call was missing the now-required
bearer header).

Retired the Goose+Nomos workstation flow (bootstrap.sh --with-nomos,
tools/setup-nomos-soul.sh, .agents/operations/nomos-agent.md) and the
Caveman auto-install tooling (tools/setup-caveman.sh, tools/caveman/) —
both superseded by the production containerized Nomos agent, which has
never used either. Kept .agents/shared/caveman.md itself (the terse
writing-style convention agents still follow by reading it).

Deleted the orphaned legacy Python oikos/ directory — nothing imports it,
and bin/homelab (the CLI it was kept for) no longer exists in the repo.

Rewrote .agents/operations/agent-enrollment.md (365 -> ~110 lines) and
commands.md to match the current architecture instead of the retired
`homelab` CLI; migrated the still-true networking prerequisites (Netbird,
split-horizon DNS, SSH key distribution) into the knowledge base as a
runbook via upsert_knowledge rather than duplicating them in markdown.
Updated all 10 .agents/skills/ runbooks referencing the dead CLI with
their real MCP tool / REST API equivalents, or flagged them as needing
verification where no equivalent is confirmed yet.

Two real bugs found and fixed, not just docs:
- The tools/setup-*.sh auto-setup glob was tools/*.setup.sh in THREE
  places (tools/post-pull.sh, bootstrap.sh, and internal/httpapi/impl.go's
  GetClientContext handler) since the mechanism's introduction on
  2026-06-02 — never matched any real filename, so no client has ever
  picked up an auto-setup script via git-pull or the context-poller sync.
  Fixed all three; the Go server-side fix is the one that actually matters
  since it's what the current context-poller mechanism depends on.
- bootstrap.sh removed dead vestigial --gitea-token/--gitea-user flags
  (parsed, never consumed) left over from an earlier clone-based model.

Also flagged, not fixed (documented as an open gap in
client-enrollment/SKILL.md): bootstrap.sh tells a freshly-enrolled client
to call POST /api/v1/clients/{slug}/activate to finish enrollment, but
that route doesn't exist in api/openapi.yaml — EnrollClient sets entities
to provisioning and nothing currently transitions them to active.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

.agents/operations/commands.md

@@ -53,34 +53,36 @@ Run from the [hubris host](../../archive/knowledge/hosts/hubris.md) as root. Whe
 
 ## Fleet apt operations
 
-Two `homelab` subcommands wrap the common patterns; both fan out to hubris + every LXC.
-
-| Command | What it does |
-| --- | --- |
-| `homelab apt-audit [--target HOST]` | Per-host table: dpkg-interrupted state, holds, upgradable count, non-apt binaries in system paths, DNS health. Exits nonzero if any host has dpkg-interrupted state. |
-| `homelab apt-upgrade --target HOST` | Launch `apt update && apt upgrade` inside a transient `systemd-run --collect` unit on the target. Survives ssh teardown. Apt configured with `Acquire::Retries=3` + `ForceIPv4=true`. |
-| `homelab apt-upgrade --all` | Same, fanned out across the standard targets. |
-| `homelab apt-upgrade ... --status` | Show running unit + tail `/var/log/homelab-apt-upgrade.log` on each target. |
-| `homelab apt-upgrade ... --safe` | Take a pre-upgrade snapshot per LXC first (`pct snapshot` → `vzdump` fallback for bind-mounted LXCs). Refuses if any snapshot fails unless `--force`. |
-| `homelab apt-upgrade ... --force` | Skip both the dpkg-audit gate and snapshot-failure refusal. |
-
-PVE/kernel deferral on hubris: `homelab apt-upgrade --target hubris` will try every upgrade, including kernel + `pve-*`. To skip those, `apt-mark hold` the relevant packages on hubris first; `homelab apt-audit` shows held packages so you can confirm.
+**No current CLI equivalent.** `homelab apt-audit`/`apt-upgrade` (dpkg-state
+audit, fanned-out apt upgrade with pre-upgrade snapshots) were part of the
+retired Python `homelab` CLI and don't have a ported replacement — apt
+patching today is ad hoc `run` MCP tool calls per host, without the
+audit/snapshot/status wrapping this used to provide. If that wrapping is
+still wanted, it needs to be rebuilt (e.g. as a runbook driving `run`, or a
+new MCP tool) — see
+[runbook-dpkg-interrupted](../skills/runbook-dpkg-interrupted/SKILL.md) for
+the dpkg-interrupted recovery procedure specifically.
 
 ## Oikos (agent OS layer)
 
-See [OIKOS.md](../OIKOS.md) for the operating model. Quick reference:
+See [OIKOS.md](../OIKOS.md) for the operating model. The `homelab` CLI this
+section used to document is retired; the actual current interface is the
+33 MCP tools cataloged in [AGENTS.md](../../AGENTS.md#3-the-mcp-server) plus
+the REST API. Closest current equivalents for what used to live here:
 
-| Command | What it does |
+| Old `homelab` command | Current equivalent |
 | --- | --- |
-| `homelab service <name> explain\|health\|docs\|log\|actions\|history` | Service Console v0 — context card, cached health (`--live` to force a probe), docs, logs, safe actions + risk class, ledger history |
-| `homelab node <name> relations` | Ontology blast-radius query: what this host/service impacts, is affected by, and its full transitive blast radius |
-| `homelab change preflight <service>` | Dry-run report before mutating: risk class, current health, config repo, verification command |
-| `homelab decide <action> <entity>` | Decision classifier: risk × blast radius × confidence → auto-act or escalate |
-| `homelab signal list\|raise\|ack\|resolve\|mute` | The attention layer — pending updates, thresholds, drift, anything needing attention |
-| `homelab approval request\|list\|reply\|check` | Escalate-route grants (Matrix-delivered via Nomos, or the Oikos Console's `/approvals` page) |
-| `homelab restart <service> [--approval-id <id>]` | `--approval-id` is required whenever the service's risk class needs approval (e.g. `caddy`, `dns`) — refuses mechanically without a valid grant |
+| `homelab service <name> explain\|health\|docs\|log` | MCP `explain`, `get_service_status`, `tail_log`, `get_entity_knowledge` |
+| `homelab node <name> relations` | MCP `get_blast_radius` |
+| `homelab change preflight <service>` | MCP `preflight` |
+| `homelab signal list\|ack\|resolve\|mute` | MCP `get_signal_history`, or REST `POST /api/v1/signals/{id}/ack\|resolve\|mute` (the control-room UI's Signals page wraps these) |
+| `homelab approval request\|list\|reply\|check` | REST `GET/POST /api/v1/approvals*` (Matrix-delivered via the notifier, or the control-room UI's Operations page) |
+| `homelab restart <service> --approval-id <id>` | MCP `run` (policy-gated — auto-executes if read-only/reversible_low, otherwise queues for the same Matrix/UI approval) |
+| `homelab decide <action> <entity>` | No direct equivalent — classification now happens inline inside `run`/`request_execution`, not as a separate dry-run call |
 
-Oikos Console (read-mostly dashboard): `oikos.hubris.network` once deployed — see [oikos/console/deploy/README.md](../../archive/oikos-cards/).
+There is no separately-deployed "Oikos Console" anymore — the control-room
+SPA (`web/`) is the operator dashboard, served standalone (see
+[plans/2026-07-12-wails-desktop-app.md](../../plans/2026-07-12-wails-desktop-app.md)).
 
 ## Related
 - [Hubris host](../../archive/knowledge/hosts/hubris.md)