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both superseded by the production containerized Nomos agent, which has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/skills/config-change-deploy/SKILL.md

@@ -2,7 +2,7 @@
 name: config-change-deploy
 risk_class: config_mutation
 inputs: [service_name, change_description]
-verification: "curl -sf <service_url> (or homelab service <name> health)"
+verification: "curl -sf <service_url> (or MCP get_service_status)"
 docs_update_checklist: [doc_page, changelog]
 ---
 
@@ -11,11 +11,10 @@ docs_update_checklist: [doc_page, changelog]
 Goal: change a tracked config repo (Caddy, Gitea customizations, an app's
 own repo) and get it live, safely.
 
-1. `homelab change preflight <service>` — current health, the service's
-   `config_repo`, its risk class, and the verification command to run
-   after. If risk class requires approval (`config_mutation` or
-   `destructive`), stop and get operator sign-off before editing — see
-   `seeds/policy.yaml`.
+1. MCP `preflight` — current health, the service's `config_repo`, its
+   risk class, and the verification command to run after. If risk class
+   requires approval (`config_mutation` or `destructive`), stop and get
+   operator sign-off before editing — see `seeds/policy.yaml`.
 2. Clone/pull the `config_repo` (never edit the backend's working tree
    directly — tracked configs change by commit + push, per
    [OIKOS.md](../../OIKOS.md) conventions).
@@ -24,10 +23,10 @@ own repo) and get it live, safely.
    [infrastructure/auto-deploy.md](../../../archive/knowledge/infrastructure/auto-deploy.md) for
    the exact receiver/reload for this service).
 5. Run the preflight's verification command. If it fails, check
-   `homelab service <name> log` for the reload/restart error.
-6. Record the change: once `oikos/ledger.py` is wired into deploy tooling
-   (Week 3), this is automatic; until then, note the change and outcome
-   in the relevant investigation/plan doc.
+   MCP `tail_log` for the reload/restart error.
+6. No manual record-keeping step needed — mutations made through the API
+   (e.g. via the `run` MCP tool) are recorded automatically in the
+   `audit_log` table.
 
 Docs-update checklist: update the service's `doc_page` if the change
 alters its behavior, ingress route, or ownership; add a changelog entry