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both superseded by the production containerized Nomos agent, which has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/dev/CONTRIBUTING.md

@@ -10,6 +10,7 @@ see [CONTRIBUTING.md](../../CONTRIBUTING.md) for a human-friendly version.
 cmd/oikos/main.go          Entry point. Subcommands: api, scheduler, notifier, migrate,
                              seed, export, secret, all
 cmd/nomos/main.go          Nomos MCP client gateway (standalone binary, formerly Hermes)
+cmd/webhook/main.go        Gitea deploy-webhook receiver (push-to-deploy on mac-mini)
 internal/httpapi/           REST + MCP server. Chi router. OpenAPI-generated types from
                              internal/httpapi/gen/api.gen.go. Strict server in impl.go.
 internal/mcp/               MCP tool implementations (get_entity, search_knowledge, etc.)
@@ -26,14 +27,19 @@ internal/domain/            Core types: entities, approvals, executions, signals
 internal/ontology/          Type hierarchy validation, relationship checks
 internal/knowledge/         Knowledge YAML seed ingestion
 internal/config/            Config loading from env vars
+web/                         Control-room SPA (Svelte 5) — standalone static build, not
+                             embedded in the oikos binary (plans/2026-07-12-wails-desktop-app.md)
 api/openapi.yaml            REST API contract. Source of truth for endpoints.
 api/codegen.yaml            oapi-codegen config → generates internal/httpapi/gen/
 migrations/                 Forward-only SQL. Format: NNN_name.up.sql. No down migrations.
 seeds/                      Bootstrap YAML. ontology.yaml, inventory.yaml, policy.yaml,
                              knowledge.yaml. Regenerated from DB via oikos export.
-compose/                    Dockerfiles. oikos/ (multi-stage), nomos/ (distroless).
+compose/                    Dockerfiles. oikos/ (2-stage, Go only — SPA is built/deployed
+                             separately), nomos/ (distroless).
                              Caddy config at compose/caddy/Caddyfile.oikos.
 scripts/                     Deploy, rollback, watchdog, verification, cutover checklist.
+checks/                      Host health-check scripts run over SSH by the scheduler.
+tools/                       Client auto-setup scripts (checks).
 nomos/                       Nomos config.yaml, SOUL.md, skills.
 .agents/                     Agent instruction files, domains, shared conventions, skills.
 plans/                       Design documents. active/ + done/.