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both superseded by the production containerized Nomos agent, which has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>

CLIENTS.md

@@ -24,9 +24,22 @@ Docker stack on mac-mini and exposes an MCP server + REST API.
 | State snapshot (health, disk, drift) | MCP `get_state_snapshot` |
 | Secrets (Infisical) | REST API + `oikos secret` CLI |
 | Approval tokens | Matrix via notifier |
+| Run a command on a host/LXC (policy-gated) | MCP `run` |
+| Record a discovered fact/relationship | MCP `update_entity_attributes`, `create_relationship`, `upsert_knowledge` |
 
-All MCP tools are read-only. Mutations use the `homelab` CLI with operator
-approval.
+Most MCP tools are read-only; a few mutate the knowledge graph (recording
+what you learned) or the live infrastructure (`run`, `request_execution`),
+gated by risk classification and — for `config_mutation`/`destructive`
+actions — operator approval. See [AGENTS.md](AGENTS.md#3-the-mcp-server) for
+the full tool catalog.
+
+## Authentication
+
+Every API/MCP call needs `Authorization: Bearer <token>` — there is no
+unauthenticated path except `POST /api/v1/clients/enroll` and `/healthz`.
+Enrollment (below) does not currently hand out a per-client bearer token;
+get the shared `OIKOS_MCP_BEARER_TOKEN` from the operator until per-client
+token issuance exists.
 
 ## Enrollment
 
@@ -41,7 +54,6 @@ curl -fsSL https://git.hubris.network/dtoro/oikos/raw/main/bootstrap.sh | sudo b
 
 # Or with optional tooling:
 curl ... | sudo bash -s -- --with-mcp      # wire Claude's MCP config
-curl ... | sudo bash -s -- --with-nomos     # install Goose + Nomos
 ```
 
 This calls `POST /api/v1/clients/enroll` on the Oikos API, which:
@@ -56,7 +68,7 @@ This calls `POST /api/v1/clients/enroll` on the Oikos API, which:
 ### What changes on your machine
 
 - `/opt/homelab/` — agent orientation files (CLIENTS.md, AGENTS.md, OIKOS.md)
-- `/opt/homelab/tools/` — tooling scripts (caveman, nomos-soul)
+- `/opt/homelab/tools/` — tooling scripts (checks)
 - `/etc/age/key.txt` — age private key for SOPS decryption (fallback)
 - `/etc/infisical/identity` — Infisical machine identity (primary secrets)
 - Context poller — launchd/systemd timer hits `GET /api/v1/clients/{slug}/context` every 5 minutes for agent file updates