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both superseded by the production containerized Nomos agent, which has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

bootstrap.sh

@@ -3,15 +3,14 @@
 #
 # Thin client model (rev 2): no git clone, no sync timer. Fetches only the
 # agent orientation files (CLIENTS.md, AGENTS.md, OIKOS.md) and tooling
-# (caveman, nomos-soul) from the raw Gitea URL. Enrolls via the Oikos API
-# to receive an age keypair and Infisical machine identity. A lightweight
-# context poller replaces the old 5-minute git pull.
+# (checks) from the raw Gitea URL. Enrolls via the Oikos API to receive an
+# age keypair and Infisical machine identity. A lightweight context poller
+# replaces the old 5-minute git pull.
 #
 # Usage:
 #   curl -fsSL https://git.hubris.network/dtoro/oikos/raw/main/bootstrap.sh \
 #     | sudo bash
 #   curl ... | sudo bash -s -- --with-mcp           # wire Claude's .mcp.json
-#   curl ... | sudo bash -s -- --with-nomos        # install Goose + Nomos
 #   curl ... | sudo bash -s -- --dry-run            # show what would happen
 #
 # Prerequisites:
@@ -28,16 +27,10 @@ REPO_RAW_URL="${HOMELAB_RAW_URL:-https://git.hubris.network/dtoro/oikos/raw/main
 OIKOS_API_URL="${HOMELAB_OIKOS_URL:-https://oikos.hubris.network/api/v1}"
 CLONE_DIR="${HOMELAB_CONTEXT_DIR:-/opt/homelab}"
 MCP_URL="${HOMELAB_MCP_URL:-https://mcp.hubris.network/mcp}"
-NOMOS_MCP_URI="${HOMELAB_NOMOS_MCP_URI:-https://mcp.hubris.network/mcp}"
-NOMOS_MODEL="${HOMELAB_NOMOS_MODEL:-nousresearch/hermes-4-405b}"
 
 WITH_MCP=0
-WITH_NOMOS=0
 DRY_RUN=0
 
-GITEA_TOKEN="${HOMELAB_GITEA_TOKEN:-}"
-GITEA_USER="${HOMELAB_GITEA_USER:-dtoro}"
-
 # ── helpers ──────────────────────────────────────────────────────────
 
 log()  { echo "[oikos] $*"; }
@@ -79,10 +72,7 @@ detect_mesh_ip() {
 while [ $# -gt 0 ]; do
     case "$1" in
         --with-mcp)       WITH_MCP=1 ;;
-        --with-nomos)    WITH_NOMOS=1 ;;
         --dry-run)        DRY_RUN=1 ;;
-        --gitea-token)    GITEA_TOKEN="$2"; shift ;;
-        --gitea-user)     GITEA_USER="$2"; shift ;;
         *) die "unknown flag: $1" ;;
     esac
     shift
@@ -148,7 +138,7 @@ done
 
 # ── fetch tools ──────────────────────────────────────────────────────
 log "fetching tools..."
-for tool in setup-caveman.sh setup-nomos-soul.sh caveman.js caveman_wrapper.sh post-pull.sh; do
+for tool in setup-checks.sh post-pull.sh; do
     url="$REPO_RAW_URL/tools/${tool}"
     dest="$CLONE_DIR/tools/${tool}"
     dry mkdir -p "$(dirname "$dest")"
@@ -161,16 +151,6 @@ for tool in setup-caveman.sh setup-nomos-soul.sh caveman.js caveman_wrapper.sh p
     fi
 done
 
-# ── fetch caveman templates ──────────────────────────────────────────
-for tmpl in git_log.txt git_status.txt test_results.txt; do
-    url="$REPO_RAW_URL/tools/caveman/templates/${tmpl}"
-    dest="$CLONE_DIR/tools/caveman/templates/${tmpl}"
-    dry mkdir -p "$(dirname "$dest")"
-    if curl -fsSL --connect-timeout 10 "$url" -o "$dest.tmp" 2>/dev/null; then
-        mv "$dest.tmp" "$dest"
-    fi
-done
-
 # ── detect control-plane (use localhost if API is reachable directly) ─
 if [ -z "${HOMELAB_OIKOS_URL:-}" ]; then
     if curl -s --connect-timeout 2 http://localhost:8090/api/v1/health >/dev/null 2>&1; then
@@ -300,7 +280,7 @@ case "$OS" in
 esac
 
 # ── run auto-setup scripts ───────────────────────────────────────────
-for setup in "$CLONE_DIR"/tools/*.setup.sh; do
+for setup in "$CLONE_DIR"/tools/setup-*.sh; do
     [ -f "$setup" ] || continue
     log "running setup: $(basename "$setup")"
     dry bash "$setup"
@@ -319,17 +299,6 @@ if [ "$WITH_MCP" -eq 1 ]; then
     log "  + MCP wired to $MCP_URL"
 fi
 
-# ── --with-nomos: install Goose + Nomos wrapper ────────────────────
-if [ "$WITH_NOMOS" -eq 1 ]; then
-    log "installing Nomos agent..."
-    GOOSE_URL="https://github.com/block/goose/releases/latest/download/goose-${OS}-${ARCH:-amd64}"
-    if [ "$OS" = Darwin ]; then GOOSE_URL="https://github.com/block/goose/releases/latest/download/goose-darwin-${ARCH:-arm64}"; fi
-    dry curl -fsSL "$GOOSE_URL" -o /usr/local/bin/goose 2>/dev/null && chmod +x /usr/local/bin/goose || warn "goose not installed"
-    # Drop Nomos persona
-    cp "$CLONE_DIR/NOMOS.md" "$CLONE_DIR/.agents/NOMOS.md" 2>/dev/null || true
-    log "  + Nomos agent installed"
-fi
-
 # ── netbird SSH JWT cache ────────────────────────────────────────────
 if command -v netbird >/dev/null 2>&1; then
     dry netbird up --management-url https://netbird.hubris.network --ssh-jwt-cache-ttl 86400 2>/dev/null || true