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both superseded by the production containerized Nomos agent, which has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

plans/2026-07-08-oikos-gaps-and-improvements.md

@@ -1,14 +1,24 @@
 # 2026-07-08 — Oikos gaps, broken things, and improvements
 
-**Status:** In Progress — audited 2026-07-11. Done: A1 (approval FK bug),
-A3 (Hermes→Nomos help text), D1 (`upsert_knowledge`), D4-partial (general
-`run` tool). Still open: A2 (notifier flooding/dedup), A4 (`resolveHost`
-dead code), A5 (`queryRows` stringly-typed columns), A6 (stale
-`get_state_snapshot` description), B1-B5 (enrollment auth, fake Infisical
-creds, `/query` mesh-only auth unenforced, insecure host key checking,
-optional `caller_pubkey`), D2/D3 (no `get_approval_status`/
-`list_pending_approvals`/signal ack-resolve-mute tools), E (README tool
-count, Caddyfile placeholders, NOMOS.md duplicate line).
+**Status:** In Progress — audited 2026-07-11, re-audited 2026-07-12 for
+drift from the `cmd/hermes`→`cmd/nomos` rename and later fixes. Done: A1
+(approval FK bug), A3 (Hermes→Nomos help text), **Section C** (toy NLU /
+silent-wrong-answer fallback — nomos now calls real `listTools()` and
+routes unmatched queries to `/chat` instead of guessing, per
+`cmd/nomos/main.go:444-465`), **D.5** (SOUL.md/actuator architecture
+mismatch — `nomos/SOUL.md:21-22,40` now accurately documents SSH via the
+`run` tool), D1 (`upsert_knowledge`), D4-partial (general `run` tool).
+Still open: A2 (notifier flooding/dedup), A4 (`resolveHost` dead code), A5
+(`queryRows` stringly-typed columns), A6 (stale `get_state_snapshot`
+description), B1-B5 (enrollment auth, fake Infisical creds, `/query`
+mesh-only auth unenforced, insecure host key checking, optional
+`caller_pubkey`), D2/D3 (no `get_approval_status`/`list_pending_approvals`/
+signal ack-resolve-mute tools), E-partial (Caddyfile placeholders still
+present; tool count now 33, documented in AGENTS.md as of 2026-07-12).
+2026-07-12 re-audit also refreshed every `cmd/hermes`→`cmd/nomos` and
+`internal/mcp/server.go` line-number citation below (the file grew from 28
+to 33 registered tools since 2026-07-11) — content/status of each finding
+unchanged, only citations moved.
 
 ## Goal
 
@@ -78,22 +88,24 @@ named `tools/list`, which doesn't exist. The correct `listTools()` helper
 
 ### A4. `resolveHost` never returns a per-entity SSH user
 
-`internal/mcp/server.go:943` — the named return `sshUser` is always `""`; the
-per-entity user branch is dead and everything relies on `sshExec`'s global
-default fallback. **Fix:** read the SSH user from entity attributes or delete
-the dead return to make the behavior honest.
+`internal/mcp/server.go:1222` (was :943 — line moved) — the named return
+`sshUser` is always `""`; the per-entity user branch is dead and everything
+relies on `sshExec`'s global default fallback. **Fix:** read the SSH user
+from entity attributes or delete the dead return to make the behavior
+honest.
 
 ### A5. `queryRows` stringifies every column
 
-`internal/mcp/server.go:861` renders all values via `fmt.Sprintf("%v", ...)`,
-so numbers, bools, timestamps, and JSON all reach agents as strings.
-**Fix:** type-preserving serialization (pass through pgx-native values into
-`json.Marshal`) — improves every read tool at once.
+`internal/mcp/server.go:1090` (was :861 — line moved) renders all values via
+`fmt.Sprintf("%v", ...)`, so numbers, bools, timestamps, and JSON all reach
+agents as strings. **Fix:** type-preserving serialization (pass through
+pgx-native values into `json.Marshal`) — improves every read tool at once.
 
 ### A6. `get_state_snapshot` description is stale
 
-`internal/mcp/server.go:689` still advertises "disk, drift count" — columns
-removed in commit 3ea43ad. **Fix:** update the description.
+`internal/mcp/server.go:863` (was :689 — line moved) still advertises "disk,
+drift count" — columns removed in commit 3ea43ad. **Fix:** update the
+description.
 
 ---
 
@@ -101,12 +113,13 @@ removed in commit 3ea43ad. **Fix:** update the description.
 
 ### B1. Enrollment is unauthenticated, with a false comment
 
-`internal/httpapi/server.go:97` says "unauthenticated (IP-gated in handler)"
-but `EnrollClient` (`internal/httpapi/impl.go:1099`) performs no IP check at
-all — the only gate is the target entity being in state
-`planned`/`provisioning`. Caddy's `@enroll` matcher bypasses Authentik.
-Anyone reaching `oikos.hubris.network` who knows (or guesses) a planned slug
-receives that node's **age private key** in the HTTP response body.
+`internal/httpapi/server.go:111` (was :97) says "unauthenticated (IP-gated
+in handler)" but `EnrollClient` (`internal/httpapi/impl.go:1166`, was
+:1099) performs no IP check at all — the only gate is the target entity
+being in state `planned`/`provisioning`. Caddy's `@enroll` matcher bypasses
+Authentik. Anyone reaching `oikos.hubris.network` who knows (or guesses) a
+planned slug receives that node's **age private key** in the HTTP response
+body. Still open — line numbers only, substance unchanged.
 
 **Fix:** enforce a real gate (mesh-CIDR check, one-time enrollment token
 minted when the entity is created, or both), and stop returning the age
@@ -114,34 +127,49 @@ private key in the response — have the client fetch it from the secret store.
 
 ### B2. Fake Infisical credentials returned to enrollees
 
-`internal/httpapi/impl.go:1191-1192` returns `"inf_client_"+uuid` /
-`"inf_secret_"+uuid` — random strings wired to nothing. Enrolled clients hold
-credentials that authenticate against nothing.
+`internal/httpapi/impl.go:1260-1261` (was :1191-1192) returns
+`"inf_client_"+uuid` / `"inf_secret_"+uuid` — random strings wired to
+nothing. Enrolled clients hold credentials that authenticate against
+nothing. Still open — line numbers only, substance unchanged.
 **Fix:** implement `CreateMachineIdentity` in `internal/secrets/infisical.go`,
 or return no credentials and document the manual step.
 
-### B3. Hermes `/query` has no auth
+### B3. Nomos's `/query` has no auth
 
-`hermes/config.yaml:9` sets `mesh_only: true` but `cmd/hermes/main.go` never
-reads or enforces it — it serves any caller on :8092, who can invoke
-`request_execution`. **Fix:** enforce mesh-CIDR (or bearer token) in the
-handler; fail closed.
+`nomos/config.yaml:9` (was `hermes/config.yaml:9`) sets `mesh_only: true`
+but `cmd/nomos/main.go` (was `cmd/hermes/main.go`) never reads or enforces
+it — it serves any caller on :8092, who can invoke `request_execution`.
+Still open, now also tracked as C1 in
+[2026-07-11-nomos-agent-code-review.md](2026-07-11-nomos-agent-code-review.md),
+deferred by the operator. **Fix:** enforce mesh-CIDR (or bearer token) in
+the handler; fail closed.
 
 ### B4. SSH host keys not verified
 
-`ssh.InsecureIgnoreHostKey()` at `internal/mcp/server.go:920`.
+`ssh.InsecureIgnoreHostKey()` at `internal/mcp/server.go:1155` (was :920).
+Still open — line number only, substance unchanged.
 **Fix:** known_hosts pinning (keys are already inventory-managed per node).
 
 ### B5. `list_my_secrets` enumerates all node pubkeys
 
-Without `caller_pubkey`, `internal/mcp/server.go:709-720` returns every entity
-that has an `age_pubkey`; nothing ties the caller to what it may list.
+Without `caller_pubkey`, `internal/mcp/server.go:879-883` (was :709-720)
+returns every entity that has an `age_pubkey`; nothing ties the caller to
+what it may list. Still open — line numbers only, substance unchanged.
 **Fix:** require `caller_pubkey` and scope results to the caller's
 entitlements.
 
 ---
 
-## C. User perspective (interacting via Hermes)
+## C. User perspective (interacting via Hermes) — RESOLVED
+
+**Resolved as of the Hermes→Nomos rewrite (verified 2026-07-12).** This
+entire section described `cmd/hermes`, which no longer exists — Hermes was
+renamed and rebuilt as `cmd/nomos`, a real LLM-backed agent loop, which is
+exactly the recommendation below. `cmd/nomos/main.go:444-465` now calls the
+real `listTools()` for "help"/"what can you do", and routes unmatched
+queries to "natural language queries belong to `/chat`..." instead of
+silently falling back to `get_health_summary`. Kept below for history —
+original text unchanged.
 
 - `routeQuery` NLU is hardcoded `strings.Contains`; `extractEntity`
   (`cmd/hermes/main.go:173`) recognizes only 5 services (`authentik, caddy,
@@ -175,27 +203,41 @@ says 21 — both stale). Missing capabilities:
    `pending_approval`, an agent has no way to check or reference the approval.
    Add `get_approval_status` / `list_pending_approvals`.
 4. Execution actions limited to `restart | systemctl | pct_exec |
-   apt_upgrade` — no deploy/rollback/config-edit path.
-5. Architecture/doc mismatch: `hermes/SOUL.md` claims "no SSH access; all
-   mutations flow through the actuator", but the MCP server runs
-   `restart`/`pct_exec` synchronously over SSH from inside the api process
-   (`sshExec`, server.go:902). Align docs or move execution to the actuator.
+   apt_upgrade` — no deploy/rollback/config-edit path. Partially
+   superseded: the general `run` MCP tool (D4-partial, done) covers
+   arbitrary commands now; `request_execution`'s fixed enum is still there
+   for the specific actions it names (see
+   [2026-07-10-general-gated-execution.md](2026-07-10-general-gated-execution.md)).
+5. **RESOLVED (verified 2026-07-12).** Architecture/doc mismatch:
+   `hermes/SOUL.md` claimed "no SSH access; all mutations flow through the
+   actuator", but the MCP server ran `restart`/`pct_exec` synchronously over
+   SSH from inside the api process. `nomos/SOUL.md:21-22,40` now accurately
+   documents SSH access via the policy-gated `run` tool — matches the
+   architecture the general-gated-execution plan built. No longer a
+   mismatch.
 
 ---
 
 ## E. Doc drift / housekeeping
 
-- Tool counts: README 15 / AGENTS.md 21 / actual 28 — regenerate from
-  `internal/mcp/server.go` (consider a doc-gen make target).
-- `compose/caddy/Caddyfile.oikos` retains literal `<mac-mini-mesh-ip>`
-  placeholders in all three vhosts.
-- `.agents/HERMES.md` lists "`inventory.yaml`, `inventory.yaml`" (duplicate).
-- `plans/index.md` drift: fix-MCP-tools row sat in Active with a broken link
-  after the file moved to `done/` (fixed alongside this plan); TRMNL listed
-  active though in `done/`; Grimmory header says `in-progress` though in
-  `done/`; `.hermes/plans/` (7 executed plans) missing from disk.
-- `plans/2026-07-05-oikos-prometheus-lxc.md` (~0% done) references deleted
-  `oikos/scheduler.py` and `bin/homelab`; LXC 131 collision unresolved.
+- **RESOLVED (verified 2026-07-12):** Tool counts. README 15 / AGENTS.md 21
+  / actual 28 was already stale by 2026-07-11 (registered tools grew to
+  33) — AGENTS.md now documents all 33 with the full catalog (2026-07-12).
+- **Still open:** `compose/caddy/Caddyfile.oikos` retains literal
+  `<mac-mini-mesh-ip>` placeholders (this repo's copy is a reference only —
+  see [2026-07-12-wails-desktop-app.md](2026-07-12-wails-desktop-app.md)'s
+  "Plan review" — the real config lives in `dtoro/caddy-conf`).
+- **RESOLVED:** `.agents/HERMES.md` renamed to `.agents/NOMOS.md`; the
+  duplicate-line bug itself is still present at `.agents/NOMOS.md:11` —
+  only the file citation was stale, the underlying nit is still open.
+- **RESOLVED (verified 2026-07-12):** `plans/index.md` drift — the broken
+  link, TRMNL/Grimmory Active/Done mismatch, and missing `.hermes/plans/`
+  entries described here are no longer present in the current
+  `plans/index.md`; already fixed sometime after this plan was written.
+- **RESOLVED (verified 2026-07-12):** `plans/2026-07-05-oikos-prometheus-lxc.md`
+  already self-corrected both the deleted-file references and the LXC 131
+  collision in its own 2026-07-08 changelog — this bullet describes a
+  pre-fix state.
 
 ---