docs: codebase review + documentation maintenance pass

Full review (plans/2026-07-17-codebase-review-and-cleanup.md) covering Go,
web SPA, and docs. Applied low-risk doc/tooling fixes; code refactors and
dead-code deletions are listed as actionable recommendations pending approval.

Doc fixes:
- AGENTS.md: remove ghost of retired request_execution (contradicted the
  retire notice above it); fix knowledge/wiki/ -> archive/knowledge/;
  replace brittle counts (33 tools, 36 docs, 20 checks) with pointers to
  source; drop point-in-time dates.
- OIKOS.md: fix broken plan link (now in done/); 001-011 -> 001-020;
  15 MCP tools -> pointer; replace hardcoded knowledge counts.
- README.md: 15 tools -> pointer; fix wails plan link (now in done/);
  complete internal/ package list (add checkdefaults, observability, safego);
  add cmd/desktop/ to repo layout.
- commands.md, page-templates.md: fix broken links; HERMES.md -> NOMOS.md.

Plans housekeeping:
- Move 4 done 2026-07-14 plans from plans/ to plans/done/.
- Reconcile plans/index.md: add the 2 missing 2026-07-14 entries and the
  2 missing 2026-07-15 done entries; add this review.
- Fix stale plan path in migrations/020 comment.

New docs:
- docs/index.md and docs/operations/README.md (folder READMEs per
  writing-style.md).

Tooling:
- web/package.json: add check/typecheck/lint scripts + svelte-check devDep.
- Makefile: desktop-package version now reads from VERSION file instead of
  hardcoded 0.1.0.

VERSION 0.7.6 -> 0.7.7 (patch: docs + tooling only).

.agents/OIKOS.md

@@ -1,8 +1,8 @@
 # Oikos — the operating model
 
 Oikos (Greek: *household*) is the agent operating system layered on this
-repo. It is not new infrastructure: `inventory.yaml` is the kernel data
-structure, the `homelab` CLI and MCP server are the syscall surface, and
+repo. It is not new infrastructure: `seeds/inventory.yaml` is the kernel data
+structure, the Oikos REST API and MCP server are the syscall surface, and
 this page defines the rules everything above them follows.
 
 Read this after [AGENTS.md](../AGENTS.md). Machine-readable companions:
@@ -100,16 +100,16 @@ via the API's `/api/v1/graph` endpoint, and the Mermaid export at
 
 The Oikos runtime was rewritten from Python to Go over 6 phases and is deployed
 in Docker on mac-mini. See
-[plans/2026-07-06-consolidate-oikos-control-plane-onto-mac-mini.md](../plans/2026-07-06-consolidate-oikos-control-plane-onto-mac-mini.md)
+[plans/done/2026-07-06-consolidate-oikos-control-plane-onto-mac-mini.md](../plans/done/2026-07-06-consolidate-oikos-control-plane-onto-mac-mini.md)
 for the full plan. The Python codebase has been removed; all functionality runs
 in the Go binary.
 
 **Phase 1 — Ontology + DB (DONE):**
-- `migrations/` (001–011): TimescaleDB hypertables, entity_status, CAGGs,
-  retention policies, knowledge entities with FTS. Forward-only, idempotent.
+- `migrations/` (001–020, forward-only): TimescaleDB hypertables, entity_status, CAGGs,
+  retention policies, knowledge entities with FTS. Idempotent.
 - `seeds/{ontology,inventory,policy,knowledge}.yaml`: DB-native bootstrap +
-  DR export. Knowledge seed contains 36 documents, 6 investigations, and 12
-  runbooks.
+  DR export. Knowledge seed contents are not hardcoded here — count them
+  from the seed or query the DB.
 - `blast_radius()` SQL CTE, type hierarchy, abstract types, relationship
   validation.
 - Go packages: `internal/db/`, `internal/ontology/`, `internal/domain/`,
@@ -139,8 +139,8 @@ in the Go binary.
 
 **Phase 4 — Agent / Nomos (DONE):**
 - Standalone Nomos MCP client binary (`cmd/nomos`) with gateway mode
-  (:8092). Structured queries + natural-language routing to 15 MCP tools.
-  Agent activity logging on every tool call. No SSH keys.
+  (:8092). Structured queries + natural-language routing to the MCP tool
+  list (see AGENTS.md §3). Agent activity logging on every tool call. No SSH keys.
 - `nomos/` directory with config, SOUL.md, homelab-ops skill.
 - Nomos Docker service in `docker-compose.yml` (profile: full).
 - Go packages: `cmd/nomos/`, `compose/nomos/`.

.agents/operations/commands.md

@@ -49,7 +49,7 @@ Run from the [hubris host](../../archive/knowledge/hosts/hubris.md) as root. Whe
 - `ras-mc-ctl --errors` — full event log
 - `cat /sys/devices/system/cpu/cpu0/cpufreq/energy_performance_preference` — should be `balance_power`
 - `cat /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor` — should be `powersave`
-- `ls /sys/fs/pstore/ /var/lib/systemd/pstore/` — panic traces from a previous crash (empty for pure hardware hangs — see [investigation](../../archive/knowledge/investigations/archive/2026-04-21-hubris-crash-loop.md))
+- `ls /sys/fs/pstore/ /var/lib/systemd/pstore/` — panic traces from a previous crash (empty for pure hardware hangs — see [investigation](../../archive/knowledge/investigations/2026-04-21-hubris-crash-loop.md))
 
 ## Fleet apt operations
 
@@ -67,7 +67,7 @@ the dpkg-interrupted recovery procedure specifically.
 
 See [OIKOS.md](../OIKOS.md) for the operating model. The `homelab` CLI this
 section used to document is retired; the actual current interface is the
-33 MCP tools cataloged in [AGENTS.md](../../AGENTS.md#3-the-mcp-server) plus
+MCP tool catalog in [AGENTS.md §3](../../AGENTS.md#3-the-mcp-server) plus
 the REST API. Closest current equivalents for what used to live here:
 
 | Old `homelab` command | Current equivalent |
@@ -82,7 +82,7 @@ the REST API. Closest current equivalents for what used to live here:
 
 There is no separately-deployed "Oikos Console" anymore — the control-room
 SPA (`web/`) is the operator dashboard, served standalone (see
-[plans/2026-07-12-wails-desktop-app.md](../../plans/2026-07-12-wails-desktop-app.md)).
+[plans/done/2026-07-12-wails-desktop-app.md](../../plans/done/2026-07-12-wails-desktop-app.md)).
 
 ## Related
 - [Hubris host](../../archive/knowledge/hosts/hubris.md)

.agents/shared/page-templates.md

@@ -9,7 +9,7 @@ in [writing-style.md](writing-style.md); the layer model (sources / wiki / index
 **Foundational / entry-point files:** ALL-CAPS
 
 - **Root level:** `AGENTS.md`, `README.md` — discovery paths for agents and humans.
-- **Agent instruction** (under `.agents/`): `OIKOS.md`, `HERMES.md` — foundational docs agents read before acting.
+- **Agent instruction** (under `.agents/`): `OIKOS.md`, `NOMOS.md` — foundational docs agents read before acting.
 - **Reference docs:** `GLOSSARY.md` — lookup reference (like classic repo conventions: LICENSE, CHANGELOG, GLOSSARY).
 
 **Content / narrative pages:** lowercase-with-dashes, date-prefixed as needed