chore: clean up superproject structure

Move content to correct locations:
- AGENTS.md → .agents/AGENTS.md (with orchestrator reference update)
- third_party/docs/ (8 reference docs) → wiki/concepts/
- manuals/ (12 Node-RED docs) → wiki/manuals/

Delete 23 unreferenced one-off scripts from scripts/ (keeping 5 active).
Delete stale Dockerfile.e2e, docker-compose.e2e.yml, test/e2e/.
Remove empty third_party/ directory.

Root is now: README, CLAUDE.md, LICENSE, package.json, Makefile,
Dockerfile, docker-compose.yml, docker/, scripts/ (5), nodes/, wiki/,
plus dotfiles (.agents, .claude, .gitea).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

wiki/index.md

@@ -20,6 +20,14 @@ updated: 2026-04-07
 
 ## Core Concepts
 - [generalFunctions API](concepts/generalfunctions-api.md) — logger, MeasurementContainer, configManager, etc.
+- [Pump Affinity Laws](concepts/pump-affinity-laws.md) — Q ∝ N, H ∝ N², P ∝ N³
+- [ASM Models](concepts/asm-models.md) — activated sludge model kinetics
+- [PID Control Theory](concepts/pid-control-theory.md) — proportional-integral-derivative control
+- [Settling Models](concepts/settling-models.md) — secondary clarifier sludge settling
+- [Signal Processing for Sensors](concepts/signal-processing-sensors.md) — sensor conditioning
+- [InfluxDB Schema Design](concepts/influxdb-schema-design.md) — telemetry data model
+- [OT Security (IEC 62443)](concepts/ot-security-iec62443.md) — industrial security standard
+- [Wastewater Compliance NL](concepts/wastewater-compliance-nl.md) — Dutch regulatory requirements
 
 ## Findings
 - [BEP-Gravitation Proof](findings/bep-gravitation-proof.md) — within 0.1% of brute-force optimum (proven)
@@ -28,21 +36,18 @@ updated: 2026-04-07
 - [Pump Switching Stability](findings/pump-switching-stability.md) — 1-2 transitions, no hysteresis (proven)
 - [Open Issues (2026-03)](findings/open-issues-2026-03.md) — diffuser, monster refactor, ML relocation, etc.
 
+## Manuals
+- [FlowFuse Dashboard Layout](manuals/node-red/flowfuse-dashboard-layout-manual.md)
+- [FlowFuse Widget Catalog](manuals/node-red/flowfuse-widgets-catalog.md)
+- [Node-RED Function Patterns](manuals/node-red/function-node-patterns.md)
+- [Node-RED Runtime](manuals/node-red/runtime-node-js.md)
+- [Messages and Editor Structure](manuals/node-red/messages-and-editor-structure.md)
+
 ## Sessions
 - [2026-04-07: Production Hardening](sessions/2026-04-07-production-hardening.md) — rotatingMachine + machineGroupControl
 
 ## Other Documentation (outside wiki)
 - `CLAUDE.md` — Claude Code project guide (root)
-- `AGENTS.md` — agent routing table, orchestrator policy (root, used by `.claude/agents/`)
+- `.agents/AGENTS.md` — agent routing table, orchestrator policy
 - `.agents/` — skills, decisions, function-anchors, improvements
 - `.claude/` — Claude Code agents and rules
-- `manuals/node-red/` — FlowFuse dashboard and Node-RED reference docs
-
-## Not Yet Documented
-- Parent-child registration protocol (Port 2 handshake)
-- Prediction health scoring algorithm (confidence 0-1)
-- MeasurementContainer internals (chainable API, delta compression)
-- PID controller implementation
-- reactor / settler / monster / measurement / valve nodes
-- pumpingStation node (uses rotatingMachine children)
-- InfluxDB telemetry format (Port 1)