docs: retire repo-mem MCP, migrate skills to .claude/skills, audit fixes

- Delete .mcp.json + .claude/rules/repo-mem.md; drop .repo-mem from .gitignore
- Remove repo-mem / substrate_score / repo_search references from all .md
- Move 15 EVOLV skills from .agents/skills/ to .claude/skills/ so they are
  auto-discovered by the Claude Code harness and invokable via the Skill tool
- Retire .agents/skills/evolv-orchestrator (duplicate of the subagent at
  .claude/agents/evolv-orchestrator.md); orchestrator lives as a subagent only
- Drop OpenAI-format agent yaml metadata from each skill (not needed for CC)
- Update CLAUDE.md, CONTRACTS.md, AGENTS.md to point at the new locations and
  disambiguate skills (.claude/skills/) vs subagents (.claude/agents/)
- Fix CLAUDE.md tick-loop wording (opt-in per-node, not a fixed 1000ms)
- Widen .claude/rules/ paths frontmatter so node-architecture and telemetry
  rules trigger on more relevant files; add frontmatter to flow-layout rule
- Bump CONTRACTS.md review date to 2026-05-19; add step 7 to the contract-
  change workflow (review example flows when topic usage changes)
- Bump nodes/generalFunctions pin (Home.md substrate_score reference removed)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

CLAUDE.md

@@ -1,8 +1,7 @@
 # EVOLV - Claude Code Project Guide
 
 > **READ FIRST, BEFORE ANY OTHER WORK:**
-> 1. [`CONTRACTS.md`](./CONTRACTS.md) — front-door map: where every contract, rule, and standard lives, and how to find them.
-> 2. [`.claude/rules/repo-mem.md`](./.claude/rules/repo-mem.md) — this repo has an MCP server (`repo-mem`) exposing a substrate-trained `repo_search` and a persistent fix-trace store. Use those instead of `grep` for concept queries, and record completed fixes via `repo_record_fix`.
+> [`CONTRACTS.md`](./CONTRACTS.md) — front-door map: where every contract, rule, and standard lives, and how to find them.
 
 ## What This Is
 Node-RED custom nodes package for wastewater treatment plant automation. Developed by Waterschap Brabantse Delta R&D team. Follows ISA-88 (S88) batch control standard.
@@ -51,11 +50,27 @@ mismatches in the meantime):
 - Nodes register under category `'EVOLV'` in Node-RED
 - S88 color scheme: Area=#0f52a5, ProcessCell=#0c99d9, Unit=#50a8d9, Equipment=#86bbdd, ControlModule=#a9daee
 - Config JSON files in `generalFunctions/src/configs/` define defaults, types, enums per node
-- Tick loop runs at 1000ms intervals for time-based updates
+- Tick loop is **opt-in per node** — default cadence 1000 ms, but each node sets `static tickInterval` (or skips it). See `.claude/refactor/OPEN_QUESTIONS.md` (2026-05-10 entry) for the design decision
 - Output ports + 3-tier architecture + file-naming + `src/editor/` layout: see `.claude/rules/node-architecture.md`
 - **Multi-tab demo flows**: see `.claude/rules/node-red-flow-layout.md` for the tab/link-channel/spacing rule set used by `examples/`
 - **Output coverage** (every output, every state, every layer): see `.claude/rules/output-coverage.md` — manifest + populated/degraded tests are mandatory for any change that touches Port 0/1/2 keys, function-node fan-outs, telemetry fields, or dashboard widget sources
 
+## Agents and Skills (use them — don't reinvent)
+- **Skills** at `.claude/skills/evolv-*/SKILL.md` (15 domain skills) — auto-discovered, invoke via the `Skill` tool. Load them when you need domain reasoning (rotating equipment, biology, telemetry, security, instrumentation, hydraulics, alarms, OT integration, regulatory, quality, commissioning, frontend, …).
+- **Subagents** at `.claude/agents/*.md` (10 Claude Code subagents) — spawnable via `Agent(subagent_type: '<name>')`. Use for independent work: `evolv-orchestrator` (multi-domain decomposition + `team` workflows), `mechanical-process-engineer`, `biological-process-engineer`, `instrumentation-measurement`, `node-red-runtime`, `telemetry-database`, `quality-test-engineer`, `commissioning-compliance`, `ot-security-integration`, `general-functions-library`.
+- **Routing table**: [`.agents/AGENTS.md`](./.agents/AGENTS.md) maps task patterns → which skill/subagent to invoke.
+- **`team` keyword**: when the user says "team", spawn `evolv-orchestrator` (subagent) — it picks specialists, runs an alignment pass, returns one integrated answer.
+
+## Tooling (Docker-first, local now, central later)
+Custom EVOLV tooling lives in `tools/` and is intended to run inside the local Docker compose stack (`tools/docker-compose.yml`). **Always prefer these tools over ad-hoc grep/curl/manual checks** — they encode the rules in `.claude/rules/` and catch regressions the human review would miss:
+- `tools/flow-lint/` — validates `examples/*.flow.json` against `.claude/rules/node-red-flow-layout.md`. Run before committing any flow change.
+- `tools/output-manifest-verify/` — diffs declared Port 0/1/2 keys vs. runtime emissions. Run on any output-shape change.
+- `tools/contract-verify/` — diffs `nodes/<n>/CONTRACT.md` vs. `src/commands/index.js`. Run after touching a command registry.
+- `tools/wiki-gen/` — regenerates topic-contract + data-model sections of `nodes/<n>/wiki/`. Run after a CONTRACT change.
+- `tools/physics-sanity/` — cross-node mass/hydraulic/energy balance assertions. Run as part of `node --test` for cross-node changes.
+- **MCP services** (Node-RED admin, InfluxDB, headless browser) live under `tools/mcp/` as Docker services. **Migration note**: these will move to a central MCP server later; the local stack is interim. The Dockerfile + compose entry stays in this repo as the canonical definition.
+- **Why use them**: every tool encodes a rule that we've previously discovered through a bug (η-null crash, ui-chart blank renders, output-key drift). Skipping them re-opens those bugs.
+
 ## Sources of truth (the canonical files)
 - **Front-door map**: [`CONTRACTS.md`](./CONTRACTS.md) — read first; lists every standard and where it lives
 - **Platform API shapes** (BaseDomain, BaseNodeAdapter, commands registry, UnitPolicy, …): `.claude/refactor/CONTRACTS.md`