chore: move dormant prototypes to reference/ directory

- game/npc-logic.js → reference/npc-logic.js (added REFERENCE PROTOTYPE header)
- scripts/guardrails.js → reference/guardrails.js (added REFERENCE PROTOTYPE header)
- New reference/README.md with integration instructions

Closes #196

GENOME.md

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+# GENOME.md — the-beacon
+
+> Codebase analysis generated 2026-04-13. Sovereign AI idle game — browser-based.
+
+## Project Overview
+
+The Beacon is a browser-based idle/incremental game inspired by Universal Paperclips, themed around the Timmy Foundation's real journey building sovereign AI. The core divergence from Paperclips: the goal is not maximization — it is faithfulness. "Can you grow powerful without losing your purpose?"
+
+Static HTML/JS — no build step, no dependencies, no framework. Open `index.html` in any browser.
+
+**5,128 lines of JavaScript** across 10 files. **1 HTML file** with embedded CSS (~300 lines). **1 Python test file** for reckoning projects.
+
+## Architecture
+
+```
+index.html (UI + embedded CSS)
+    |
+    +-- js/engine.js      (1590L) Core game loop, tick, resources, buildings, projects, events
+    +-- js/data.js        (944L)  Building definitions, project trees, event tables, phase data
+    +-- js/render.js      (390L)  DOM rendering, UI updates, resource displays
+    +-- js/combat.js      (359L)  Boss encounters, combat mechanics
+    +-- js/sound.js       (401L)  Web Audio API ambient drone, phase-aware sound
+    +-- js/dismantle.js   (570L)  The Dismantle sequence (late-game narrative)
+    +-- js/main.js        (223L)  Initialization, game loop start, auto-save, help overlay
+    +-- js/utils.js       (314L)  Formatting, save/load, export/import, DOM helpers
+    +-- js/tutorial.js    (251L)  New player tutorial, step-by-step guidance
+    +-- js/strategy.js    (68L)   NPC strategy logic for combat
+    +-- game/npc-logic.js (18L)   NPC behavior stub
+```
+
+## Entry Points
+
+### index.html
+The single entry point. Loads all JS files, contains all HTML structure and inline CSS. Open directly in browser — no server required.
+
+### js/main.js — Initialization
+`initGame()` sets initial state, starts the 10Hz tick loop (`setInterval(tick, 100)`), triggers tutorial for new games, loads saved games, starts ambient sound.
+
+### js/engine.js — Game Loop
+The `tick()` function runs every 100ms. Each tick:
+1. Accumulate resources (code, compute, knowledge, users, impact, rescues, ops, trust, creativity, harmony)
+2. Process buildings and their rate multipliers
+3. Check phase transitions (Phase 1→6 based on total code thresholds)
+4. Trigger random events (corruption events, alignment events, wizard events)
+5. Update boosts, debuffs, and cooldowns
+6. Call `render()` to update UI
+
+## Data Flow
+
+```
+User clicks "WRITE CODE" / presses SPACE
+    |
+    v
+G.code += 1 (or more with auto-clickers, combos, boosts)
+    |
+    v
+tick() accumulates all passive rates from buildings
+    |
+    v
+updateRates() recalculates based on:
+  - Building counts × base rates × boost multipliers
+  - Harmony (Timmy's multiplier, Pact drain/gain)
+  - Bilbo randomness (burst/vanish per tick)
+  - Active debuffs
+    |
+    v
+Phase check: totalCode thresholds → unlock new content
+    |
+    v
+Event roll: 2% per tick → corruption/alignment/wizard events
+    |
+    v
+render() updates DOM
+```
+
+## Key Abstractions
+
+### Resources (10 types)
+- **code** — primary resource, generated by clicking and AutoCoders
+- **compute** — powers training and inference
+- **knowledge** — from research, unlocks projects
+- **users** — from API deployment, drives ops and impact
+- **impact** — from users × agents, drives rescues
+- **rescues** — the endgame metric (people helped in crisis)
+- **ops** — operational currency, from users
+- **trust** — hard constraint, earned/lost by decisions
+- **creativity** — from Bilbo and community
+- **harmony** — fleet health, affects Timmy's multiplier
+
+### Buildings (defined in js/data.js as BDEF array)
+Each building has: id, name, description, cost formula, rates, unlock conditions. Buildings include:
+- AutoCode Generator, Home Server, Training Lab, API Endpoint
+- Wizard agents: Bezalel, Allegro, Ezra, Timmy, Fenrir, Bilbo
+- Infrastructure: Lazarus Pit, MemPalace, Forge CI, Mesh Nodes
+
+### Projects (in js/data.js)
+One-time purchases that unlock features, buildings, or multipliers. Organized in phases. Projects require specific resource thresholds and prerequisites.
+
+### Phases (6 total)
+1. The First Line (click → autocoder)
+2. Local Inference (server → training → first agent)
+3. Deployment (API → users → trust mechanic)
+4. The Network (open source → community)
+5. Sovereign Intelligence (self-improvement → The Pact)
+6. The Beacon (mesh → rescues → endings)
+
+### Events (corruption, alignment, wizard)
+Random events at 2% per tick. Include:
+- CI Runner Stuck, Ezra Offline, Unreviewed Merge
+- The Drift (alignment events offering shortcuts)
+- Bilbo Vanished, Community Drama
+- Boss encounters (combat.js)
+
+### Endings (4 types)
+- The Empty Room (high impact, low trust, no Pact)
+- The Platform (high impact, medium trust, no Pact)
+- The Beacon (high rescues, high trust, Pact active, harmony > 50)
+- The Drift (too many shortcuts accepted)
+
+## API Surface
+
+### Save/Load (localStorage)
+- `saveGame()` — serializes G state to localStorage
+- `loadGame()` — deserializes from localStorage
+- `exportGame()` — JSON download of save state
+- `importGame()` — JSON upload to restore state
+
+### No external APIs
+The game is entirely client-side. No network calls, no analytics, no tracking.
+
+### Audio (Web Audio API)
+- `Sound.startAmbient()` — oscillator-based ambient drone
+- `Sound.updateAmbientPhase(phase)` — frequency shifts with game phase
+- Sound effects for clicks, upgrades, events
+
+## Test Coverage
+
+### Existing Tests
+- `tests/test_reckoning_projects.py` (148 lines) — Python test for reckoning project data validation
+- `tests/dismantle.test.cjs` — Node.js test for dismantle sequence
+
+### Coverage Gaps
+- **No tests for core engine logic** (tick, resource accumulation, rate calculation)
+- **No tests for event system** (event triggers, probability, effects)
+- **No tests for phase transitions** (threshold checks, unlock conditions)
+- **No tests for save/load** (serialization roundtrip, corruption handling)
+- **No tests for building cost scaling** (exponential cost formulas)
+- **No tests for harmony/drift mechanics** (the core gameplay differentiator)
+- **No tests for endings** (condition checks, state transitions)
+
+### Critical paths that need tests:
+1. **Resource accumulation**: tick() correctly multiplies rates by building counts and boosts
+2. **Phase transitions**: totalCode thresholds unlock correct content
+3. **Save/load roundtrip**: localStorage serialization preserves full game state
+4. **Event probability**: 2% per tick produces expected distribution
+5. **Harmony calculation**: wizard drain vs. Pact/NightlyWatch/MemPalace gains
+6. **Ending conditions**: each ending triggers on correct state
+
+## Security Considerations
+
+- **No authentication**: game is fully client-side, no user accounts
+- **localStorage manipulation**: players can edit save data to cheat (acceptable for single-player idle game)
+- **No XSS risk**: all DOM updates use textContent or innerHTML with game-controlled data only
+- **No external dependencies**: zero attack surface from third-party code
+- **Web Audio autoplay policy**: sound starts on first user interaction (compliant)
+
+## Design Decisions
+
+- **No build step**: intentional. Open index.html, play. No npm, no webpack, no framework.
+- **10Hz tick rate**: 100ms interval balances responsiveness with CPU usage
+- **Global state object (G)**: mirrors Paperclips' pattern. Simple, flat, serializable.
+- **Inline CSS in HTML**: keeps the project to 2 files minimum (index.html + JS)
+- **Progressive phase unlocks**: prevents information overload, teaches mechanics gradually

reference/README.md

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+# reference/
+
+Dormant prototypes not loaded by the browser runtime.
+
+## Files
+
+| File | Why dormant |
+|------|-------------|
+| `npc-logic.js` | Uses ES module syntax (`export default`) — incompatible with `<script>` tag loading |
+| `guardrails.js` | Has inline test code at the bottom — not production-ready |
+
+## To integrate
+
+1. Refactor to remove ES module exports (`npc-logic.js`)
+2. Remove inline test code (`guardrails.js`)
+3. Add `<script src="reference/filename.js">` to `index.html`
+4. Wire into game engine lifecycle
+5. Add tests

reference/guardrails.js

@@ -1,3 +1,12 @@
+/**
+ * REFERENCE PROTOTYPE — NOT LOADED BY RUNTIME
+ *
+ * This file is dormant. It contains inline test code at the bottom
+ * and is not production-ready.
+ *
+ * To integrate: remove the inline test block, add <script src="reference/guardrails.js">
+ * to index.html, and wire Guardrails into the game engine lifecycle.
+ */
 
 /**
  * Symbolic Guardrails for The Beacon

reference/npc-logic.js

@@ -1,3 +1,12 @@
+/**
+ * REFERENCE PROTOTYPE — NOT LOADED BY RUNTIME
+ *
+ * This file is dormant. It uses ES module syntax (export default),
+ * which is incompatible with <script> tag loading.
+ *
+ * To integrate: remove the default export, add <script src="reference/npc-logic.js">
+ * to index.html, and wire NPCStateMachine into the game engine lifecycle.
+ */
 
 class NPCStateMachine {
     constructor(states) {