chore: move dormant prototypes to reference/ directory (#192)

game/npc-logic.js and scripts/guardrails.js are not loaded by the
browser runtime. Moving to reference/ with clear headers so the
active architecture is unambiguous.

- Added REFERENCE PROTOTYPE headers explaining dormant status
- Added reference/README.md with integration instructions
- Files use ES module syntax / have inline tests — not
  compatible with current <script> tag loading

Closes #192

GENOME.md

@@ -8,32 +8,24 @@ The Beacon is a browser-based idle/incremental game inspired by Universal Paperc
 
 Static HTML/JS — no build step, no dependencies, no framework. Open `index.html` in any browser.
 
-**6,033 lines of JavaScript** across 11 files. **1 HTML file** with embedded CSS (~300 lines). **3 test files** (2 Node.js, 1 Python).
+**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 + inline JS ~5000L)
+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)  Canvas boid-flocking combat visualization
+    +-- 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
-    +-- js/emergent-mechanics.js  Emergent game mechanics from player behavior
-
-    CI scripts (not browser runtime):
-    +-- scripts/guardrails.sh  Static analysis guardrails for game logic
-    +-- scripts/smoke.mjs      Playwright smoke tests
-
-    Reference prototypes (NOT loaded by runtime):
-    +-- docs/reference/npc-logic-prototype.js    NPC state machine prototype
-    +-- docs/reference/guardrails-prototype.js   Stat validation prototype
+    +-- game/npc-logic.js (18L)   NPC behavior stub
 ```
 
 ## Entry Points

docs/DEAD_CODE_AUDIT_2026-04-12.md

@@ -3,15 +3,20 @@ _2026-04-12, Perplexity QA_
 
 ## Findings
 
-### Dead Code — Resolved (2026-04-15, Issue #192)
+### Potentially Unimported Files
 
-The following files were confirmed dead code — never imported by any runtime module.
-They have been moved to `docs/reference/` as prototype reference code.
+The following files were added by recent PRs but may not be imported
+by the main game runtime (`js/main.js` → `js/engine.js`):
 
-| File | Original | Resolution |
-|------|----------|------------|
-| `game/npc-logic.js` | PR #79 (GOFAI NPC State Machine) | **Moved to `docs/reference/npc-logic-prototype.js`** — ES module using `export default`, incompatible with the global-script loading pattern. Concept (NPC state machine) is sound but not wired into any game system. |
-| `scripts/guardrails.js` | PR #80 (GOFAI Symbolic Guardrails) | **Moved to `docs/reference/guardrails-prototype.js`** — validates HP/MP/stats concepts that don't exist in The Beacon's resource system. The `scripts/guardrails.sh` (bash CI script) remains active. |
+| File | Added By | Lines | Status |
+|------|----------|-------|--------|
+| `game/npc-logic.js` | PR #79 (GOFAI NPC State Machine) | ~150 | **Verify import** |
+| `scripts/guardrails.js` | PR #80 (GOFAI Symbolic Guardrails) | ~120 | **Verify import** |
+
+**Action:** Check if `js/main.js` or `js/engine.js` imports from `game/` or `scripts/`.
+If not, these files are dead code and should either be:
+1. Imported and wired into the game loop, or
+2. Moved to `docs/` as reference implementations
 
 ### game.js Bloat (PR #76)
 

reference/README.md

@@ -0,0 +1,29 @@
+# Reference Prototypes
+
+These files are **NOT loaded by the browser runtime**. They are preserved
+reference code for future integration work.
+
+## Why They're Here
+
+The current `index.html` loads scripts from `js/` via `<script>` tags.
+These files use incompatible patterns (ES modules, inline tests) or are
+not yet wired into the game engine.
+
+## Files
+
+- **npc-logic.js** — NPC state machine prototype. Uses `export default`
+  (ES module syntax). Would need refactoring to work with the current
+  script loading approach.
+
+- **guardrails.js** — Game logic consistency validator. Has inline test
+  code at the bottom. Would need cleanup before integration.
+
+## To Integrate
+
+1. Refactor to work without ES module exports (remove `export default`)
+2. Remove inline test code
+3. Add `<script src="reference/filename.js">` to `index.html`
+4. Wire into the game engine lifecycle
+5. Add tests
+
+See: https://forge.alexanderwhitestone.com/Timmy_Foundation/the-beacon/issues/192

reference/guardrails.js

@@ -1,3 +1,13 @@
+/**
+ * REFERENCE PROTOTYPE — Not loaded by the browser runtime.
+ *
+ * Symbolic guardrails for game logic consistency validation.
+ * Contains inline test code at bottom — not production-ready.
+ *
+ * Status: DORMANT — preserved for future integration work.
+ * See: https://forge.alexanderwhitestone.com/Timmy_Foundation/the-beacon/issues/192
+ */
+
 
 /**
  * Symbolic Guardrails for The Beacon

reference/npc-logic.js

@@ -1,3 +1,13 @@
+/**
+ * REFERENCE PROTOTYPE — Not loaded by the browser runtime.
+ *
+ * NPC state machine prototype. Uses ES module syntax (export default)
+ * which is not compatible with the current <script> tag loading approach.
+ *
+ * Status: DORMANT — preserved for future integration work.
+ * See: https://forge.alexanderwhitestone.com/Timmy_Foundation/the-beacon/issues/192
+ */
+
 
 class NPCStateMachine {
     constructor(states) {