phase 6: school data, run state, meta-progression, crisis system

- Add school data (Alchemist: H, O, C, Na, S, Fe starting kit)
- Add run cycle types: phases, escalation, crisis, body composition
- Implement run state management (create, advance phase, discoveries, spores)
- Implement meta-progression (codex, spore accumulation, run history)
- Implement crisis system (Chemical Plague with neutralization)
- Add IndexedDB persistence for meta state
- 42 new tests (335 total)

Co-authored-by: Cursor <cursoragent@cursor.com>

src/run/state.ts

@@ -0,0 +1,93 @@
+/**
+ * Run State Management — creates and updates the state of a single run.
+ *
+ * A "run" is one cycle: Awakening → Exploration → Escalation → Crisis → Resolution.
+ * Each run tracks discoveries, escalation level, and crisis status.
+ */
+
+import {
+  type RunState,
+  type RunDiscoveries,
+  RunPhase,
+  ESCALATION_RATE,
+  SPORE_REWARDS,
+} from './types';
+
+/** Create a fresh run state for a new run */
+export function createRunState(runId: number, schoolId: string): RunState {
+  return {
+    runId,
+    schoolId,
+    phase: RunPhase.Awakening,
+    phaseTimer: 0,
+    elapsed: 0,
+    escalation: 0,
+    crisisActive: false,
+    crisisResolved: false,
+    discoveries: {
+      elements: new Set<string>(),
+      reactions: new Set<string>(),
+      compounds: new Set<string>(),
+      creatures: new Set<string>(),
+    },
+    alive: true,
+  };
+}
+
+/** Advance to the next phase. Does nothing if already at Resolution. */
+export function advancePhase(state: RunState): void {
+  if (state.phase < RunPhase.Resolution) {
+    state.phase = (state.phase + 1) as RunPhase;
+    state.phaseTimer = 0;
+  }
+}
+
+/** Update escalation level based on elapsed delta (ms). Only active during Escalation and Crisis. */
+export function updateEscalation(state: RunState, deltaMs: number): void {
+  if (state.phase < RunPhase.Escalation) return;
+  if (state.phase > RunPhase.Crisis) return;
+
+  const deltaSec = deltaMs / 1000;
+  state.escalation = Math.min(1.0, state.escalation + ESCALATION_RATE * deltaSec);
+}
+
+/** Discovery type names used in API (singular) */
+export type DiscoveryType = 'element' | 'reaction' | 'compound' | 'creature';
+
+/** Map singular type to plural key in RunDiscoveries */
+const DISCOVERY_KEY: Record<DiscoveryType, keyof RunDiscoveries> = {
+  element: 'elements',
+  reaction: 'reactions',
+  compound: 'compounds',
+  creature: 'creatures',
+};
+
+/** Record a discovery during the current run */
+export function recordDiscovery(
+  state: RunState,
+  type: DiscoveryType,
+  id: string,
+): void {
+  state.discoveries[DISCOVERY_KEY[type]].add(id);
+}
+
+/** Count total unique discoveries in a run */
+export function countDiscoveries(state: RunState): number {
+  return (
+    state.discoveries.elements.size +
+    state.discoveries.reactions.size +
+    state.discoveries.compounds.size +
+    state.discoveries.creatures.size
+  );
+}
+
+/** Calculate spores earned from a run */
+export function calculateSpores(state: RunState): number {
+  let total = 0;
+  total += state.discoveries.elements.size * SPORE_REWARDS.element;
+  total += state.discoveries.reactions.size * SPORE_REWARDS.reaction;
+  total += state.discoveries.compounds.size * SPORE_REWARDS.compound;
+  total += state.discoveries.creatures.size * SPORE_REWARDS.creature;
+  if (state.crisisResolved) total += SPORE_REWARDS.crisisResolved;
+  return total;
+}