intentdna 1.0.0

package/dist/evolution/index.js

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+/**
+ * Intent DNA — Evolution Engine
+ *
+ * Orchestrates the epigenetic learning loop:
+ *   1. Record outcome (via collector)
+ *   2. Generate/update markers (via marker-gen)
+ *   3. Store markers (via store)
+ *   4. Compilation pipeline reads markers on next run
+ */
+import { DEFAULT_EVOLUTION_CONFIG } from "./types.js";
+import { EvolutionStore } from "./store.js";
+import { OutcomeCollector } from "./collector.js";
+import { generateMarkers, describeMarkerChanges } from "./marker-gen.js";
+export { EvolutionStore } from "./store.js";
+export { OutcomeCollector } from "./collector.js";
+export { generateMarkers, describeMarkerChanges } from "./marker-gen.js";
+export { computeGeneFitness, computeModulationFactor, computeMarkerStrength } from "./fitness.js";
+/**
+ * The Evolution Engine: ties together collection, marker generation, and storage.
+ */
+export class EvolutionEngine {
+    store;
+    collector;
+    config;
+    constructor(config) {
+        this.config = { ...DEFAULT_EVOLUTION_CONFIG, ...config };
+        this.store = new EvolutionStore(this.config);
+        this.collector = new OutcomeCollector(this.store);
+    }
+    /**
+     * Record an execution outcome.
+     */
+    async recordOutcome(input) {
+        return this.collector.record(input);
+    }
+    /**
+     * Evolve: generate/update epigenetic markers based on accumulated outcomes.
+     * Returns the new marker set.
+     */
+    async evolve(dnaId) {
+        const outcomes = await this.store.listOutcomes(dnaId);
+        const existing = await this.store.loadMarkers(dnaId);
+        const markers = generateMarkers(outcomes, existing, this.config);
+        await this.store.saveMarkers(dnaId, markers);
+        return markers;
+    }
+    /**
+     * Preview what markers would be generated without persisting.
+     */
+    async preview(dnaId) {
+        const outcomes = await this.store.listOutcomes(dnaId);
+        const existing = await this.store.loadMarkers(dnaId);
+        return describeMarkerChanges(outcomes, existing, this.config);
+    }
+    /**
+     * Load stored markers for use in compilation.
+     * This is the integration point with the compiler pipeline.
+     */
+    async loadMarkers(dnaId) {
+        return this.store.loadMarkers(dnaId);
+    }
+    /**
+     * Get outcome summary for a DNA.
+     */
+    async summary(dnaId) {
+        return this.collector.getSummary(dnaId);
+    }
+}
+//# sourceMappingURL=index.js.map

package/dist/evolution/index.js.map

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package/dist/evolution/marker-gen.d.ts

@@ -0,0 +1,31 @@
+/**
+ * Intent DNA — Marker Generator
+ *
+ * Converts execution outcomes into epigenetic markers.
+ * This is the core learning loop: outcomes → markers → gene modulation.
+ *
+ * Rules:
+ *   - A gene needs >= min_outcomes_for_marker feedback entries to generate a marker
+ *   - Markers are merged if they target the same gene (update count + recalculate factor)
+ *   - Markers exceeding max_markers are pruned by lowest strength
+ */
+import type { EpigeneticMarker } from "../schema/types.js";
+import type { ExecutionOutcome, EvolutionConfig } from "./types.js";
+/**
+ * Generate or update epigenetic markers from a set of outcomes.
+ * Returns the updated marker array.
+ */
+export declare function generateMarkers(outcomes: ExecutionOutcome[], existingMarkers: EpigeneticMarker[], config?: Partial<EvolutionConfig>): EpigeneticMarker[];
+/**
+ * Get a human-readable summary of what markers would be generated.
+ */
+export declare function describeMarkerChanges(outcomes: ExecutionOutcome[], existingMarkers: EpigeneticMarker[], config?: Partial<EvolutionConfig>): MarkerChange[];
+export interface MarkerChange {
+    gene: string;
+    type: "create" | "update" | "neutral" | "insufficient_data";
+    action?: "amplify" | "suppress";
+    factor?: number;
+    feedback_count: number;
+    needed?: number;
+}
+//# sourceMappingURL=marker-gen.d.ts.map

package/dist/evolution/marker-gen.d.ts.map

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package/dist/evolution/marker-gen.js

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+/**
+ * Intent DNA — Marker Generator
+ *
+ * Converts execution outcomes into epigenetic markers.
+ * This is the core learning loop: outcomes → markers → gene modulation.
+ *
+ * Rules:
+ *   - A gene needs >= min_outcomes_for_marker feedback entries to generate a marker
+ *   - Markers are merged if they target the same gene (update count + recalculate factor)
+ *   - Markers exceeding max_markers are pruned by lowest strength
+ */
+import { randomBytes } from "node:crypto";
+import { DEFAULT_EVOLUTION_CONFIG } from "./types.js";
+import { computeModulationFactor, computeMarkerStrength } from "./fitness.js";
+/**
+ * Generate or update epigenetic markers from a set of outcomes.
+ * Returns the updated marker array.
+ */
+export function generateMarkers(outcomes, existingMarkers, config = {}) {
+    const cfg = { ...DEFAULT_EVOLUTION_CONFIG, ...config };
+    // Collect all genes that received feedback
+    const geneFeedbackCounts = new Map();
+    for (const outcome of outcomes) {
+        for (const fb of outcome.constraint_feedback) {
+            geneFeedbackCounts.set(fb.gene, (geneFeedbackCounts.get(fb.gene) ?? 0) + 1);
+        }
+    }
+    // Start with existing markers (clone)
+    const markers = existingMarkers.map(m => ({ ...m, effects: [...m.effects] }));
+    const markerByGene = new Map();
+    for (const m of markers) {
+        for (const e of m.effects) {
+            if (e.gene) {
+                markerByGene.set(e.gene, m);
+            }
+        }
+    }
+    // Generate/update markers for genes with enough feedback
+    for (const [geneName, feedbackCount] of geneFeedbackCounts) {
+        if (feedbackCount < cfg.min_outcomes_for_marker)
+            continue;
+        const factor = computeModulationFactor(geneName, outcomes);
+        // Skip if modulation is negligible
+        if (Math.abs(factor - 1.0) < 0.05)
+            continue;
+        const action = factor > 1.0 ? "amplify" : "suppress";
+        const existing = markerByGene.get(geneName);
+        if (existing) {
+            // Update existing marker
+            existing.timestamp = new Date().toISOString();
+            existing.count = (existing.count ?? 1) + feedbackCount;
+            existing.decay = cfg.default_decay;
+            // Update the effect for this gene
+            const effect = existing.effects.find(e => e.gene === geneName);
+            if (effect) {
+                effect.action = action;
+                effect.factor = factor;
+            }
+        }
+        else {
+            // Create new marker
+            const triggersFromOutcomes = outcomes
+                .flatMap(o => o.constraint_feedback)
+                .filter(fb => fb.gene === geneName)
+                .map(fb => fb.detail ?? fb.effect)
+                .slice(0, 3);
+            const marker = {
+                id: `epi_${geneName}_${randomBytes(4).toString("hex")}`,
+                trigger: `outcome_feedback:${geneName}`,
+                timestamp: new Date().toISOString(),
+                count: feedbackCount,
+                effects: [{
+                        gene: geneName,
+                        action,
+                        factor,
+                    }],
+                decay: cfg.default_decay,
+            };
+            markers.push(marker);
+            markerByGene.set(geneName, marker);
+        }
+    }
+    // Prune decayed markers
+    const active = markers.filter(m => computeMarkerStrength(m) >= cfg.prune_threshold);
+    // Enforce max markers limit (keep highest strength)
+    if (active.length > cfg.max_markers) {
+        active.sort((a, b) => computeMarkerStrength(b) - computeMarkerStrength(a));
+        return active.slice(0, cfg.max_markers);
+    }
+    return active;
+}
+/**
+ * Get a human-readable summary of what markers would be generated.
+ */
+export function describeMarkerChanges(outcomes, existingMarkers, config = {}) {
+    const cfg = { ...DEFAULT_EVOLUTION_CONFIG, ...config };
+    const changes = [];
+    const geneFeedbackCounts = new Map();
+    for (const outcome of outcomes) {
+        for (const fb of outcome.constraint_feedback) {
+            geneFeedbackCounts.set(fb.gene, (geneFeedbackCounts.get(fb.gene) ?? 0) + 1);
+        }
+    }
+    const existingGenes = new Set();
+    for (const m of existingMarkers) {
+        for (const e of m.effects) {
+            if (e.gene)
+                existingGenes.add(e.gene);
+        }
+    }
+    for (const [geneName, feedbackCount] of geneFeedbackCounts) {
+        if (feedbackCount < cfg.min_outcomes_for_marker) {
+            changes.push({
+                gene: geneName,
+                type: "insufficient_data",
+                feedback_count: feedbackCount,
+                needed: cfg.min_outcomes_for_marker,
+            });
+            continue;
+        }
+        const factor = computeModulationFactor(geneName, outcomes);
+        if (Math.abs(factor - 1.0) < 0.05) {
+            changes.push({
+                gene: geneName,
+                type: "neutral",
+                factor,
+                feedback_count: feedbackCount,
+            });
+            continue;
+        }
+        changes.push({
+            gene: geneName,
+            type: existingGenes.has(geneName) ? "update" : "create",
+            action: factor > 1.0 ? "amplify" : "suppress",
+            factor,
+            feedback_count: feedbackCount,
+        });
+    }
+    return changes;
+}
+//# sourceMappingURL=marker-gen.js.map

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package/dist/evolution/store.d.ts

@@ -0,0 +1,24 @@
+/**
+ * Intent DNA — Evolution Store
+ *
+ * File-based persistence for execution outcomes and epigenetic markers.
+ * Adapted from Mycelium's store pattern.
+ *
+ * Layout:
+ *   {store_dir}/outcomes/{dna_id}/{id}.json  — execution outcomes
+ *   {store_dir}/markers/{dna_id}.json        — epigenetic markers for a DNA
+ */
+import type { ExecutionOutcome, EvolutionConfig } from "./types.js";
+import type { EpigeneticMarker } from "../schema/types.js";
+export declare class EvolutionStore {
+    private config;
+    constructor(config?: Partial<EvolutionConfig>);
+    private outcomesDir;
+    private markersPath;
+    saveOutcome(outcome: ExecutionOutcome): Promise<void>;
+    listOutcomes(dnaId: string): Promise<ExecutionOutcome[]>;
+    getOutcome(dnaId: string, outcomeId: string): Promise<ExecutionOutcome | null>;
+    loadMarkers(dnaId: string): Promise<EpigeneticMarker[]>;
+    saveMarkers(dnaId: string, markers: EpigeneticMarker[]): Promise<void>;
+}
+//# sourceMappingURL=store.d.ts.map

package/dist/evolution/store.d.ts.map

@@ -0,0 +1 @@
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package/dist/evolution/store.js

@@ -0,0 +1,78 @@
+/**
+ * Intent DNA — Evolution Store
+ *
+ * File-based persistence for execution outcomes and epigenetic markers.
+ * Adapted from Mycelium's store pattern.
+ *
+ * Layout:
+ *   {store_dir}/outcomes/{dna_id}/{id}.json  — execution outcomes
+ *   {store_dir}/markers/{dna_id}.json        — epigenetic markers for a DNA
+ */
+import { readFile, writeFile, mkdir, readdir } from "node:fs/promises";
+import { join } from "node:path";
+import { DEFAULT_EVOLUTION_CONFIG } from "./types.js";
+export class EvolutionStore {
+    config;
+    constructor(config) {
+        this.config = { ...DEFAULT_EVOLUTION_CONFIG, ...config };
+    }
+    outcomesDir(dnaId) {
+        return join(this.config.store_dir, "outcomes", dnaId);
+    }
+    markersPath(dnaId) {
+        return join(this.config.store_dir, "markers", `${dnaId}.json`);
+    }
+    // ── Outcomes ─────────────────────────────────────────────────
+    async saveOutcome(outcome) {
+        const dir = this.outcomesDir(outcome.dna_id);
+        await mkdir(dir, { recursive: true });
+        const filePath = join(dir, `${outcome.id}.json`);
+        await writeFile(filePath, JSON.stringify(outcome, null, 2), "utf-8");
+    }
+    async listOutcomes(dnaId) {
+        const dir = this.outcomesDir(dnaId);
+        await mkdir(dir, { recursive: true });
+        const files = await readdir(dir);
+        const outcomes = [];
+        for (const file of files) {
+            if (!file.endsWith(".json"))
+                continue;
+            try {
+                const raw = await readFile(join(dir, file), "utf-8");
+                outcomes.push(JSON.parse(raw));
+            }
+            catch {
+                // Skip corrupt files
+            }
+        }
+        // Sort by timestamp descending (newest first)
+        outcomes.sort((a, b) => b.timestamp.localeCompare(a.timestamp));
+        return outcomes;
+    }
+    async getOutcome(dnaId, outcomeId) {
+        try {
+            const filePath = join(this.outcomesDir(dnaId), `${outcomeId}.json`);
+            const raw = await readFile(filePath, "utf-8");
+            return JSON.parse(raw);
+        }
+        catch {
+            return null;
+        }
+    }
+    // ── Markers ──────────────────────────────────────────────────
+    async loadMarkers(dnaId) {
+        try {
+            const raw = await readFile(this.markersPath(dnaId), "utf-8");
+            return JSON.parse(raw);
+        }
+        catch {
+            return [];
+        }
+    }
+    async saveMarkers(dnaId, markers) {
+        const dir = join(this.config.store_dir, "markers");
+        await mkdir(dir, { recursive: true });
+        await writeFile(this.markersPath(dnaId), JSON.stringify(markers, null, 2), "utf-8");
+    }
+}
+//# sourceMappingURL=store.js.map

package/dist/evolution/store.js.map

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package/dist/evolution/types.d.ts

@@ -0,0 +1,73 @@
+/**
+ * Intent DNA — Evolution Types
+ *
+ * Adapted from Mycelium evolution types for Intent DNA's epigenetic system.
+ * Core flow: agent executes → outcome recorded → markers generated → DNA modulated
+ */
+export interface ConstraintFeedback {
+    /** Which gene's constraint was involved */
+    gene: string;
+    /** Did this constraint help, hinder, or have no effect? */
+    effect: "helped" | "hindered" | "neutral";
+    /** Optional detail about what happened */
+    detail?: string;
+}
+export interface OutcomeMetrics {
+    duration_ms?: number;
+    tokens?: number;
+    cost_usd?: number;
+    retries?: number;
+}
+/**
+ * Record of what happened when an agent executed under DNA constraints.
+ * This is the raw input to the epigenetic system.
+ */
+export interface ExecutionOutcome {
+    id: string;
+    timestamp: string;
+    /** Which DNA was active */
+    dna_id: string;
+    /** Which context was active (if any) */
+    context?: string;
+    /** Description of what the agent was doing */
+    action: string;
+    /** Which genes were active during execution */
+    active_genes: string[];
+    /** Which constraints were applied */
+    constraints_applied: string[];
+    /** Did the overall action succeed? */
+    success: boolean;
+    /** Per-constraint feedback */
+    constraint_feedback: ConstraintFeedback[];
+    /** Execution metrics */
+    metrics?: OutcomeMetrics;
+}
+/**
+ * Fitness tracking for an epigenetic marker.
+ * Tracks how effective the marker's modulation has been.
+ */
+export interface MarkerFitness {
+    /** How often outcomes were positive when this marker was active */
+    success_rate: number;
+    /** Number of times this marker influenced execution */
+    activation_count: number;
+    /** Normalized fitness score (0-1), computed from success_rate + recency */
+    score: number;
+}
+/**
+ * Configuration for the epigenetic evolution engine.
+ */
+export interface EvolutionConfig {
+    /** Directory for storing outcomes and markers. Default: ".intentdna" */
+    store_dir: string;
+    /** Minimum outcome count before generating markers. Default: 3 */
+    min_outcomes_for_marker: number;
+    /** Initial decay rate for new markers. Default: 0.9 */
+    default_decay: number;
+    /** Threshold below which markers are pruned. Default: 0.01 */
+    prune_threshold: number;
+    /** Maximum markers per DNA. Default: 50 */
+    max_markers: number;
+}
+export declare const DEFAULT_EVOLUTION_CONFIG: EvolutionConfig;
+//# sourceMappingURL=types.d.ts.map

package/dist/evolution/types.d.ts.map

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package/dist/evolution/types.js

@@ -0,0 +1,14 @@
+/**
+ * Intent DNA — Evolution Types
+ *
+ * Adapted from Mycelium evolution types for Intent DNA's epigenetic system.
+ * Core flow: agent executes → outcome recorded → markers generated → DNA modulated
+ */
+export const DEFAULT_EVOLUTION_CONFIG = {
+    store_dir: ".intentdna",
+    min_outcomes_for_marker: 3,
+    default_decay: 0.9,
+    prune_threshold: 0.01,
+    max_markers: 50,
+};
+//# sourceMappingURL=types.js.map

package/dist/evolution/types.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,4 @@
+export * from "./schema/index.js";
+export * from "./compiler/index.js";
+export * from "./runtime/index.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/index.js

@@ -0,0 +1,4 @@
+export * from "./schema/index.js";
+export * from "./compiler/index.js";
+export * from "./runtime/index.js";
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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package/dist/log/logger.d.ts

@@ -0,0 +1,15 @@
+/**
+ * Intent DNA — Outcome Logger
+ *
+ * Append-only JSONL log for execution outcomes.
+ * Adapted from Mycelium's SignalLogger.
+ */
+import type { ExecutionOutcome } from "../evolution/types.js";
+export declare class OutcomeLogger {
+    private ready;
+    readonly path: string;
+    constructor(logPath: string);
+    log(outcome: ExecutionOutcome): Promise<void>;
+    readAll(): Promise<ExecutionOutcome[]>;
+}
+//# sourceMappingURL=logger.d.ts.map

package/dist/log/logger.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"logger.d.ts","sourceRoot":"","sources":["../../src/log/logger.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAIH,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAE9D,qBAAa,aAAa;IACxB,OAAO,CAAC,KAAK,CAAgB;IAC7B,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;gBAEV,OAAO,EAAE,MAAM;IAKrB,GAAG,CAAC,OAAO,EAAE,gBAAgB,GAAG,OAAO,CAAC,IAAI,CAAC;IAM7C,OAAO,IAAI,OAAO,CAAC,gBAAgB,EAAE,CAAC;CAa7C"}

package/dist/log/logger.js

@@ -0,0 +1,36 @@
+/**
+ * Intent DNA — Outcome Logger
+ *
+ * Append-only JSONL log for execution outcomes.
+ * Adapted from Mycelium's SignalLogger.
+ */
+import { appendFile, mkdir, readFile } from "node:fs/promises";
+import { dirname } from "node:path";
+export class OutcomeLogger {
+    ready;
+    path;
+    constructor(logPath) {
+        this.path = logPath;
+        this.ready = mkdir(dirname(logPath), { recursive: true }).then(() => { });
+    }
+    async log(outcome) {
+        await this.ready;
+        const line = JSON.stringify(outcome) + "\n";
+        await appendFile(this.path, line, "utf-8");
+    }
+    async readAll() {
+        await this.ready;
+        try {
+            const raw = await readFile(this.path, "utf-8");
+            return raw
+                .trim()
+                .split("\n")
+                .filter(Boolean)
+                .map(line => JSON.parse(line));
+        }
+        catch {
+            return [];
+        }
+    }
+}
+//# sourceMappingURL=logger.js.map

package/dist/log/logger.js.map

@@ -0,0 +1 @@
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package/dist/runtime/agent-md.d.ts

@@ -0,0 +1,56 @@
+/**
+ * Intent DNA — Agent MD Adapter
+ *
+ * Compiles RoleDef definitions into Claude Code agent markdown files.
+ * Each role produces a .md file with YAML frontmatter (name, tools,
+ * disallowedTools, model) and a markdown body containing role description,
+ * scope rules, and DNA behavioral guidelines.
+ *
+ * Output directory: .claude/agents/<name>.md
+ */
+import type { RoleDef, ConstraintIR } from "../schema/types.js";
+/** Agent MD compilation options */
+export interface AgentMDOptions {
+    /** Output directory (default ".claude/agents") */
+    outputDir?: string;
+    /** Whether to include DNA behavioral guidelines in body */
+    includeDNAGuidelines?: boolean;
+    /** Role name prefix (e.g. "dna-") */
+    namePrefix?: string;
+}
+/** Single agent MD compilation result */
+export interface AgentMDResult {
+    /** Role name (original key, e.g. "reviewer") */
+    roleName: string;
+    /** Generated file name (e.g. "dna-reviewer.md") */
+    fileName: string;
+    /** Full MD content (frontmatter + body) */
+    content: string;
+}
+/**
+ * Convert camelCase or snake_case to kebab-case.
+ */
+export declare function toKebabCase(name: string): string;
+/**
+ * Compile a single RoleDef into an agent MD file.
+ * Pure function, no side effects.
+ */
+export declare function compileRoleToAgentMD(roleName: string, role: RoleDef, ir?: ConstraintIR, options?: AgentMDOptions): AgentMDResult;
+/**
+ * Compile all roles from IntentDNA into agent MD files.
+ * Returns compilation results for each role.
+ */
+export declare function compileAllRolesToAgentMD(roles: Record<string, RoleDef>, ir?: ConstraintIR, options?: AgentMDOptions): AgentMDResult[];
+/**
+ * Write agent MD results to the file system.
+ * Creates the output directory if it doesn't exist.
+ * Returns list of written file paths.
+ */
+export declare function writeAgentMDFiles(results: AgentMDResult[], outputDir: string): Promise<string[]>;
+/**
+ * Remove Intent DNA generated agent MD files from a directory.
+ * Only removes files that contain the sentinel comment.
+ * Returns number of files removed.
+ */
+export declare function removeAgentMDFiles(outputDir: string): Promise<number>;
+//# sourceMappingURL=agent-md.d.ts.map

package/dist/runtime/agent-md.d.ts.map

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