nexus-prime 0.2.0

package/dist/engines/memory.d.ts

@@ -0,0 +1,76 @@
+/**
+ * Memory Engine — Persistent Zettelkasten
+ *
+ * Three-tier memory system backed by SQLite for cross-session persistence.
+ * Memories link to each other (Zettelkasten) — recall returns context networks,
+ * not just isolated facts. High-value memories trigger fission (broadcast).
+ *
+ * Persistence: ~/.nexus-prime/memory.db
+ * Load on MCP start. Flush on exit.
+ */
+export interface MemoryItem {
+    id: string;
+    content: string;
+    priority: number;
+    timestamp: number;
+    tags: string[];
+    tier: 'prefrontal' | 'hippocampus' | 'cortex';
+    sessionId?: string;
+    accessCount: number;
+    links?: string[];
+    parentId?: string;
+    depth?: number;
+}
+export interface MemoryLink {
+    fromId: string;
+    toId: string;
+    weight: number;
+    type: 'semantic' | 'temporal' | 'tagged';
+}
+export interface MemoryStats {
+    prefrontal: number;
+    hippocampus: number;
+    cortex: number;
+    totalLinks: number;
+    oldestEntry: number | null;
+    topTags: string[];
+}
+export declare class MemoryEngine {
+    private db;
+    private sessionId;
+    private prefrontal;
+    private maxPrefrontal;
+    private maxHippocampus;
+    private embedder;
+    private vectorIdToMemoryId;
+    private memoryIdToVectorId;
+    private nextVectorId;
+    constructor(dbPath?: string);
+    private initSchema;
+    /** Restore hippocampus + cortex from DB on startup */
+    load(): void;
+    /** Flush prefrontal to DB (called on MCP shutdown) */
+    flush(): void;
+    store(content: string, priority?: number, tags?: string[], parentId?: string, depth?: number): string;
+    recall(query: string, k?: number): Promise<string[]>;
+    private vectorEmbeddings;
+    private indexMemory;
+    private autoLink;
+    /** Get a memory's connected context network */
+    getNetwork(id: string, depth?: number): MemoryItem[];
+    private fission;
+    private consolidate;
+    private wordOverlap;
+    private rowToItem;
+    private getAllItems;
+    getStats(): MemoryStats;
+    clear(): void;
+    /**
+     * Query memories by tag using direct SQL — precise, no fuzzy matching.
+     * Returns memories that contain ANY of the specified tags.
+     */
+    queryByTags(tags: string[], limit?: number): MemoryItem[];
+    close(): void;
+}
+export declare const createMemoryEngine: (dbPath?: string) => MemoryEngine;
+//# sourceMappingURL=memory.d.ts.map

package/dist/engines/memory.d.ts.map

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package/dist/engines/memory.js

@@ -0,0 +1,431 @@
+/**
+ * Memory Engine — Persistent Zettelkasten
+ *
+ * Three-tier memory system backed by SQLite for cross-session persistence.
+ * Memories link to each other (Zettelkasten) — recall returns context networks,
+ * not just isolated facts. High-value memories trigger fission (broadcast).
+ *
+ * Persistence: ~/.nexus-prime/memory.db
+ * Load on MCP start. Flush on exit.
+ */
+import Database from 'better-sqlite3';
+import * as os from 'os';
+import * as path from 'path';
+import * as fs from 'fs';
+import { randomUUID } from 'crypto';
+import { Embedder, HyperbolicMath } from './embedder.js';
+import { podNetwork } from './pod-network.js';
+// ─────────────────────────────────────────────────────────────────────────────
+// MemoryEngine
+// ─────────────────────────────────────────────────────────────────────────────
+export class MemoryEngine {
+    db;
+    sessionId;
+    // In-RAM working tiers (flushed to DB periodically)
+    prefrontal = [];
+    maxPrefrontal = 7;
+    maxHippocampus = 200;
+    // Vector index (in-memory TF-IDF) — rebuilt on load
+    embedder;
+    // Maps vector item id → memory id
+    vectorIdToMemoryId = new Map();
+    memoryIdToVectorId = new Map();
+    nextVectorId = 1;
+    constructor(dbPath) {
+        const dbDir = path.join(os.homedir(), '.nexus-prime');
+        fs.mkdirSync(dbDir, { recursive: true });
+        const resolvedPath = dbPath ?? path.join(dbDir, 'memory.db');
+        this.db = new Database(resolvedPath);
+        this.sessionId = randomUUID();
+        this.embedder = new Embedder();
+        this.initSchema();
+        this.load();
+    }
+    // ─────────────────────────────────────────────────────────────────────────
+    // Schema
+    // ─────────────────────────────────────────────────────────────────────────
+    initSchema() {
+        this.db.exec(`
+      CREATE TABLE IF NOT EXISTS memories (
+        id          TEXT PRIMARY KEY,
+        content     TEXT NOT NULL,
+        priority    REAL NOT NULL DEFAULT 1.0,
+        timestamp   INTEGER NOT NULL,
+        tags        TEXT NOT NULL DEFAULT '[]',
+        tier        TEXT NOT NULL DEFAULT 'hippocampus',
+        session_id  TEXT,
+        access_count INTEGER NOT NULL DEFAULT 0,
+        parent_id   TEXT,
+        depth       INTEGER DEFAULT 0
+      );
+    `);
+        // Migration logic for existing tables
+        const tableInfo = this.db.prepare("PRAGMA table_info(memories)").all();
+        const columns = tableInfo.map(c => c.name);
+        if (!columns.includes('parent_id')) {
+            this.db.exec("ALTER TABLE memories ADD COLUMN parent_id TEXT");
+        }
+        if (!columns.includes('depth')) {
+            this.db.exec("ALTER TABLE memories ADD COLUMN depth INTEGER DEFAULT 0");
+        }
+        this.db.exec(`
+      CREATE TABLE IF NOT EXISTS memory_links(
+      from_id  TEXT NOT NULL,
+      to_id    TEXT NOT NULL,
+      weight   REAL NOT NULL DEFAULT 0.5,
+      type     TEXT NOT NULL DEFAULT 'semantic',
+      PRIMARY KEY(from_id, to_id),
+      FOREIGN KEY(from_id) REFERENCES memories(id) ON DELETE CASCADE,
+      FOREIGN KEY(to_id)   REFERENCES memories(id) ON DELETE CASCADE
+    );
+
+      CREATE INDEX IF NOT EXISTS idx_memories_tier      ON memories(tier);
+      CREATE INDEX IF NOT EXISTS idx_memories_priority  ON memories(priority DESC);
+      CREATE INDEX IF NOT EXISTS idx_memories_timestamp ON memories(timestamp DESC);
+      CREATE INDEX IF NOT EXISTS idx_links_from         ON memory_links(from_id);
+    `);
+    }
+    // ─────────────────────────────────────────────────────────────────────────
+    // Persistence
+    // ─────────────────────────────────────────────────────────────────────────
+    /** Restore hippocampus + cortex from DB on startup */
+    load() {
+        const rows = this.db.prepare(`SELECT * FROM memories ORDER BY priority DESC, timestamp DESC LIMIT 500`).all();
+        // Fit TF-IDF vocabulary on all stored content
+        const allContent = rows.map(r => r.content);
+        if (allContent.length > 0) {
+            this.embedder.fitVocabulary(allContent);
+        }
+        for (const row of rows) {
+            const item = {
+                id: row.id,
+                content: row.content,
+                priority: row.priority,
+                timestamp: row.timestamp,
+                tags: JSON.parse(row.tags),
+                tier: row.tier,
+                sessionId: row.session_id,
+                accessCount: row.access_count
+            };
+            // Restore prefrontal items to RAM
+            if (item.tier === 'prefrontal') {
+                this.prefrontal.push(item);
+            }
+            // Rebuild in-memory vector index (synchronously via local embed)
+            this.indexMemory(item.id, item.content);
+        }
+    }
+    /** Flush prefrontal to DB (called on MCP shutdown) */
+    flush() {
+        const upsert = this.db.prepare(`
+      INSERT INTO memories(id, content, priority, timestamp, tags, tier, session_id, access_count, parent_id, depth)
+    VALUES(@id, @content, @priority, @timestamp, @tags, @tier, @session_id, @access_count, @parent_id, @depth)
+      ON CONFLICT(id) DO UPDATE SET
+    priority = excluded.priority,
+      access_count = excluded.access_count,
+      tier = excluded.tier,
+      parent_id = excluded.parent_id,
+      depth = excluded.depth
+        `);
+        const txn = this.db.transaction((items) => {
+            for (const item of items) {
+                upsert.run({
+                    id: item.id,
+                    content: item.content,
+                    priority: item.priority,
+                    timestamp: item.timestamp,
+                    tags: JSON.stringify(item.tags),
+                    tier: item.tier,
+                    session_id: item.sessionId ?? null,
+                    access_count: item.accessCount,
+                    parent_id: item.parentId ?? null,
+                    depth: item.depth ?? 0
+                });
+            }
+        });
+        txn(this.prefrontal);
+    }
+    // ─────────────────────────────────────────────────────────────────────────
+    // Core Operations
+    // ─────────────────────────────────────────────────────────────────────────
+    store(content, priority = 1.0, tags = [], parentId, depth = 0) {
+        const id = randomUUID();
+        const item = {
+            id,
+            content,
+            priority,
+            timestamp: Date.now(),
+            tags,
+            tier: 'prefrontal',
+            sessionId: this.sessionId,
+            accessCount: 0,
+            parentId,
+            depth
+        };
+        // Write to DB immediately (don't wait for flush)
+        this.db.prepare(`
+      INSERT INTO memories(id, content, priority, timestamp, tags, tier, session_id, access_count, parent_id, depth)
+    VALUES(?, ?, ?, ?, ?, 'prefrontal', ?, 0, ?, ?)
+      `).run(id, content, priority, item.timestamp, JSON.stringify(tags), this.sessionId, parentId, depth);
+        // Update vocabulary and add to vector index
+        this.embedder.fitVocabulary([content]);
+        this.indexMemory(id, content);
+        // Auto-link to semantically similar recent memories
+        this.autoLink(item);
+        // Add to RAM prefrontal
+        this.prefrontal.push(item);
+        if (this.prefrontal.length > this.maxPrefrontal) {
+            this.consolidate();
+        }
+        // Fission: broadcast high-value memories
+        if (priority > 0.9) {
+            this.fission(item);
+        }
+        return id;
+    }
+    async recall(query, k = 5) {
+        // ── Stage 1: Vector search (semantic) ────────────────────────────────────
+        const queryVector = await this.embedder.embed(query);
+        const vectorMatches = new Map();
+        const allItems = this.getAllItems();
+        for (const item of allItems) {
+            const itemVector = this.embedder.localEmbed(item.content);
+            const hDist = HyperbolicMath.dist(queryVector, itemVector);
+            let score = 1 / (1 + hDist);
+            // Hierarchy Boost: if item has a parent that matches query, boost child
+            if (item.parentId) {
+                const parent = allItems.find(i => i.id === item.parentId);
+                if (parent) {
+                    const parentVector = this.embedder.localEmbed(parent.content);
+                    const pDist = HyperbolicMath.dist(queryVector, parentVector);
+                    if (pDist < 0.3)
+                        score *= 1.4; // Boost child if parent is relevant
+                }
+            }
+            vectorMatches.set(item.id, score);
+        }
+        // ── Stage 2: SQL scoring (priority + recency) ─────────────────────────────
+        const podFindings = podNetwork.recall([]);
+        const queryLower = query.toLowerCase();
+        const rows = this.db.prepare(`
+    SELECT *, access_count FROM memories
+      ORDER BY priority DESC, timestamp DESC
+      LIMIT 300
+    `).all();
+        const scored = rows.map(row => {
+            const vectorScore = vectorMatches.get(row.id) ?? 0;
+            const recencyScore = Math.exp(-(Date.now() - row.timestamp) / (7 * 24 * 3600 * 1000));
+            const priorityScore = row.priority;
+            const accessBonus = Math.min(row.access_count * 0.05, 0.3);
+            return {
+                content: row.content,
+                id: row.id,
+                score: vectorScore * 0.5 + priorityScore * 0.25 + recencyScore * 0.15 + accessBonus * 0.1
+            };
+        });
+        const podMatches = podFindings
+            .filter(f => f.content.toLowerCase().includes(queryLower))
+            .map(f => ({ content: f.content, score: 0.95 }));
+        const top = [...scored, ...podMatches]
+            .sort((a, b) => b.score - a.score)
+            .slice(0, k);
+        // Increment access count for recalled items
+        if (top.length > 0) {
+            const ids = top.filter(t => t.id).map(t => `'${t.id}'`).join(',');
+            if (ids) {
+                this.db.exec(`UPDATE memories SET access_count = access_count + 1 WHERE id IN(${ids})`);
+            }
+        }
+        return top.map(r => r.content);
+    }
+    // ─────────────────────────────────────────────────────────────────────────
+    // Vector Index Helpers
+    // ─────────────────────────────────────────────────────────────────────────
+    // In-RAM embedding store (id → float[] vector)
+    vectorEmbeddings = new Map();
+    indexMemory(memoryId, content) {
+        const vector = this.embedder.localEmbed(content);
+        const vid = this.nextVectorId++;
+        this.vectorEmbeddings.set(vid, vector);
+        this.vectorIdToMemoryId.set(vid, memoryId);
+        this.memoryIdToVectorId.set(memoryId, vid);
+    }
+    // ─────────────────────────────────────────────────────────────────────────
+    // Zettelkasten — semantic linking
+    // ─────────────────────────────────────────────────────────────────────────
+    autoLink(newItem) {
+        const recentRows = this.db.prepare(`
+      SELECT id, content, tags FROM memories
+      WHERE id != ? ORDER BY timestamp DESC LIMIT 50
+      `).all(newItem.id);
+        const newWords = newItem.content.toLowerCase().split(/\s+/);
+        for (const row of recentRows) {
+            const existingWords = row.content.toLowerCase().split(/\s+/);
+            const similarity = this.wordOverlap(newWords, existingWords);
+            if (similarity > 0.25) {
+                this.db.prepare(`
+          INSERT OR IGNORE INTO memory_links(from_id, to_id, weight, type)
+    VALUES(?, ?, ?, 'semantic')
+      `).run(newItem.id, row.id, similarity);
+            }
+            // Tag-based linking
+            const sharedTags = newItem.tags.filter(t => JSON.parse(row.tags ?? '[]').includes(t));
+            if (sharedTags.length > 0) {
+                this.db.prepare(`
+          INSERT OR IGNORE INTO memory_links(from_id, to_id, weight, type)
+    VALUES(?, ?, ?, 'tagged')
+      `).run(newItem.id, row.id, 0.6 + sharedTags.length * 0.1);
+            }
+        }
+    }
+    /** Get a memory's connected context network */
+    getNetwork(id, depth = 1) {
+        const visited = new Set([id]);
+        const result = [];
+        let frontier = [id];
+        for (let d = 0; d < depth; d++) {
+            const next = [];
+            for (const fromId of frontier) {
+                const links = this.db.prepare(`
+          SELECT to_id FROM memory_links WHERE from_id = ? ORDER BY weight DESC LIMIT 5
+      `).all(fromId);
+                for (const link of links) {
+                    const toId = link.to_id;
+                    if (!visited.has(toId)) {
+                        visited.add(toId);
+                        next.push(toId);
+                        const row = this.db.prepare('SELECT * FROM memories WHERE id = ?').get(toId);
+                        if (row)
+                            result.push(this.rowToItem(row));
+                    }
+                }
+            }
+            frontier = next;
+        }
+        return result;
+    }
+    // ─────────────────────────────────────────────────────────────────────────
+    // Fission: broadcast high-value discoveries
+    // ─────────────────────────────────────────────────────────────────────────
+    fission(item) {
+        // Promote to cortex immediately (permanently important)
+        this.db.prepare(`
+      UPDATE memories SET tier = 'cortex', priority = MIN(priority * 1.2, 2.0)
+      WHERE id = ?
+      `).run(item.id);
+        // Strengthen links TO this item (makes it easier to discover via related queries)
+        this.db.prepare(`
+      UPDATE memory_links SET weight = MIN(weight * 1.3, 1.0) WHERE to_id = ?
+      `).run(item.id);
+    }
+    // ─────────────────────────────────────────────────────────────────────────
+    // Tier Management
+    // ─────────────────────────────────────────────────────────────────────────
+    consolidate() {
+        const sorted = [...this.prefrontal].sort((a, b) => b.priority - a.priority);
+        const keepInRam = sorted.slice(0, Math.ceil(this.maxPrefrontal / 2));
+        const toPromote = sorted.slice(Math.ceil(this.maxPrefrontal / 2));
+        this.prefrontal = keepInRam;
+        if (toPromote.length > 0) {
+            const promoteStmt = this.db.prepare(`UPDATE memories SET tier = 'hippocampus' WHERE id = ? `);
+            const txn = this.db.transaction((items) => {
+                for (const item of items) {
+                    promoteStmt.run(item.id);
+                    item.tier = 'hippocampus';
+                }
+            });
+            txn(toPromote);
+        }
+        // Compact hippocampus to cortex if overfull
+        const hippoCount = this.db.prepare(`SELECT COUNT(*) as c FROM memories WHERE tier = 'hippocampus'`).get().c;
+        if (hippoCount > this.maxHippocampus) {
+            this.db.prepare(`
+        UPDATE memories SET tier = 'cortex'
+        WHERE tier = 'hippocampus'
+        AND id IN(
+        SELECT id FROM memories WHERE tier = 'hippocampus'
+          ORDER BY priority DESC LIMIT ?
+        )
+      `).run(hippoCount - this.maxHippocampus);
+        }
+    }
+    // ─────────────────────────────────────────────────────────────────────────
+    // Utilities
+    // ─────────────────────────────────────────────────────────────────────────
+    wordOverlap(a, b) {
+        const setA = new Set(a.filter(w => w.length > 2));
+        const setB = new Set(b.filter(w => w.length > 2));
+        if (setA.size === 0 || setB.size === 0)
+            return 0;
+        const intersection = [...setA].filter(x => setB.has(x));
+        const union = new Set([...setA, ...setB]);
+        return intersection.length / union.size;
+    }
+    rowToItem(row) {
+        return {
+            id: row.id,
+            content: row.content,
+            priority: row.priority,
+            timestamp: row.timestamp,
+            tags: JSON.parse(row.tags ?? '[]'),
+            tier: row.tier,
+            sessionId: row.session_id,
+            accessCount: row.access_count,
+            parentId: row.parent_id,
+            depth: row.depth
+        };
+    }
+    getAllItems() {
+        const rows = this.db.prepare('SELECT * FROM memories').all();
+        return rows.map(row => this.rowToItem(row));
+    }
+    getStats() {
+        const counts = this.db.prepare(`
+      SELECT tier, COUNT(*) as c FROM memories GROUP BY tier
+      `).all();
+        const tierMap = {};
+        for (const row of counts)
+            tierMap[row.tier] = row.c;
+        const linkCount = this.db.prepare('SELECT COUNT(*) as c FROM memory_links').get().c;
+        const oldest = this.db.prepare('SELECT MIN(timestamp) as t FROM memories').get().t;
+        const topTagsRaw = this.db.prepare(`
+      SELECT value as tag, COUNT(*) as c
+      FROM memories, json_each(memories.tags)
+      GROUP BY value ORDER BY c DESC LIMIT 5
+      `).all();
+        return {
+            prefrontal: tierMap['prefrontal'] ?? 0,
+            hippocampus: tierMap['hippocampus'] ?? 0,
+            cortex: tierMap['cortex'] ?? 0,
+            totalLinks: linkCount,
+            oldestEntry: oldest,
+            topTags: topTagsRaw.map(r => r.tag)
+        };
+    }
+    clear() {
+        this.prefrontal = [];
+        this.db.exec('DELETE FROM memory_links; DELETE FROM memories;');
+    }
+    /**
+     * Query memories by tag using direct SQL — precise, no fuzzy matching.
+     * Returns memories that contain ANY of the specified tags.
+     */
+    queryByTags(tags, limit = 20) {
+        if (tags.length === 0)
+            return [];
+        const placeholders = tags.map(() => '?').join(',');
+        const rows = this.db.prepare(`
+      SELECT DISTINCT m.* FROM memories m, json_each(m.tags) jt
+      WHERE jt.value IN (${placeholders})
+      ORDER BY m.priority DESC, m.timestamp DESC
+      LIMIT ?
+    `).all(...tags, limit);
+        return rows.map(row => this.rowToItem(row));
+    }
+    close() {
+        this.flush();
+        this.db.close();
+    }
+}
+export const createMemoryEngine = (dbPath) => new MemoryEngine(dbPath);
+//# sourceMappingURL=memory.js.map

package/dist/engines/memory.js.map

@@ -0,0 +1 @@
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package/dist/engines/meta-learner.d.ts

@@ -0,0 +1,87 @@
+/**
+ * Meta-Learner for Adaptive Compression
+ *
+ * Implements adaptive interpolation and token retention.
+ */
+export interface CompressionFeatures {
+    entropy: number;
+    taskEmbedding: number[];
+    layerDepth: number;
+    magnitudeRatio: number;
+    cosineSimilarity: number;
+}
+export declare class AdaptiveInterpolator {
+    private w1;
+    private w2;
+    private b;
+    /**
+     * Adaptive interpolation: t^{l,l-1} = σ(w1 * mag_ratio + w2 * cos_sim + b)
+     * Bounds t to [0.3, 0.7]
+     */
+    computeT(features: CompressionFeatures): number;
+    /**
+     * Update weights (simple gradient descent)
+     */
+    update(features: CompressionFeatures, targetT: number, learningRate?: number): void;
+    /**
+     * Extract features from layer outputs
+     */
+    extractFeatures(attentionMatrix: number[][], taskQuery: string, layerIndex: number, totalLayers: number, currentLayer: number[], previousLayer: number[]): CompressionFeatures;
+    private computeEntropy;
+    private simpleEmbedding;
+    private magnitudeRatio;
+    private cosineSimilarity;
+}
+export declare class TokenRetention {
+    private gamma;
+    setGamma(g: number): void;
+    /**
+     * Token Retention Threshold:
+     * I = {i | d_i < d_min + (d_max - d_min) * γ}
+     * where d_i = (1/π) * arccos(cos_sim_i) is angular distance
+     */
+    computeRetentionMask(currentLayer: number[][], previousLayer: number[][]): boolean[];
+    /**
+     * Get retained tokens
+     */
+    getRetained(layer: number[][], mask: boolean[]): number[][];
+    /**
+     * Get removed tokens
+     */
+    getRemoved(layer: number[][], mask: boolean[]): number[][];
+    /**
+     * Estimate retention ratio
+     */
+    getRetentionRatio(mask: boolean[]): number;
+    private cosineSimilarity;
+}
+export declare class MetaLearner {
+    private interpolator;
+    private retention;
+    constructor();
+    /**
+     * Predict compression decision
+     */
+    predict(attentionMatrix: number[][], taskQuery: string, layerIndex: number, totalLayers: number, currentLayer: number[], previousLayer: number[]): {
+        shouldMerge: boolean;
+        t: number;
+        gamma: number;
+    };
+    /**
+     * Apply compression and get result
+     */
+    compress(currentLayer: number[][], previousLayer: number[][], taskQuery: string, layerIndex: number, totalLayers: number, attentionMatrix: number[][]): {
+        merged: number[][];
+        retained: number[][];
+        removed: number[][];
+        mask: boolean[];
+    };
+    /**
+     * Update from feedback (simple learning)
+     */
+    update(features: CompressionFeatures, actualQuality: number, expectedQuality: number): void;
+}
+export declare const createMetaLearner: () => MetaLearner;
+export declare const createAdaptiveInterpolator: () => AdaptiveInterpolator;
+export declare const createTokenRetention: () => TokenRetention;
+//# sourceMappingURL=meta-learner.d.ts.map

package/dist/engines/meta-learner.d.ts.map

@@ -0,0 +1 @@
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