@rbalchii/anchor-engine 4.7.0

package/engine/dist/core/db.js

@@ -0,0 +1,563 @@
+/**
+ * Database Module for Sovereign Context Engine
+ *
+ * This module manages the PGlite database connection and provides
+ * database operations for the context engine.
+ */
+console.log("[DB] Loading Config...");
+import { config } from "../config/index.js";
+import fs from "fs";
+import { fileURLToPath } from "url";
+import { PGlite } from "@electric-sql/pglite";
+const __filename = fileURLToPath(import.meta.url);
+import { pathManager } from '../utils/path-manager.js';
+export class Database {
+    dbInstance = null;
+    _isInitialized = false;
+    inTransaction = false;
+    preparedStatements = new Map();
+    constructor() {
+        // Database connection is now established in init()
+    }
+    get isInitialized() {
+        return this._isInitialized;
+    }
+    /**
+     * Begin a transaction
+     *
+     * NOTE: Nested transactions are not supported. If a transaction is already
+     * open, this call is a no-op. PGlite does not support SAVEPOINTs via this
+     * wrapper. For nested transactional logic, use raw SQL SAVEPOINTs:
+     *   await db.run('SAVEPOINT my_save');
+     *   ...on error... await db.run('ROLLBACK TO SAVEPOINT my_save');
+     */
+    async beginTransaction() {
+        if (!this.inTransaction) {
+            await this.run('BEGIN');
+            this.inTransaction = true;
+        }
+    }
+    /**
+     * Commit a transaction
+     */
+    async commit() {
+        if (this.inTransaction) {
+            await this.run('COMMIT');
+            this.inTransaction = false;
+        }
+    }
+    /**
+     * Rollback a transaction
+     */
+    async rollback() {
+        if (this.inTransaction) {
+            await this.run('ROLLBACK');
+            this.inTransaction = false;
+        }
+    }
+    /**
+     * Execute a function within a transaction
+     */
+    async transaction(fn) {
+        await this.beginTransaction();
+        try {
+            const result = await fn();
+            await this.commit();
+            return result;
+        }
+        catch (error) {
+            await this.rollback();
+            throw error;
+        }
+    }
+    /**
+     * Initialize the database with required schemas
+     * Wipes existing database on startup to prevent corruption
+     */
+    async init() {
+        // 0. Initialize the database connection
+        if (this.dbInstance === null) {
+            // Use pathManager for consistent absolute path (Standard 051)
+            const dbPath = process.env.PGLITE_DB_PATH || pathManager.getDatabasePath();
+            // Wipe and recreate the database directory on every startup (Standard 051 - Ephemeral Index)
+            // Controlled by user_settings.json: database.wipe_on_startup (default: true)
+            const shouldWipe = config.DATABASE?.WIPE_ON_STARTUP !== false;
+            try {
+                console.log(`[DB] Using database directory: ${dbPath}`);
+                if (shouldWipe) {
+                    // Remove existing database directory to prevent corruption from unclean shutdowns
+                    if (fs.existsSync(dbPath)) {
+                        console.log(`[DB] Removing existing database directory (preventing corruption): ${dbPath}`);
+                        try {
+                            fs.rmSync(dbPath, { recursive: true, force: true });
+                            console.log(`[DB] Old database directory removed successfully`);
+                        }
+                        catch (rmError) {
+                            console.warn(`[DB] Warning: Could not remove old database directory: ${rmError.message}`);
+                            console.warn(`[DB] Will attempt to overwrite on init`);
+                        }
+                    }
+                }
+                else {
+                    console.log(`[DB] Retaining existing database (wipe_on_startup=false). Index may be stale.`);
+                }
+                console.log(`[DB] Database directory ready: ${dbPath}`);
+            }
+            catch (cleanupError) {
+                console.error(`[DB] Error during database directory preparation:`, cleanupError);
+                // Don't crash if wipe fails, just try to continue
+            }
+            try {
+                console.log(`[DB] Initializing PGlite at: ${dbPath}`);
+                // Initialize PGlite with optimized memory settings (Standard 127)
+                // Memory reduction tactics for embedded deployment (phones + laptops)
+                this.dbInstance = await new PGlite(dbPath, {
+                    // Don't set maxMemory limit - let Node.js GC manage heap (6GB from --max-old-space-size)
+                    // OOM prevention is handled by:
+                    // 1. Search serialization (one search at a time)
+                    // 2. Memory pressure detection (downgrade max-recall if heap >3.2GB)
+                    // 3. Forced GC after ingestion and search completion
+                    relaxedDurability: true, // Skip fsync during ingestion (Standard 059)
+                    settings: {
+                        // Reduce PGlite WASM buffer cache from default 1GB
+                        'shared_buffers': '256MB',
+                        // Bound planner's estimate to prevent unbounded CTE memory
+                        'effective_cache_size': '512MB',
+                        // Per-operation memory for sorts/hashes (physics walker CTEs)
+                        'work_mem': '16MB',
+                        // Memory for VACUUM, CREATE INDEX, etc.
+                        'maintenance_work_mem': '64MB',
+                        // WAL buffer size
+                        'wal_buffers': '4MB',
+                        // Spread checkpoint writes over 90% of checkpoint interval
+                        'checkpoint_completion_target': 0.9,
+                        // Random page access cost estimate (helps planner choose seq scans)
+                        'random_page_cost': 1.1,
+                        // Sequential scan cost estimate
+                        'seq_page_cost': 1.0,
+                    }
+                });
+                console.log(`[DB] PGlite initialized successfully: ${dbPath}`);
+                console.log(`[DB] Memory settings: shared_buffers=256MB, effective_cache_size=512MB, work_mem=16MB`);
+                // Additional runtime memory bounds (applied after init)
+                // These complement the constructor settings above
+                await this.dbInstance.exec("SET effective_cache_size = '512MB'");
+                await this.dbInstance.exec("SET work_mem = '16MB'");
+                await this.dbInstance.exec("SET maintenance_work_mem = '64MB'");
+            }
+            catch (e) {
+                console.error(`[DB] Failed to initialize PGlite: ${e.message}`);
+                throw e;
+            }
+        }
+        // Create Synonyms table for automatic query expansion
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS synonyms (
+          term TEXT PRIMARY KEY,
+          synonyms TEXT,
+          created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+        );
+      `);
+            console.log("[DB] 'synonyms' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating synonyms table:", e);
+            throw e;
+        }
+        // Create atoms table schema - simplified for PGlite compatibility
+        try {
+            // Create sequence for vector_ids
+            await this.run('CREATE SEQUENCE IF NOT EXISTS vector_id_seq START 1;');
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS atoms (
+          id TEXT PRIMARY KEY,
+          content TEXT,
+          source_path TEXT,
+          timestamp REAL,
+          simhash TEXT,
+          embedding TEXT,
+          vector_id BIGINT,
+          provenance TEXT,
+          created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+        );
+      `);
+            console.log("[DB] 'atoms' table initialized.");
+            // Add missing columns if they don't exist (for existing databases)
+            const columnsToAdd = [
+                { name: 'vector_id', type: 'BIGINT' },
+                { name: 'buckets', type: 'TEXT[]' },
+                { name: 'tags', type: 'TEXT[]' },
+                { name: 'epochs', type: 'TEXT[]' },
+                { name: 'sequence', type: 'INTEGER' },
+                { name: 'type', type: 'TEXT' },
+                { name: 'hash', type: 'TEXT' },
+                { name: 'molecular_signature', type: 'TEXT' },
+                { name: 'compound_id', type: 'TEXT' },
+                { name: 'start_byte', type: 'INTEGER' },
+                { name: 'end_byte', type: 'INTEGER' },
+                { name: 'numeric_value', type: 'REAL' },
+                { name: 'numeric_unit', type: 'TEXT' },
+                { name: 'source_id', type: 'TEXT' },
+                { name: 'tags', type: 'JSONB' },
+                { name: 'entities', type: 'JSONB' },
+                { name: 'payload', type: 'JSONB' } // Crystal Atom Structure (Hybrid Architecture)
+            ];
+            for (const col of columnsToAdd) {
+                try {
+                    await this.run(`ALTER TABLE atoms ADD COLUMN IF NOT EXISTS ${col.name} ${col.type};`);
+                }
+                catch (alterErr) {
+                    // Column might already exist, which is fine
+                    console.debug(`[DB] Column ${col.name} addition:`, alterErr.message);
+                }
+            }
+            // Add index for compound_id (CRITICAL for Physics Walker)
+            try {
+                await this.run('CREATE INDEX IF NOT EXISTS idx_atoms_compound_id ON atoms(compound_id);');
+            }
+            catch (idxErr) {
+                console.warn("[DB] Could not create compound_id index:", idxErr.message);
+            }
+        }
+        catch (e) {
+            console.error("[DB] Error initializing atoms table:", e);
+            throw e;
+        }
+        // Create the tags table (The "Nervous System")
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS tags (
+          atom_id TEXT,
+          tag TEXT,
+          bucket TEXT,
+          PRIMARY KEY (atom_id, tag, bucket)
+        );
+      `);
+            // Create indexes - optimized for PhysicsWalker queries
+            try {
+                await this.run('CREATE INDEX IF NOT EXISTS idx_tags_tag ON tags(tag);');
+            }
+            catch (indexErr) {
+                console.warn("[DB] Could not create tag index:", indexErr.message);
+            }
+            try {
+                await this.run('CREATE INDEX IF NOT EXISTS idx_tags_bucket ON tags(bucket);');
+            }
+            catch (indexErr) {
+                console.warn("[DB] Could not create bucket index:", indexErr.message);
+            }
+            // NEW INDEX (2026-02-23): For fast atom_id lookups in PhysicsWalker
+            try {
+                await this.run('CREATE INDEX IF NOT EXISTS idx_tags_atom_id ON tags(atom_id);');
+            }
+            catch (indexErr) {
+                console.warn("[DB] Could not create atom_id index:", indexErr.message);
+            }
+            console.log("[DB] 'tags' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating tags table:", e);
+            throw e;
+        }
+        // Create Edges table (The Graph Connections)
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS edges (
+          source_id TEXT,
+          target_id TEXT,
+          relation TEXT,
+          weight REAL,
+          PRIMARY KEY (source_id, target_id, relation)
+        );
+      `);
+            console.log("[DB] 'edges' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating edges table:", e);
+            throw e;
+        }
+        // Create Source Table (Container)
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS sources (
+          path TEXT PRIMARY KEY,
+          hash TEXT,
+          total_atoms INTEGER,
+          last_ingest REAL
+        );
+      `);
+            console.log("[DB] 'sources' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating sources table:", e);
+            throw e;
+        }
+        // Create molecules table (The Document Sentences)
+        try {
+            await this.run(`
+          CREATE TABLE IF NOT EXISTS molecules (
+            id TEXT PRIMARY KEY,
+            content TEXT,
+            compound_id TEXT,
+            sequence INTEGER,
+            start_byte INTEGER,
+            end_byte INTEGER,
+            type TEXT,
+            numeric_value REAL,
+            numeric_unit TEXT,
+            molecular_signature TEXT,
+            embedding TEXT,
+            timestamp REAL,
+            tags JSONB,
+            entities JSONB
+          );
+        `);
+            // Add indices for molecules
+            try {
+                await this.run('CREATE INDEX IF NOT EXISTS idx_molecules_compound ON molecules(compound_id);');
+            }
+            catch (idxErr) {
+                console.warn("[DB] Could not create molecule compound index:", idxErr.message);
+            }
+            // Ensure new columns exist for existing databases
+            const molColumnsToAdd = [
+                { name: 'tags', type: 'JSONB' },
+                { name: 'entities', type: 'JSONB' }
+            ];
+            for (const col of molColumnsToAdd) {
+                try {
+                    await this.run(`ALTER TABLE molecules ADD COLUMN IF NOT EXISTS ${col.name} ${col.type};`);
+                }
+                catch (alterErr) {
+                    // Column might already exist
+                }
+            }
+            console.log("[DB] 'molecules' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating molecules table:", e);
+            throw e;
+        }
+        // Create Compounds table (Atomic Architecture)
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS compounds (
+          id TEXT PRIMARY KEY,
+          compound_body TEXT,
+          path TEXT,
+          timestamp REAL,
+          provenance TEXT,
+          molecular_signature TEXT,
+          atoms TEXT,
+          molecules TEXT,
+          embedding TEXT
+        );
+      `);
+            console.log("[DB] 'compounds' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating compounds table:", e);
+            throw e;
+        }
+        // Create Engrams table (Lexical Sidecar)
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS engrams (
+          key TEXT PRIMARY KEY,
+          value TEXT
+        );
+      `);
+            console.log("[DB] 'engrams' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating engrams table:", e);
+            throw e;
+        }
+        // Create Atom Positions table (Lazy Molecule Inflation)
+        // Tracks where atoms (keywords) appear in compounds for radial inflation
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS atom_positions (
+          compound_id TEXT NOT NULL,
+          atom_label TEXT NOT NULL,
+          byte_offset INTEGER NOT NULL,
+          PRIMARY KEY (compound_id, atom_label, byte_offset)
+        );
+      `);
+            await this.run(`
+        CREATE INDEX IF NOT EXISTS idx_atom_positions_label 
+        ON atom_positions(atom_label);
+      `);
+            console.log("[DB] 'atom_positions' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating atom_positions table:", e);
+            throw e;
+        }
+        // Create Summary Nodes Table (Dreamer Abstractions)
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS summary_nodes (
+          id TEXT PRIMARY KEY,
+          type TEXT,
+          content TEXT,
+          span_start REAL,
+          span_end REAL,
+          embedding TEXT
+        );
+      `);
+            console.log("[DB] 'summary_nodes' table initialized.");
+        }
+        catch (e) {
+            console.error("[DB] Error creating summary_nodes table:", e);
+            throw e;
+        }
+        // Create GitHub Repos Table (Standard 115: GitHub Repository Ingestion)
+        try {
+            await this.run(`
+        CREATE TABLE IF NOT EXISTS github_repos (
+          id TEXT PRIMARY KEY,
+          owner TEXT NOT NULL,
+          repo TEXT NOT NULL,
+          branch TEXT DEFAULT 'main',
+          bucket TEXT NOT NULL,
+          github_url TEXT NOT NULL,
+          last_synced_at TIMESTAMP,
+          last_sync_status TEXT,
+          last_error TEXT,
+          total_files INTEGER DEFAULT 0,
+          total_atoms INTEGER DEFAULT 0,
+          total_size_bytes INTEGER DEFAULT 0,
+          created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+          updated_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+        );
+      `);
+            console.log("[DB] 'github_repos' table initialized.");
+            // Create index for owner/repo lookup
+            await this.run(`
+        CREATE INDEX IF NOT EXISTS idx_github_repos_owner_repo 
+        ON github_repos(owner, repo);
+      `);
+        }
+        catch (e) {
+            console.error("[DB] Error creating github_repos table:", e);
+            throw e;
+        }
+        // Create FTS index for content search
+        try {
+            await this.run(`
+        CREATE INDEX IF NOT EXISTS idx_atoms_content_gin
+        ON atoms
+        USING GIN(to_tsvector('simple', content));
+      `);
+            console.log("[DB] FTS index created for content search.");
+        }
+        catch (e) {
+            console.warn("[DB] Could not create FTS index:", e.message);
+            // Try creating a simpler index if GIN fails
+            try {
+                await this.run(`
+          CREATE INDEX IF NOT EXISTS idx_atoms_content_text
+          ON atoms (content);
+        `);
+                console.log("[DB] Text index created as fallback.");
+            }
+            catch (fallbackErr) {
+                console.warn("[DB] Could not create fallback text index:", fallbackErr.message);
+            }
+        }
+        // Create FTS index for molecules content search (Tag-Walker anchor stage)
+        try {
+            await this.run(`
+        CREATE INDEX IF NOT EXISTS idx_molecules_content_gin
+        ON molecules
+        USING GIN(to_tsvector('simple', content));
+      `);
+            console.log("[DB] FTS index created for molecules content search.");
+        }
+        catch (e) {
+            console.warn("[DB] Could not create molecules FTS index:", e.message);
+            // Try creating a simpler index if GIN fails
+            try {
+                await this.run(`
+          CREATE INDEX IF NOT EXISTS idx_molecules_content_text
+          ON molecules (content);
+        `);
+                console.log("[DB] Molecules text index created as fallback.");
+            }
+            catch (fallbackErr) {
+                console.warn("[DB] Could not create molecules fallback text index:", fallbackErr.message);
+            }
+        }
+        // Create JSONB GIN Index (Crystal Atom Optimization)
+        try {
+            await this.run(`
+        CREATE INDEX IF NOT EXISTS idx_atoms_payload_gin
+        ON atoms
+        USING GIN (payload);
+      `);
+            console.log("[DB] GIN index created for payload (Crystal Atom).");
+        }
+        catch (e) {
+            console.warn("[DB] Could not create payload GIN index:", e.message);
+        }
+        // Mark as initialized after all setup is complete
+        this._isInitialized = true;
+        console.log("Database initialized successfully");
+    }
+    /**
+     * Close the database connection
+     */
+    async close() {
+        // Close the database connection
+        if (this.dbInstance) {
+            await this.dbInstance.close();
+        }
+    }
+    /**
+     * Run a query against the database
+     */
+    async run(query, params) {
+        const { config } = await import("../config/index.js");
+        if (config.LOG_LEVEL === "DEBUG") {
+            console.log(`[DB] Executing Query: ${query.substring(0, 80)}...`);
+            if (params && params.length > 0)
+                console.log(`[DB] Params:`, params);
+        }
+        try {
+            if (this.dbInstance === null) {
+                throw new Error("Database not initialized");
+            }
+            // PGlite returns objects by default which works with our named fields
+            const result = await this.dbInstance.query(query, params || []);
+            return result;
+        }
+        catch (e) {
+            // Don't log transaction control statements as errors
+            if (!query.trim().match(/^(BEGIN|COMMIT|ROLLBACK)/i)) {
+                console.error(`[DB] Query Failed: ${e.message}`);
+                console.error(`[DB] Query: ${query}`);
+            }
+            throw e;
+        }
+    }
+    /**
+     * Run a FTS search query
+     */
+    async search(query) {
+        if (this.dbInstance === null) {
+            throw new Error("Database not initialized");
+        }
+        // For now, use a simple LIKE query since full-text search may not be available
+        const result = await this.dbInstance.query(`SELECT * FROM atoms WHERE content LIKE ?`, [`%${query}%`]);
+        return result;
+    }
+    // Helper methods for file system operations
+    existsSync = fs.existsSync;
+    rmdirSync = fs.rmSync;
+    mkdirSync = fs.mkdirSync;
+}
+// Export a singleton instance
+export const db = new Database();
+//# sourceMappingURL=db.js.map

package/engine/dist/core/db.js.map

@@ -0,0 +1 @@
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package/engine/dist/core/inference/ChatWorker.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=ChatWorker.d.ts.map

package/engine/dist/core/inference/ChatWorker.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ChatWorker.d.ts","sourceRoot":"","sources":["../../../src/core/inference/ChatWorker.ts"],"names":[],"mappings":""}

package/engine/dist/core/inference/ChatWorker.js

@@ -0,0 +1,28 @@
+/**
+ * ChatWorker — Local inference stub.
+ *
+ * node-llama-cpp has been removed from this project (user intent: pare to working core).
+ * Local LLM inference is NOT available. Configure LLM_PROVIDER=remote in user_settings.json
+ * to use a remote OpenAI-compatible endpoint instead.
+ *
+ * To restore local inference:
+ *   1. Re-add node-llama-cpp to engine/package.json
+ *   2. Restore the original ChatWorker implementation from git history
+ */
+import { parentPort } from 'worker_threads';
+// Worker stub — signals ready immediately, returns errors for all requests
+async function init() {
+    console.warn('[ChatWorker] Local inference is disabled. node-llama-cpp has been removed.');
+    parentPort?.postMessage({ type: 'ready' });
+}
+parentPort?.on('message', (message) => {
+    const err = 'Local inference not available. node-llama-cpp removed. Use LLM_PROVIDER=remote.';
+    if (message.type === 'dispose') {
+        parentPort?.postMessage({ type: 'disposed' });
+    }
+    else {
+        parentPort?.postMessage({ type: 'error', error: err });
+    }
+});
+init();
+//# sourceMappingURL=ChatWorker.js.map

package/engine/dist/core/inference/ChatWorker.js.map

@@ -0,0 +1 @@
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package/engine/dist/core/inference/context_manager.d.ts

@@ -0,0 +1,49 @@
+import type { UserContext } from '../../types/context-protocol.js';
+export interface ContextAtom {
+    id: string;
+    content: string;
+    source: string;
+    timestamp: number;
+    score: number;
+    tags?: string[];
+    type?: string;
+    provenance?: string;
+    connections?: string[];
+}
+export interface ContextResult {
+    prompt: string;
+    stats: {
+        tokenCount: number;
+        charCount: number;
+        filledPercent: number;
+        atomCount: number;
+    };
+}
+/**
+ * Rolling Context Slicer (Feature 8) - Neuro-Symbolic Bridge Edition
+ *
+ * Implements "Middle-Out" Context Budgeting with Structured Graph Output.
+ * Prioritizes atoms based on a mix of Relevance (Vector Similarity) and Recency.
+ *
+ * Strategy:
+ * 1. Rank Candidates: Score = (Relevance * 0.7) + (RecencyNorm * 0.3).
+ * 2. Select: Fill budget with highest ranked atoms.
+ * 3. Smart Slice: If an atom fits partially, slice around the keyword match (windowing).
+ * 4. Order: Sort selected atoms Chronologically (or by Sequence) for linear readability.
+ */
+export declare function composeRollingContext(query: string, results: ContextAtom[], tokenBudget?: number): ContextResult;
+/**
+ * Compose context using the Graph-Context Protocol.
+ *
+ * This produces the sovereign prompt format:
+ *   System: "You are the interface for Anchor OS..."
+ *   User:   [CONTEXT_GRAPH_START]...[CONTEXT_GRAPH_END] + query
+ *
+ * Use this instead of composeRollingContext when you have physics metadata.
+ */
+export declare function composeGraphContext(query: string, anchors: ContextAtom[], walkerResults: ContextAtom[], user: UserContext, tokenBudget?: number): {
+    system: string;
+    user: string;
+    stats: ContextResult['stats'];
+};
+//# sourceMappingURL=context_manager.d.ts.map

package/engine/dist/core/inference/context_manager.d.ts.map

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