@iflow-mcp/jkheadley-instar 0.26.2

package/dist/memory/MemoryIndex.d.ts

@@ -0,0 +1,76 @@
+/**
+ * MemoryIndex — FTS5 full-text search over agent memory files.
+ *
+ * @deprecated Use SemanticMemory instead. MemoryIndex will be removed in v1.0.
+ * SemanticMemory provides the same FTS5 search plus semantic types, confidence
+ * tracking, knowledge graph relations, and optional vector search (Phase 5).
+ * Use `instar memory export` or POST /semantic/export-memory to generate
+ * MEMORY.md from SemanticMemory.
+ *
+ * Uses SQLite with FTS5 for fast full-text search. The database is
+ * a derived cache — delete it, run reindex, and it rebuilds perfectly
+ * from the markdown source files.
+ *
+ * Security:
+ *   - FTS5 special syntax is stripped from queries to prevent manipulation
+ *   - Source paths are validated before indexing
+ *   - Highlight output uses pre-escaped text
+ */
+import type { MemorySearchConfig, MemorySearchResult, MemoryIndexStats } from '../core/types.js';
+export declare class MemoryIndex {
+    private db;
+    private readonly stateDir;
+    private readonly config;
+    private readonly dbPath;
+    constructor(stateDir: string, config?: Partial<MemorySearchConfig>);
+    /**
+     * Open the database and create tables if needed.
+     */
+    open(): Promise<void>;
+    /**
+     * Close the database connection.
+     */
+    close(): void;
+    /**
+     * Create database schema.
+     */
+    private createSchema;
+    /**
+     * Incremental sync — hash check, re-index changed files.
+     */
+    sync(): {
+        added: number;
+        updated: number;
+        removed: number;
+    };
+    /**
+     * Full rebuild from scratch.
+     */
+    reindex(): {
+        added: number;
+    };
+    /**
+     * Full-text search with ranking.
+     */
+    search(query: string, options?: {
+        limit?: number;
+        source?: string;
+    }): MemorySearchResult[];
+    /**
+     * Get index statistics.
+     */
+    stats(): MemoryIndexStats;
+    /**
+     * Index a single file.
+     */
+    private indexFile;
+    /**
+     * Remove a file's chunks from the index.
+     */
+    removeFile(relativePath: string): void;
+    /**
+     * Collect all files matching configured sources.
+     */
+    private collectSourceFiles;
+}
+//# sourceMappingURL=MemoryIndex.d.ts.map

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

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package/dist/memory/MemoryIndex.js

@@ -0,0 +1,413 @@
+/**
+ * MemoryIndex — FTS5 full-text search over agent memory files.
+ *
+ * @deprecated Use SemanticMemory instead. MemoryIndex will be removed in v1.0.
+ * SemanticMemory provides the same FTS5 search plus semantic types, confidence
+ * tracking, knowledge graph relations, and optional vector search (Phase 5).
+ * Use `instar memory export` or POST /semantic/export-memory to generate
+ * MEMORY.md from SemanticMemory.
+ *
+ * Uses SQLite with FTS5 for fast full-text search. The database is
+ * a derived cache — delete it, run reindex, and it rebuilds perfectly
+ * from the markdown source files.
+ *
+ * Security:
+ *   - FTS5 special syntax is stripped from queries to prevent manipulation
+ *   - Source paths are validated before indexing
+ *   - Highlight output uses pre-escaped text
+ */
+import fs from 'node:fs';
+import path from 'node:path';
+import crypto from 'node:crypto';
+import { chunkMarkdown, chunkJson, chunkJsonl } from './Chunker.js';
+const DEFAULT_CONFIG = {
+    enabled: false,
+    dbPath: 'memory.db',
+    sources: [
+        { path: 'AGENT.md', type: 'markdown', evergreen: true },
+        { path: 'USER.md', type: 'markdown', evergreen: true },
+        { path: 'MEMORY.md', type: 'markdown', evergreen: true },
+        { path: 'relationships/', type: 'json', evergreen: true },
+    ],
+    chunkSize: 400,
+    chunkOverlap: 80,
+    indexSessionLogs: false,
+    temporalDecayFactor: 0.693,
+};
+const SCHEMA_VERSION = '1';
+/**
+ * Strip FTS5 special syntax characters from a query.
+ * Prevents query manipulation (AND, OR, NOT, NEAR, *, column filters).
+ */
+function sanitizeQuery(query) {
+    return query
+        .replace(/\b(AND|OR|NOT|NEAR)\b/gi, '')
+        .replace(/[*:"^{}().]/g, '') // Strip FTS5 special chars including period (column separator)
+        .replace(/\s+/g, ' ')
+        .trim();
+}
+/**
+ * HTML-escape text for safe output.
+ */
+function escapeHtml(text) {
+    return text
+        .replace(/&/g, '&')
+        .replace(/</g, '&lt;')
+        .replace(/>/g, '&gt;')
+        .replace(/"/g, '&quot;');
+}
+/**
+ * Compute search score combining FTS5 rank with temporal decay.
+ */
+function computeScore(ftsRank, sourceModifiedAt, isEvergreen, decayFactor) {
+    // Normalize BM25 rank to a positive score (BM25 returns negative, lower = more relevant)
+    const normalizedScore = 1 / (1 + Math.abs(ftsRank));
+    if (isEvergreen)
+        return normalizedScore;
+    const ageHours = (Date.now() - sourceModifiedAt.getTime()) / (1000 * 60 * 60);
+    const decay = Math.exp(-decayFactor * ageHours / (24 * 30)); // 30-day half-life
+    return normalizedScore * decay;
+}
+export class MemoryIndex {
+    db = null;
+    stateDir;
+    config;
+    dbPath;
+    constructor(stateDir, config) {
+        this.stateDir = path.resolve(stateDir);
+        this.config = { ...DEFAULT_CONFIG, ...config };
+        this.dbPath = path.isAbsolute(this.config.dbPath)
+            ? this.config.dbPath
+            : path.join(this.stateDir, this.config.dbPath);
+    }
+    /**
+     * Open the database and create tables if needed.
+     */
+    async open() {
+        if (this.db)
+            return;
+        let BetterSqlite3;
+        try {
+            BetterSqlite3 = await import('better-sqlite3');
+        }
+        catch {
+            throw new Error('Memory search enabled but better-sqlite3 is not installed. ' +
+                'Run: npm install better-sqlite3. Memory search will be unavailable until installed.');
+        }
+        // Handle both ESM default export and CJS module.exports
+        const constructor = BetterSqlite3.default || BetterSqlite3;
+        // Ensure parent directory exists
+        const dbDir = path.dirname(this.dbPath);
+        if (!fs.existsSync(dbDir)) {
+            fs.mkdirSync(dbDir, { recursive: true });
+        }
+        this.db = constructor(this.dbPath);
+        this.db.pragma('journal_mode = WAL');
+        this.db.pragma('busy_timeout = 5000');
+        this.db.pragma('foreign_keys = ON');
+        this.createSchema();
+    }
+    /**
+     * Close the database connection.
+     */
+    close() {
+        if (this.db) {
+            this.db.close();
+            this.db = null;
+        }
+    }
+    /**
+     * Create database schema.
+     */
+    createSchema() {
+        if (!this.db)
+            return;
+        this.db.exec(`
+      CREATE TABLE IF NOT EXISTS meta (
+        key TEXT PRIMARY KEY,
+        value TEXT
+      );
+
+      CREATE TABLE IF NOT EXISTS tracked_files (
+        path TEXT PRIMARY KEY,
+        hash TEXT NOT NULL,
+        mtime TEXT NOT NULL,
+        type TEXT NOT NULL,
+        evergreen INTEGER DEFAULT 0,
+        indexed_at TEXT NOT NULL,
+        chunk_count INTEGER DEFAULT 0
+      );
+
+      CREATE TABLE IF NOT EXISTS chunks (
+        id INTEGER PRIMARY KEY AUTOINCREMENT,
+        source TEXT NOT NULL,
+        offset INTEGER NOT NULL,
+        length INTEGER NOT NULL,
+        text TEXT NOT NULL,
+        token_count INTEGER,
+        created_at TEXT NOT NULL,
+        indexed_at TEXT NOT NULL,
+        FOREIGN KEY (source) REFERENCES tracked_files(path) ON DELETE CASCADE
+      );
+
+      CREATE VIRTUAL TABLE IF NOT EXISTS chunks_fts USING fts5(
+        text,
+        source UNINDEXED,
+        content='chunks',
+        content_rowid='id',
+        tokenize='porter unicode61'
+      );
+
+      CREATE TRIGGER IF NOT EXISTS chunks_ai AFTER INSERT ON chunks BEGIN
+        INSERT INTO chunks_fts(rowid, text, source) VALUES (new.id, new.text, new.source);
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS chunks_ad AFTER DELETE ON chunks BEGIN
+        INSERT INTO chunks_fts(chunks_fts, rowid, text, source)
+          VALUES('delete', old.id, old.text, old.source);
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS chunks_au AFTER UPDATE ON chunks BEGIN
+        INSERT INTO chunks_fts(chunks_fts, rowid, text, source)
+          VALUES('delete', old.id, old.text, old.source);
+        INSERT INTO chunks_fts(rowid, text, source) VALUES (new.id, new.text, new.source);
+      END;
+    `);
+        // Set schema version
+        this.db.prepare('INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)').run('schema_version', SCHEMA_VERSION);
+    }
+    /**
+     * Incremental sync — hash check, re-index changed files.
+     */
+    sync() {
+        if (!this.db)
+            throw new Error('Database not open. Call open() first.');
+        const result = { added: 0, updated: 0, removed: 0 };
+        const now = new Date().toISOString();
+        // Collect all source file paths
+        const sourceFiles = this.collectSourceFiles();
+        // Process each file
+        for (const { filePath, relativePath, source } of sourceFiles) {
+            if (!fs.existsSync(filePath))
+                continue;
+            const stat = fs.statSync(filePath);
+            const content = fs.readFileSync(filePath, 'utf-8');
+            const hash = crypto.createHash('sha256').update(content).digest('hex');
+            const mtime = stat.mtime.toISOString();
+            // Check if file has changed
+            const existing = this.db.prepare('SELECT hash FROM tracked_files WHERE path = ?').get(relativePath);
+            if (existing && existing.hash === hash)
+                continue; // Unchanged
+            if (existing) {
+                result.updated++;
+            }
+            else {
+                result.added++;
+            }
+            this.indexFile(relativePath, content, source.type, source.evergreen, hash, mtime, now);
+        }
+        // Remove files that no longer exist
+        const trackedPaths = this.db.prepare('SELECT path FROM tracked_files').all().map(r => r.path);
+        const currentPaths = new Set(sourceFiles.map(f => f.relativePath));
+        for (const tracked of trackedPaths) {
+            if (!currentPaths.has(tracked)) {
+                this.removeFile(tracked);
+                result.removed++;
+            }
+        }
+        // Update last indexed time
+        this.db.prepare('INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)').run('last_indexed_at', now);
+        return result;
+    }
+    /**
+     * Full rebuild from scratch.
+     */
+    reindex() {
+        if (!this.db)
+            throw new Error('Database not open. Call open() first.');
+        // Clear everything
+        this.db.exec('DELETE FROM chunks');
+        this.db.exec('DELETE FROM tracked_files');
+        const now = new Date().toISOString();
+        let added = 0;
+        const sourceFiles = this.collectSourceFiles();
+        for (const { filePath, relativePath, source } of sourceFiles) {
+            if (!fs.existsSync(filePath))
+                continue;
+            const stat = fs.statSync(filePath);
+            const content = fs.readFileSync(filePath, 'utf-8');
+            const hash = crypto.createHash('sha256').update(content).digest('hex');
+            const mtime = stat.mtime.toISOString();
+            this.indexFile(relativePath, content, source.type, source.evergreen, hash, mtime, now);
+            added++;
+        }
+        this.db.prepare('INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)').run('last_indexed_at', now);
+        return { added };
+    }
+    /**
+     * Full-text search with ranking.
+     */
+    search(query, options) {
+        if (!this.db)
+            throw new Error('Database not open. Call open() first.');
+        const sanitized = sanitizeQuery(query);
+        if (!sanitized)
+            return [];
+        const limit = options?.limit ?? 10;
+        // FTS5 search with BM25 ranking
+        let sql = `
+      SELECT
+        c.text,
+        c.source,
+        c.offset,
+        chunks_fts.rank as fts_rank,
+        highlight(chunks_fts, 0, '<b>', '</b>') as highlight,
+        tf.mtime as source_mtime,
+        tf.evergreen
+      FROM chunks_fts
+      JOIN chunks c ON c.id = chunks_fts.rowid
+      JOIN tracked_files tf ON tf.path = c.source
+      WHERE chunks_fts MATCH ?
+    `;
+        const params = [sanitized];
+        if (options?.source) {
+            sql += ` AND c.source = ?`;
+            params.push(escapeHtml(options.source));
+        }
+        sql += ` ORDER BY chunks_fts.rank LIMIT ?`;
+        params.push(limit);
+        const rows = this.db.prepare(sql).all(...params);
+        return rows.map(row => ({
+            text: row.text,
+            source: escapeHtml(row.source),
+            offset: row.offset,
+            score: computeScore(row.fts_rank, new Date(row.source_mtime), row.evergreen === 1, this.config.temporalDecayFactor),
+            highlight: row.highlight,
+            sourceModifiedAt: row.source_mtime,
+        }));
+    }
+    /**
+     * Get index statistics.
+     */
+    stats() {
+        if (!this.db)
+            throw new Error('Database not open. Call open() first.');
+        const totalFiles = this.db.prepare('SELECT COUNT(*) as cnt FROM tracked_files').get().cnt;
+        const totalChunks = this.db.prepare('SELECT COUNT(*) as cnt FROM chunks').get().cnt;
+        const lastIndexedAt = this.db.prepare("SELECT value FROM meta WHERE key = 'last_indexed_at'").get()?.value || '';
+        let dbSizeBytes = 0;
+        try {
+            dbSizeBytes = fs.statSync(this.dbPath).size;
+        }
+        catch {
+            // DB file may not exist yet
+        }
+        // Count stale files
+        let staleFiles = 0;
+        const sourceFiles = this.collectSourceFiles();
+        for (const { filePath, relativePath } of sourceFiles) {
+            if (!fs.existsSync(filePath))
+                continue;
+            const content = fs.readFileSync(filePath, 'utf-8');
+            const hash = crypto.createHash('sha256').update(content).digest('hex');
+            const existing = this.db.prepare('SELECT hash FROM tracked_files WHERE path = ?').get(relativePath);
+            if (!existing || existing.hash !== hash) {
+                staleFiles++;
+            }
+        }
+        return {
+            totalFiles,
+            totalChunks,
+            dbSizeBytes,
+            lastIndexedAt,
+            staleFiles,
+            vectorSearchAvailable: false,
+        };
+    }
+    /**
+     * Index a single file.
+     */
+    indexFile(relativePath, content, type, evergreen, hash, mtime, now) {
+        if (!this.db)
+            return;
+        // Remove old chunks for this file
+        this.db.prepare('DELETE FROM chunks WHERE source = ?').run(relativePath);
+        this.db.prepare('DELETE FROM tracked_files WHERE path = ?').run(relativePath);
+        // Chunk based on type
+        let chunks;
+        switch (type) {
+            case 'markdown':
+                chunks = chunkMarkdown(content, this.config.chunkSize, this.config.chunkOverlap);
+                break;
+            case 'json':
+                chunks = chunkJson(content);
+                break;
+            case 'jsonl':
+                chunks = chunkJsonl(content);
+                break;
+            default:
+                chunks = chunkMarkdown(content, this.config.chunkSize, this.config.chunkOverlap);
+        }
+        // Insert tracked file
+        this.db.prepare(`
+      INSERT INTO tracked_files (path, hash, mtime, type, evergreen, indexed_at, chunk_count)
+      VALUES (?, ?, ?, ?, ?, ?, ?)
+    `).run(relativePath, hash, mtime, type, evergreen ? 1 : 0, now, chunks.length);
+        // Insert chunks (batched in a transaction)
+        const insertChunk = this.db.prepare(`
+      INSERT INTO chunks (source, offset, length, text, token_count, created_at, indexed_at)
+      VALUES (?, ?, ?, ?, ?, ?, ?)
+    `);
+        const insertMany = this.db.transaction((chunks) => {
+            for (const chunk of chunks) {
+                insertChunk.run(relativePath, chunk.offset, chunk.length, chunk.text, chunk.tokenCount, now, now);
+            }
+        });
+        insertMany(chunks);
+    }
+    /**
+     * Remove a file's chunks from the index.
+     */
+    removeFile(relativePath) {
+        if (!this.db)
+            return;
+        this.db.prepare('DELETE FROM chunks WHERE source = ?').run(relativePath);
+        this.db.prepare('DELETE FROM tracked_files WHERE path = ?').run(relativePath);
+    }
+    /**
+     * Collect all files matching configured sources.
+     */
+    collectSourceFiles() {
+        const files = [];
+        for (const source of this.config.sources) {
+            const fullPath = path.join(this.stateDir, source.path);
+            if (source.path.endsWith('/')) {
+                // Directory source
+                if (fs.existsSync(fullPath) && fs.statSync(fullPath).isDirectory()) {
+                    for (const entry of fs.readdirSync(fullPath)) {
+                        const entryPath = path.join(fullPath, entry);
+                        if (fs.statSync(entryPath).isFile()) {
+                            files.push({
+                                filePath: entryPath,
+                                relativePath: path.join(source.path, entry),
+                                source,
+                            });
+                        }
+                    }
+                }
+            }
+            else {
+                // Single file source
+                if (fs.existsSync(fullPath) && fs.statSync(fullPath).isFile()) {
+                    files.push({
+                        filePath: fullPath,
+                        relativePath: source.path,
+                        source,
+                    });
+                }
+            }
+        }
+        return files;
+    }
+}
+//# sourceMappingURL=MemoryIndex.js.map

package/dist/memory/MemoryIndex.js.map

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

@@ -0,0 +1,103 @@
+/**
+ * MemoryMigrator — Ingests knowledge from legacy memory systems into SemanticMemory.
+ *
+ * Phase 2 of the memory architecture (PROP-memory-architecture.md).
+ * Transforms flat files (MEMORY.md, JSON, JSONL) into typed entities
+ * with relationships and confidence scores.
+ *
+ * Supported sources:
+ *   - MEMORY.md → fact/pattern entities (confidence 0.7)
+ *   - RelationshipManager JSON → person entities + edges
+ *   - CanonicalState quick-facts → fact entities (confidence 0.95)
+ *   - CanonicalState anti-patterns → lesson entities
+ *   - CanonicalState projects → project entities
+ *   - DecisionJournal JSONL → decision entities
+ *
+ * Key design decisions:
+ *   - Idempotent: uses sourceKey-based dedup to skip already-migrated items
+ *   - Incremental: can be run repeatedly as sources grow
+ *   - No mocking in tests: real filesystem, real SQLite
+ */
+import type { SemanticMemory } from './SemanticMemory.js';
+export interface MigrationSource {
+    source: string;
+    entitiesCreated: number;
+    entitiesSkipped: number;
+    edgesCreated: number;
+    errors: string[];
+    durationMs: number;
+}
+export interface MigrationReport extends MigrationSource {
+}
+export interface FullMigrationReport {
+    sources: MigrationSource[];
+    totalEntitiesCreated: number;
+    totalEdgesCreated: number;
+    totalErrors: number;
+    durationMs: number;
+}
+export interface MemoryMigratorConfig {
+    stateDir: string;
+    semanticMemory: SemanticMemory;
+}
+export declare class MemoryMigrator {
+    private stateDir;
+    private memory;
+    constructor(config: MemoryMigratorConfig);
+    /**
+     * Parse a MEMORY.md file into SemanticMemory entities.
+     * Each H2/H3 section becomes a separate entity.
+     * Sections about patterns → 'pattern' type; others → 'fact' type.
+     */
+    migrateMemoryMd(filePath: string): Promise<MigrationReport>;
+    /**
+     * Migrate RelationshipManager JSON files into person entities.
+     * Each .json file in {stateDir}/relationships/ becomes a person entity.
+     */
+    migrateRelationships(): Promise<MigrationReport>;
+    /**
+     * Migrate CanonicalState files (quick-facts, anti-patterns, projects)
+     * into SemanticMemory entities.
+     */
+    migrateCanonicalState(): Promise<MigrationReport>;
+    private migrateQuickFacts;
+    private migrateAntiPatterns;
+    private migrateProjects;
+    /**
+     * Migrate DecisionJournal JSONL entries into decision entities.
+     */
+    migrateDecisionJournal(): Promise<MigrationReport>;
+    /**
+     * Run all migration sources. Returns aggregate report.
+     */
+    migrateAll(options: {
+        memoryMdPath?: string;
+    }): Promise<FullMigrationReport>;
+    /**
+     * Check if an entity with this source key already exists.
+     * Uses direct SQL lookup on the indexed source column.
+     */
+    private entityExistsForSource;
+    /**
+     * Parse markdown content into heading + content sections.
+     * Extracts H2 and H3 sections (ignoring H1 which is usually the title).
+     */
+    private parseMarkdownSections;
+    /**
+     * Infer entity type from section heading and content.
+     */
+    private inferEntityType;
+    /**
+     * Extract simple tags from heading and content.
+     */
+    private extractTags;
+    /**
+     * Infer a domain from heading and content.
+     */
+    private inferDomain;
+    /**
+     * Safely load a JSON file, returning default on error.
+     */
+    private loadJson;
+}
+//# sourceMappingURL=MemoryMigrator.d.ts.map

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

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