@monoes/monomindcli 2.8.3 → 2.9.1

package/dist/src/memory/memory-crud.js.map

@@ -1 +1 @@
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package/dist/src/memory/memory-initializer.d.ts

@@ -10,10 +10,10 @@
  */
 export { MEMORY_SCHEMA } from './memory-schema.js';
 export { getHNSWIndex, addToHNSWIndex, searchHNSWIndex, getHNSWStatus, clearHNSWIndex, rebuildSearchIndex, quantizeInt8, dequantizeInt8, quantizedCosineSim, getQuantizationStats, batchCosineSim, softmaxAttention, topKIndices, flashAttentionSearch, } from './hnsw-operations.js';
-export { ensureSchemaColumns, checkAndMigrateLegacy, } from './memory-migrations.js';
+export { ensureSchemaColumns, } from './memory-migrations.js';
 export { loadEmbeddingModel, generateEmbedding, generateBatchEmbeddings, generateHashEmbedding, } from './embedding-operations.js';
 export { verifyMemoryInit, storeEntry, searchEntries, listEntries, getEntry, deleteEntry, } from './memory-crud.js';
-import { checkAndMigrateLegacy, ensureSchemaColumns } from './memory-migrations.js';
+import { ensureSchemaColumns } from './memory-migrations.js';
 import { rebuildSearchIndex } from './hnsw-operations.js';
 import { verifyMemoryInit, storeEntry, searchEntries, listEntries, getEntry, deleteEntry } from './memory-crud.js';
 import { loadEmbeddingModel, generateEmbedding } from './embedding-operations.js';
@@ -54,7 +54,6 @@ export declare function initializeMemoryDatabase(options: {
     dbPath?: string;
     force?: boolean;
     verbose?: boolean;
-    migrate?: boolean;
 }): Promise<MemoryInitResult>;
 /**
  * Check if memory database is properly initialized
@@ -82,7 +81,6 @@ export declare function applyTemporalDecay(dbPath?: string): Promise<{
 declare const _default: {
     initializeMemoryDatabase: typeof initializeMemoryDatabase;
     checkMemoryInitialization: typeof checkMemoryInitialization;
-    checkAndMigrateLegacy: typeof checkAndMigrateLegacy;
     ensureSchemaColumns: typeof ensureSchemaColumns;
     applyTemporalDecay: typeof applyTemporalDecay;
     loadEmbeddingModel: typeof loadEmbeddingModel;

package/dist/src/memory/memory-initializer.d.ts.map

@@ -1 +1 @@
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package/dist/src/memory/memory-initializer.js

@@ -11,6 +11,8 @@
 import * as fs from 'fs';
 import * as path from 'path';
 import { BRIDGE_EMBEDDING_DIMS } from './memory-bridge.js';
+import { withDbLock } from '../utils/db-mutex.js';
+import { secureDbFilePermissions } from './file-permissions.js';
 /** Maximum SQLite database file size accepted before read (256 MB). */
 const MAX_DB_FILE_BYTES = 256 * 1024 * 1024;
 // ADR-053: Lazy import of SQLite-backed memory bridge
@@ -34,14 +36,14 @@ async function getBridge() {
 // ============================================================================
 export { MEMORY_SCHEMA } from './memory-schema.js';
 export { getHNSWIndex, addToHNSWIndex, searchHNSWIndex, getHNSWStatus, clearHNSWIndex, rebuildSearchIndex, quantizeInt8, dequantizeInt8, quantizedCosineSim, getQuantizationStats, batchCosineSim, softmaxAttention, topKIndices, flashAttentionSearch, } from './hnsw-operations.js';
-export { ensureSchemaColumns, checkAndMigrateLegacy, } from './memory-migrations.js';
+export { ensureSchemaColumns, } from './memory-migrations.js';
 export { loadEmbeddingModel, generateEmbedding, generateBatchEmbeddings, generateHashEmbedding, } from './embedding-operations.js';
 export { verifyMemoryInit, storeEntry, searchEntries, listEntries, getEntry, deleteEntry, } from './memory-crud.js';
 // ============================================================================
 // Local imports for use in this file
 // ============================================================================
 import { MEMORY_SCHEMA } from './memory-schema.js';
-import { checkAndMigrateLegacy, ensureSchemaColumns } from './memory-migrations.js';
+import { ensureSchemaColumns } from './memory-migrations.js';
 import { rebuildSearchIndex } from './hnsw-operations.js';
 import { verifyMemoryInit, storeEntry, searchEntries, listEntries, getEntry, deleteEntry, } from './memory-crud.js';
 import { loadEmbeddingModel, generateEmbedding, } from './embedding-operations.js';
@@ -121,7 +123,7 @@ async function activateControllerRegistry(dbPath, verbose) {
  * Initialize the memory database properly using sql.js
  */
 export async function initializeMemoryDatabase(options) {
-    const { backend = 'hybrid', dbPath: customPath, force = false, verbose = false, migrate = true } = options;
+    const { backend = 'hybrid', dbPath: customPath, force = false, verbose = false, } = options;
     const swarmDir = path.join(process.cwd(), '.swarm');
     const dbPath = customPath || path.join(swarmDir, 'memory.db');
     const dbDir = path.dirname(dbPath);
@@ -130,13 +132,6 @@ export async function initializeMemoryDatabase(options) {
         if (!fs.existsSync(dbDir)) {
             fs.mkdirSync(dbDir, { recursive: true });
         }
-        // Check for legacy installations
-        if (migrate) {
-            const legacyCheck = await checkAndMigrateLegacy({ dbPath, verbose });
-            if (legacyCheck.needsMigration && verbose) {
-                console.log(`Found legacy database (v${legacyCheck.legacyVersion}) with ${legacyCheck.legacyEntries} entries`);
-            }
-        }
         // Check existing database
         if (fs.existsSync(dbPath) && !force) {
             return {
@@ -188,6 +183,7 @@ export async function initializeMemoryDatabase(options) {
             const dbTmp = dbPath + '.tmp';
             fs.writeFileSync(dbTmp, buffer);
             fs.renameSync(dbTmp, dbPath);
+            secureDbFilePermissions(dbPath);
             // Close database
             db.close();
             // Also create schema file for reference (atomic)
@@ -240,53 +236,31 @@ export async function initializeMemoryDatabase(options) {
             };
         }
         else {
-            // Fall back to schema file approach (atomic writes)
-            const schemaPath = path.join(dbDir, 'schema.sql');
-            const schemaTmpFb = schemaPath + '.tmp';
-            fs.writeFileSync(schemaTmpFb, MEMORY_SCHEMA + '\n' + getInitialMetadata(backend));
-            fs.renameSync(schemaTmpFb, schemaPath);
-            // Create minimal valid SQLite file
-            const sqliteHeader = Buffer.alloc(4096, 0);
-            // SQLite format 3 header
-            Buffer.from('SQLite format 3\0').copy(sqliteHeader, 0);
-            sqliteHeader[16] = 0x10; // page size high byte (4096)
-            sqliteHeader[17] = 0x00; // page size low byte
-            sqliteHeader[18] = 0x01; // file format write version
-            sqliteHeader[19] = 0x01; // file format read version
-            sqliteHeader[24] = 0x00; // max embedded payload
-            sqliteHeader[25] = 0x40;
-            sqliteHeader[26] = 0x20; // min embedded payload
-            sqliteHeader[27] = 0x20; // leaf payload
-            const dbTmpFb = dbPath + '.tmp';
-            fs.writeFileSync(dbTmpFb, sqliteHeader);
-            fs.renameSync(dbTmpFb, dbPath);
-            // ADR-053: Activate ControllerRegistry even on fallback path
-            const controllerResult = await activateControllerRegistry(dbPath, verbose);
+            // R2: sql.js is missing. The previous code wrote a hand-crafted 4 KB
+            // "SQLite format 3" buffer to disk and reported success:true — every
+            // subsequent read on that file fails (it isn't a real SQLite DB) and
+            // checkMemoryInitialization loops forever reporting "not initialized"
+            // on a file the user thinks is fresh. Honest behavior: report failure
+            // with a clear error so the caller can either install sql.js, switch
+            // to the native backend, or skip memory entirely.
+            if (verbose) {
+                console.error('[memory-initializer] sql.js is not installed and the native @monoes/memory backend is unavailable; refusing to write a fake SQLite header. Install sql.js (npm install sql.js) or @monoes/memory to enable memory.');
+            }
             return {
-                success: true,
+                success: false,
                 backend,
                 dbPath,
                 schemaVersion: '3.0.0',
-                tablesCreated: [
-                    'memory_entries (pending)',
-                    'patterns (pending)',
-                    'pattern_history (pending)',
-                    'trajectories (pending)',
-                    'trajectory_steps (pending)',
-                    'migration_state (pending)',
-                    'sessions (pending)',
-                    'vector_indexes (pending)',
-                    'metadata (pending)'
-                ],
+                tablesCreated: [],
                 indexesCreated: [],
                 features: {
-                    vectorEmbeddings: true,
-                    patternLearning: true,
-                    temporalDecay: true,
-                    hnswIndexing: true,
-                    migrationTracking: true
+                    vectorEmbeddings: false,
+                    patternLearning: false,
+                    temporalDecay: false,
+                    hnswIndexing: false,
+                    migrationTracking: false
                 },
-                controllers: controllerResult,
+                error: 'sql.js is not installed and the native @monoes/memory backend is unavailable. Install one of them to enable persistent memory; refusing to write a placeholder SQLite file.'
             };
         }
     }
@@ -370,38 +344,42 @@ export async function applyTemporalDecay(dbPath) {
     const swarmDir = path.join(process.cwd(), '.swarm');
     const path_ = dbPath || path.join(swarmDir, 'memory.db');
     try {
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        // Guard against excessively large DB files to prevent OOM.
-        const decayStat = fs.statSync(path_);
-        if (decayStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, patternsDecayed: 0, error: `Database file too large: ${decayStat.size} bytes` };
-        }
-        const fileBuffer = fs.readFileSync(path_);
-        const db = new SQL.Database(fileBuffer);
-        // Apply decay: confidence *= exp(-decay_rate * days_since_last_use)
-        const now = Date.now();
-        const decayQuery = `
+        return await withDbLock(path_, async () => {
+            const initSqlJs = (await import('sql.js')).default;
+            const SQL = await initSqlJs();
+            const decayStat = fs.statSync(path_);
+            if (decayStat.size > MAX_DB_FILE_BYTES) {
+                return { success: false, patternsDecayed: 0, error: `Database file too large: ${decayStat.size} bytes` };
+            }
+            const fileBuffer = fs.readFileSync(path_);
+            const db = new SQL.Database(fileBuffer);
+            const now = Date.now();
+            // #87: the decay formula is linear (`confidence * (1 - rate * days)`), which
+            // goes negative after ~20 days at the default rate 0.05 — downstream code
+            // rejects confidence outside [0,1], so stale patterns silently vanished.
+            // Clamp at 0.0 so confidence decays to zero instead of wrapping negative.
+            const decayQuery = `
       UPDATE patterns
       SET
-        confidence = confidence * (1.0 - decay_rate * ((? - COALESCE(last_matched_at, created_at)) / 86400000.0)),
+        confidence = MAX(0.0, confidence * (1.0 - decay_rate * ((? - COALESCE(last_matched_at, created_at)) / 86400000.0))),
         updated_at = ?
       WHERE status = 'active'
         AND confidence > 0.1
         AND (? - COALESCE(last_matched_at, created_at)) > 86400000
     `;
-        db.run(decayQuery, [now, now, now]);
-        const changes = db.getRowsModified();
-        // Save atomically
-        const data = db.export();
-        const dbTmpDecay = path_ + '.tmp';
-        fs.writeFileSync(dbTmpDecay, Buffer.from(data));
-        fs.renameSync(dbTmpDecay, path_);
-        db.close();
-        return {
-            success: true,
-            patternsDecayed: changes
-        };
+            db.run(decayQuery, [now, now, now]);
+            const changes = db.getRowsModified();
+            const data = db.export();
+            const dbTmpDecay = path_ + '.tmp';
+            fs.writeFileSync(dbTmpDecay, Buffer.from(data));
+            fs.renameSync(dbTmpDecay, path_);
+            secureDbFilePermissions(path_);
+            db.close();
+            return {
+                success: true,
+                patternsDecayed: changes
+            };
+        });
     }
     catch (error) {
         return {
@@ -414,7 +392,6 @@ export async function applyTemporalDecay(dbPath) {
 export default {
     initializeMemoryDatabase,
     checkMemoryInitialization,
-    checkAndMigrateLegacy,
     ensureSchemaColumns,
     applyTemporalDecay,
     loadEmbeddingModel,

package/dist/src/memory/memory-initializer.js.map

@@ -1 +1 @@
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package/dist/src/memory/memory-migrations.d.ts

@@ -1,6 +1,6 @@
 /**
  * Memory Migrations
- * Schema column migration and legacy database detection.
+ * Schema column migration for older databases.
  * Extracted from memory-initializer.ts (ARCH-4)
  *
  * @module v1/cli/memory-migrations
@@ -14,17 +14,4 @@ export declare function ensureSchemaColumns(dbPath: string): Promise<{
     columnsAdded: string[];
     error?: string;
 }>;
-/**
- * Check for legacy database installations and migrate if needed
- */
-export declare function checkAndMigrateLegacy(options: {
-    dbPath: string;
-    verbose?: boolean;
-}): Promise<{
-    needsMigration: boolean;
-    legacyVersion?: string;
-    legacyEntries?: number;
-    migrated?: boolean;
-    migratedCount?: number;
-}>;
 //# sourceMappingURL=memory-migrations.d.ts.map

package/dist/src/memory/memory-migrations.d.ts.map

@@ -1 +1 @@
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package/dist/src/memory/memory-migrations.js

@@ -1,12 +1,13 @@
 /**
  * Memory Migrations
- * Schema column migration and legacy database detection.
+ * Schema column migration for older databases.
  * Extracted from memory-initializer.ts (ARCH-4)
  *
  * @module v1/cli/memory-migrations
  */
 import * as fs from 'fs';
-import * as path from 'path';
+import { withDbLock } from '../utils/db-mutex.js';
+import { secureDbFilePermissions } from './file-permissions.js';
 /** Maximum SQLite database file size accepted before read (256 MB). */
 const MAX_DB_FILE_BYTES = 256 * 1024 * 1024;
 /**
@@ -19,58 +20,57 @@ export async function ensureSchemaColumns(dbPath) {
         if (!fs.existsSync(dbPath)) {
             return { success: true, columnsAdded: [] };
         }
-        const initSqlJs = (await import('sql.js')).default;
-        const SQL = await initSqlJs();
-        // Guard against excessively large DB files to prevent OOM.
-        const ensureStat = fs.statSync(dbPath);
-        if (ensureStat.size > MAX_DB_FILE_BYTES) {
-            return { success: false, columnsAdded, error: `Database file too large: ${ensureStat.size} bytes` };
-        }
-        const fileBuffer = fs.readFileSync(dbPath);
-        const db = new SQL.Database(fileBuffer);
-        // Get current columns in memory_entries
-        const tableInfo = db.exec("PRAGMA table_info(memory_entries)");
-        const existingColumns = new Set(tableInfo[0]?.values?.map(row => row[1]) || []);
-        // Required columns that may be missing in older schemas
-        // Issue #977: 'type' column was missing from this list, causing store failures on older DBs
-        const requiredColumns = [
-            { name: 'content', definition: "content TEXT DEFAULT ''" },
-            { name: 'type', definition: "type TEXT DEFAULT 'semantic'" },
-            { name: 'embedding', definition: 'embedding TEXT' },
-            { name: 'embedding_model', definition: "embedding_model TEXT DEFAULT 'local'" },
-            { name: 'embedding_dimensions', definition: 'embedding_dimensions INTEGER' },
-            { name: 'tags', definition: 'tags TEXT' },
-            { name: 'metadata', definition: 'metadata TEXT' },
-            { name: 'owner_id', definition: 'owner_id TEXT' },
-            { name: 'expires_at', definition: 'expires_at INTEGER' },
-            { name: 'last_accessed_at', definition: 'last_accessed_at INTEGER' },
-            { name: 'access_count', definition: 'access_count INTEGER DEFAULT 0' },
-            { name: 'status', definition: "status TEXT DEFAULT 'active'" }
-        ];
-        let modified = false;
-        for (const col of requiredColumns) {
-            if (!existingColumns.has(col.name)) {
-                try {
-                    db.run(`ALTER TABLE memory_entries ADD COLUMN ${col.definition}`);
-                    columnsAdded.push(col.name);
-                    modified = true;
-                }
-                catch (e) {
-                    // Column might already exist or other error - continue
-                    if (process.env.DEBUG || process.env.MONOMIND_DEBUG)
-                        console.error(`[ensureSchemaColumns] failed to add column '${col.name}':`, e);
+        return await withDbLock(dbPath, async () => {
+            const initSqlJs = (await import('sql.js')).default;
+            const SQL = await initSqlJs();
+            // Guard against excessively large DB files to prevent OOM.
+            const ensureStat = fs.statSync(dbPath);
+            if (ensureStat.size > MAX_DB_FILE_BYTES) {
+                return { success: false, columnsAdded, error: `Database file too large: ${ensureStat.size} bytes` };
+            }
+            const fileBuffer = fs.readFileSync(dbPath);
+            const db = new SQL.Database(fileBuffer);
+            // Get current columns in memory_entries
+            const tableInfo = db.exec("PRAGMA table_info(memory_entries)");
+            const existingColumns = new Set(tableInfo[0]?.values?.map(row => row[1]) || []);
+            const requiredColumns = [
+                { name: 'content', definition: "content TEXT DEFAULT ''" },
+                { name: 'type', definition: "type TEXT DEFAULT 'semantic'" },
+                { name: 'embedding', definition: 'embedding TEXT' },
+                { name: 'embedding_model', definition: "embedding_model TEXT DEFAULT 'local'" },
+                { name: 'embedding_dimensions', definition: 'embedding_dimensions INTEGER' },
+                { name: 'tags', definition: 'tags TEXT' },
+                { name: 'metadata', definition: 'metadata TEXT' },
+                { name: 'owner_id', definition: 'owner_id TEXT' },
+                { name: 'expires_at', definition: 'expires_at INTEGER' },
+                { name: 'last_accessed_at', definition: 'last_accessed_at INTEGER' },
+                { name: 'access_count', definition: 'access_count INTEGER DEFAULT 0' },
+                { name: 'status', definition: "status TEXT DEFAULT 'active'" }
+            ];
+            let modified = false;
+            for (const col of requiredColumns) {
+                if (!existingColumns.has(col.name)) {
+                    try {
+                        db.run(`ALTER TABLE memory_entries ADD COLUMN ${col.definition}`);
+                        columnsAdded.push(col.name);
+                        modified = true;
+                    }
+                    catch (e) {
+                        if (process.env.DEBUG || process.env.MONOMIND_DEBUG)
+                            console.error(`[ensureSchemaColumns] failed to add column '${col.name}':`, e);
+                    }
                 }
             }
-        }
-        if (modified) {
-            // Save updated database (atomic to avoid corruption on crash)
-            const data = db.export();
-            const tmp = dbPath + '.tmp';
-            fs.writeFileSync(tmp, Buffer.from(data));
-            fs.renameSync(tmp, dbPath);
-        }
-        db.close();
-        return { success: true, columnsAdded };
+            if (modified) {
+                const data = db.export();
+                const tmp = dbPath + '.tmp';
+                fs.writeFileSync(tmp, Buffer.from(data));
+                fs.renameSync(tmp, dbPath);
+                secureDbFilePermissions(dbPath);
+            }
+            db.close();
+            return { success: true, columnsAdded };
+        });
     }
     catch (error) {
         return {
@@ -80,57 +80,4 @@ export async function ensureSchemaColumns(dbPath) {
         };
     }
 }
-/**
- * Check for legacy database installations and migrate if needed
- */
-export async function checkAndMigrateLegacy(options) {
-    const { dbPath, verbose = false } = options;
-    // Check for legacy locations
-    const legacyPaths = [
-        path.join(process.cwd(), 'memory.db'),
-        path.join(process.cwd(), '.claude/memory.db'),
-        path.join(process.cwd(), 'data/memory.db'),
-        path.join(process.cwd(), '.monomind/memory.db')
-    ];
-    for (const legacyPath of legacyPaths) {
-        if (fs.existsSync(legacyPath) && legacyPath !== dbPath) {
-            try {
-                const initSqlJs = (await import('sql.js')).default;
-                const SQL = await initSqlJs();
-                // Guard against excessively large legacy DB files to prevent OOM.
-                const legacyStat = fs.statSync(legacyPath);
-                if (legacyStat.size > MAX_DB_FILE_BYTES) {
-                    if (verbose) {
-                        console.warn(`[memory] Skipping legacy DB at ${legacyPath}: file too large (${legacyStat.size} bytes)`);
-                    }
-                    continue;
-                }
-                const legacyBuffer = fs.readFileSync(legacyPath);
-                const legacyDb = new SQL.Database(legacyBuffer);
-                // Check if it has data
-                const countResult = legacyDb.exec('SELECT COUNT(*) FROM memory_entries');
-                const count = countResult[0]?.values[0]?.[0] || 0;
-                // Get version if available
-                let version = 'unknown';
-                try {
-                    const versionResult = legacyDb.exec("SELECT value FROM metadata WHERE key='schema_version'");
-                    version = versionResult[0]?.values[0]?.[0] || 'unknown';
-                }
-                catch { /* no metadata table */ }
-                legacyDb.close();
-                if (count > 0) {
-                    return {
-                        needsMigration: true,
-                        legacyVersion: version,
-                        legacyEntries: count
-                    };
-                }
-            }
-            catch {
-                // Not a valid SQLite database, skip
-            }
-        }
-    }
-    return { needsMigration: false };
-}
 //# sourceMappingURL=memory-migrations.js.map

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