@monoes/memory 2.24.1 → 2.24.4

package/README.md

@@ -27,17 +27,19 @@ npm install @monoes/memory
 ### Schema Architecture & Storage Engine
 - **Storage Driver**: Operates over SQLite with WAL mode (`PRAGMA journal_mode = WAL`) using `better-sqlite3` with a WASM `sql.js` fallback.
 - **Dual Schema Support**:
-  - Standalone `@monoes/memory` core schema ([`packages/@monomind/memory/src/sql-schema.ts:28`](packages/@monomind/memory/src/sql-schema.ts#L28)): `SCHEMA_VERSION = 2` managing **4 tables** (`memory_entries`, `memory_embeddings`, `memory_entry_tags`, `agent_reads`).
-  - CLI project memory schema ([`packages/@monomind/cli/src/memory/memory-schema.ts:15`](packages/@monomind/cli/src/memory/memory-schema.ts#L15)): Schema version `3.0.0` managing **9 tables** (`memory_entries`, `patterns`, `pattern_history`, `trajectories`, `trajectory_steps`, `migration_state`, `sessions`, `vector_indexes`, `metadata`).
+  - Standalone `@monoes/memory` core schema ([`src/sql-schema.ts`](src/sql-schema.ts)): `SCHEMA_VERSION = 4` (stored in `PRAGMA user_version`) managing **4 tables** (`memory_entries`, `memory_embeddings`, `memory_entry_tags`, `agent_reads`).
+  - CLI project memory schema ([`packages/@monomind/cli/src/memory/memory-schema.ts`](../cli/src/memory/memory-schema.ts)): Schema version `3.0.0` managing **9 tables** (`memory_entries`, `patterns`, `pattern_history`, `trajectories`, `trajectory_steps`, `migration_state`, `sessions`, `vector_indexes`, `metadata`).
 
 ## Hybrid Search: ONNX ModernBERT 768d + BM25 RRF
 
+> The retrieval pipeline below (BM25, RRF, query router, OKF, EWC, SONA) is implemented in `@monoes/monomindcli` (`packages/@monomind/cli/src/memory/` and `src/knowledge/`), on top of the storage primitives this package exports.
+
 Retrieval uses a dual-arm hybrid search architecture combined with Reciprocal Rank Fusion (RRF):
 
 1. **Dense Vector Search**:
    - Model: `Alibaba-NLP/gte-modernbert-base` (768 dimensions).
    - Embedding Pipeline: `@xenova/transformers` ONNX feature extraction.
-   - Acceleration: Standalone pure-JS `HNSWIndex` (`dimensions=768`, `M=16`, `efConstruction=200`, `metric='cosine'`).
+   - Acceleration: Standalone pure-JS `HNSWIndex` (set `dimensions: 768` for this model; defaults are `dimensions=1536`, `M=16`, `efConstruction=200`, `metric='cosine'`).
 2. **Lexical Arm (In-Process Okapi BM25)**:
    - Parameters: $k_1 = 1.2$, $b = 0.75$.
    - Tokenizer: Exact parity with the evaluation harness (`text-tokens.ts`).
@@ -69,11 +71,11 @@ Supports document and memory export/import via Open Knowledge Format (OKF) Markd
 | Export | What it does |
 |---|---|
 | `SQLiteBackend` / `SqlJsBackend` | Structured key-value storage in SQLite WAL mode (native + WASM fallback) |
-| `HNSWIndex` | Standalone pure-JS approximate nearest-neighbor index (`768d`) |
+| `HNSWIndex` | Standalone pure-JS approximate nearest-neighbor index (`dimensions` configurable, default `1536`) |
 | `chunkDocument`, `KnowledgeStore`, `KnowledgeRetriever` | Document chunking + retrieval pipeline |
 | `QueryBuilder` / `query()` | Fluent query construction |
 | `CacheManager` | In-memory LRU caching with size/TTL limits |
-| `SwarmCheckpointer` | Persist/restore swarm agent state snapshots |
+| `MonoswarmCheckpointer` | Persist/restore swarm agent state snapshots |
 | `MemoryMigrator` | Import from SQLite, JSON, or Markdown sources |
 | `PromptVersionStore` | Prompt version history & prompt experiment tracking |
 
@@ -91,5 +93,5 @@ everywhere including Windows without a toolchain).
 
 ## License
 
-MIT
+Apache-2.0
 

package/dist/hnsw-distance.d.ts

@@ -10,6 +10,7 @@
 import type { HNSWNode } from './hnsw-index.js';
 import type { DistanceMetric } from './types.js';
 export declare function distance(metric: DistanceMetric, a: Float32Array, b: Float32Array): number;
+/** 1 - cosine similarity; 1 (no similarity) for empty, zero-norm or mismatched-length vectors. */
 export declare function cosineDistance(a: Float32Array, b: Float32Array): number;
 /**
  * OPTIMIZED: Cosine distance using pre-normalized vectors

package/dist/hnsw-distance.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"hnsw-distance.d.ts","sourceRoot":"","sources":["../src/hnsw-distance.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAEhD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAEjD,wBAAgB,QAAQ,CAAC,MAAM,EAAE,cAAc,EAAE,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM,CAazF;AAED,kGAAkG;AAClG,wBAAgB,cAAc,CAAC,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM,CAEvE;AAED;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM,CAYjF;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,YAAY,GAAG,YAAY,CAiBlE;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,cAAc,EACtB,KAAK,EAAE,YAAY,EACnB,eAAe,EAAE,YAAY,GAAG,IAAI,EACpC,IAAI,EAAE,QAAQ,GACb,MAAM,CAQR;AAED,wBAAgB,iBAAiB,CAAC,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM,CAO1E;AAED,wBAAgB,kBAAkB,CAAC,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM,CAO3E;AAED,wBAAgB,iBAAiB,CAAC,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM,CAM1E"}

package/dist/hnsw-distance.js

@@ -7,6 +7,7 @@
  *
  * @module v1/memory/hnsw-distance
  */
+import { cosineSimilarity, warnVectorLengthMismatch } from './math-utils.js';
 export function distance(metric, a, b) {
     switch (metric) {
         case 'cosine':
@@ -21,20 +22,9 @@ export function distance(metric, a, b) {
             return cosineDistance(a, b);
     }
 }
+/** 1 - cosine similarity; 1 (no similarity) for empty, zero-norm or mismatched-length vectors. */
 export function cosineDistance(a, b) {
-    let dotProduct = 0;
-    let normA = 0;
-    let normB = 0;
-    for (let i = 0; i < a.length; i++) {
-        dotProduct += a[i] * b[i];
-        normA += a[i] * a[i];
-        normB += b[i] * b[i];
-    }
-    const denom = Math.sqrt(normA) * Math.sqrt(normB);
-    if (denom === 0)
-        return 1; // zero vector has maximum distance
-    const similarity = dotProduct / denom;
-    return 1 - similarity; // Convert to distance
+    return 1 - cosineSimilarity(a, b);
 }
 /**
  * OPTIMIZED: Cosine distance using pre-normalized vectors
@@ -42,6 +32,10 @@ export function cosineDistance(a, b) {
  * Performance: O(n) with ~2x speedup over standard cosine
  */
 export function cosineDistanceNormalized(a, b) {
+    if (a.length !== b.length) {
+        warnVectorLengthMismatch(a.length, b.length);
+        return 1;
+    }
     let dotProduct = 0;
     for (let i = 0; i < a.length; i++) {
         dotProduct += a[i] * b[i];

package/dist/hnsw-distance.js.map

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package/dist/hnsw-index.d.ts.map

@@ -1 +1 @@
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package/dist/hnsw-index.js

@@ -111,12 +111,10 @@ export class HNSWIndex extends EventEmitter {
         const normalizedQuery = this.config.metric === 'cosine' ? normalizeVector(queryVector) : null;
         // Start from entry point and search down the layers
         let currentNode = this.entryPoint;
-        let _currentDist = distanceOptimized(this.config.metric, queryVector, normalizedQuery, this.nodes.get(currentNode));
         // Search through layers from top to 1
         for (let level = this.maxLevel; level > 0; level--) {
             const layerResult = searchLayerOptimized(this.nodes, this.config.metric, queryVector, normalizedQuery, currentNode, 1, level);
             currentNode = layerResult[0]?.id || currentNode;
-            _currentDist = distanceOptimized(this.config.metric, queryVector, normalizedQuery, this.nodes.get(currentNode));
         }
         // Search layer 0 with ef candidates using heap-based search
         const candidates = searchLayerOptimized(this.nodes, this.config.metric, queryVector, normalizedQuery, currentNode, searchEf, 0);

package/dist/hnsw-index.js.map

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package/dist/index.d.ts

@@ -17,6 +17,7 @@ export { HNSWIndex } from './hnsw-index.js';
 export type { ChunkRecord, KnowledgeExcerpt, MetadataRecord, RetrievalResult, SearchFn, TextChunk, } from './knowledge/index.js';
 export { chunkDocument, KnowledgeRetriever, KnowledgeStore } from './knowledge/index.js';
 export { createMigrator, MemoryMigrator, migrateMultipleSources } from './migration.js';
+export type { PatternStore, StoredPatternRecord } from './pattern-store.js';
 export type { DiffResult, PromptExperiment, PromptVersion, } from './prompt-version-store.js';
 export { PromptVersionStore } from './prompt-version-store.js';
 export type { SortDirection, SortField } from './query-builder.js';

package/dist/index.d.ts.map

@@ -1 +1 @@
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package/dist/index.js.map

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package/dist/math-utils.d.ts

@@ -1,6 +1,15 @@
 /**
  * Shared math utilities — single source of truth for the memory package.
  */
+/**
+ * Warn, at most once per process, that two vectors of different lengths were
+ * compared. That usually means the embedding model changed under a stored index.
+ */
+export declare function warnVectorLengthMismatch(a: number, b: number): void;
+/**
+ * Cosine similarity in [-1, 1]. Returns 0 for empty or zero-norm vectors, and
+ * for vectors of different lengths (with a one-time warning).
+ */
 export declare function cosineSimilarity(a: ArrayLike<number>, b: ArrayLike<number>): number;
 export declare function createHashEmbedding(text: string, dim?: number): Float32Array;
 //# sourceMappingURL=math-utils.d.ts.map

package/dist/math-utils.d.ts.map

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package/dist/math-utils.js

@@ -1,8 +1,30 @@
 /**
  * Shared math utilities — single source of truth for the memory package.
  */
+/** Shared across every monomind cosine copy so the process warns at most once. */
+const LENGTH_MISMATCH_WARNED = Symbol.for('monomind.cosine.lengthMismatchWarned');
+/**
+ * Warn, at most once per process, that two vectors of different lengths were
+ * compared. That usually means the embedding model changed under a stored index.
+ */
+export function warnVectorLengthMismatch(a, b) {
+    const g = globalThis;
+    if (g[LENGTH_MISMATCH_WARNED])
+        return;
+    g[LENGTH_MISMATCH_WARNED] = true;
+    console.warn(`[monomind] cosine similarity: vector length mismatch (${a} vs ${b}), scored as 0. ` +
+        'The embedding model probably changed under a stored index; rebuild it.');
+}
+/**
+ * Cosine similarity in [-1, 1]. Returns 0 for empty or zero-norm vectors, and
+ * for vectors of different lengths (with a one-time warning).
+ */
 export function cosineSimilarity(a, b) {
-    if (a.length !== b.length || a.length === 0)
+    if (a.length !== b.length) {
+        warnVectorLengthMismatch(a.length, b.length);
+        return 0;
+    }
+    if (a.length === 0)
         return 0;
     const len = a.length;
     let dot = 0, normA = 0, normB = 0;

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package/dist/pattern-store.d.ts

@@ -0,0 +1,39 @@
+/**
+ * PatternStore - storage-agnostic contract for learned-pattern persistence.
+ *
+ * The CLI's JSON-file ReasoningBank (`LocalReasoningBank`) implements this
+ * today without any change to its on-disk format; a SQLite-backed store can
+ * implement the same interface later.
+ */
+/** A learned pattern as persisted by a PatternStore. */
+export interface StoredPatternRecord {
+    id: string;
+    type: string;
+    embedding: number[];
+    content: string;
+    confidence: number;
+    usageCount: number;
+    createdAt: number;
+    lastUsedAt: number;
+    metadata?: Record<string, unknown>;
+}
+export interface PatternStore {
+    /** Insert or update a pattern; usage/created/lastUsed default when omitted. */
+    store(pattern: Omit<StoredPatternRecord, 'usageCount' | 'createdAt' | 'lastUsedAt'> & Partial<StoredPatternRecord>): void;
+    /** Cosine-similarity search; a pure read that does not touch usage metrics. */
+    findSimilar(queryEmbedding: number[], options: {
+        k?: number;
+        threshold?: number;
+        type?: string;
+    }): StoredPatternRecord[];
+    /** Record a usage hit for a pattern. */
+    recordUsage(id: string): void;
+    get(id: string): StoredPatternRecord | undefined;
+    getAll(): StoredPatternRecord[];
+    getByType(type: string): StoredPatternRecord[];
+    delete(id: string): boolean;
+    clear(): void;
+    /** Write any pending changes to durable storage. */
+    flushToDisk(): void;
+}
+//# sourceMappingURL=pattern-store.d.ts.map

package/dist/pattern-store.d.ts.map

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

@@ -0,0 +1,9 @@
+/**
+ * PatternStore - storage-agnostic contract for learned-pattern persistence.
+ *
+ * The CLI's JSON-file ReasoningBank (`LocalReasoningBank`) implements this
+ * today without any change to its on-disk format; a SQLite-backed store can
+ * implement the same interface later.
+ */
+export {};
+//# sourceMappingURL=pattern-store.js.map

package/dist/pattern-store.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pattern-store.js","sourceRoot":"","sources":["../src/pattern-store.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG"}

package/dist/schema-migrations.d.ts

@@ -0,0 +1,59 @@
+/**
+ * Versioned schema migrations for the memory SQLite store.
+ *
+ * Dependency-free and driver-agnostic: it only uses the SqlDriver contract, so
+ * it runs the same on better-sqlite3 and sql.js.
+ *
+ * Applied migrations are recorded in a `schema_migrations` table rather than
+ * in `PRAGMA user_version`. The pragma is already taken: releases before this
+ * runner stamp it with their own SCHEMA_VERSION on every open (overwriting a
+ * higher value), and the global brain is opened by whichever monomind version
+ * happens to run. A counter that an older install silently rewinds cannot
+ * tell which migrations ran; a table that older code never touches can.
+ *
+ * Guarantees:
+ *   - each migration runs in its own transaction, together with the row that
+ *     records it, so a migration that throws leaves no trace and is retried
+ *     on the next open;
+ *   - already-recorded migrations are skipped, so re-running is a no-op;
+ *   - a database that records a migration this build does not know was
+ *     written by a newer release, and is refused before anything is written;
+ *   - an untracked database the caller recognises as already being at some
+ *     version is stamped with that baseline, without running its migrations.
+ */
+import type { SqlDriver } from './sql-driver.js';
+export interface SchemaMigration {
+    /** 1-based, contiguous, in the order the migrations run. Never renumber a shipped one. */
+    readonly id: number;
+    readonly description: string;
+    /** Must be synchronous and must not open its own transaction (the runner holds one). */
+    up(driver: SqlDriver): void;
+}
+export interface MigrationRunReport {
+    /** Version recorded before this run, after any baseline stamp. */
+    from: number;
+    /** Version after this run. */
+    to: number;
+    /** Migrations whose `up` ran in this call. */
+    applied: number[];
+    /** Migrations recorded as a baseline in this call, without running `up`. */
+    baselined: number[];
+}
+export interface RunMigrationsOptions {
+    /**
+     * Called only when the tracking table has no rows. Returns the version an
+     * existing database is already at (0 for a fresh one); migrations up to it
+     * are recorded as baseline instead of being run.
+     */
+    baseline?: (driver: SqlDriver) => number;
+}
+export declare class SchemaTooNewError extends Error {
+    readonly databaseVersion: number;
+    readonly supportedVersion: number;
+    readonly code = "MEMORY_SCHEMA_TOO_NEW";
+    constructor(databaseVersion: number, supportedVersion: number);
+}
+/** Highest recorded migration id; 0 for an untracked database. */
+export declare function schemaMigrationVersion(driver: SqlDriver): number;
+export declare function runMigrations(driver: SqlDriver, migrations: readonly SchemaMigration[], options?: RunMigrationsOptions): MigrationRunReport;
+//# sourceMappingURL=schema-migrations.d.ts.map

package/dist/schema-migrations.d.ts.map

@@ -0,0 +1 @@
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package/dist/schema-migrations.js

@@ -0,0 +1,97 @@
+/**
+ * Versioned schema migrations for the memory SQLite store.
+ *
+ * Dependency-free and driver-agnostic: it only uses the SqlDriver contract, so
+ * it runs the same on better-sqlite3 and sql.js.
+ *
+ * Applied migrations are recorded in a `schema_migrations` table rather than
+ * in `PRAGMA user_version`. The pragma is already taken: releases before this
+ * runner stamp it with their own SCHEMA_VERSION on every open (overwriting a
+ * higher value), and the global brain is opened by whichever monomind version
+ * happens to run. A counter that an older install silently rewinds cannot
+ * tell which migrations ran; a table that older code never touches can.
+ *
+ * Guarantees:
+ *   - each migration runs in its own transaction, together with the row that
+ *     records it, so a migration that throws leaves no trace and is retried
+ *     on the next open;
+ *   - already-recorded migrations are skipped, so re-running is a no-op;
+ *   - a database that records a migration this build does not know was
+ *     written by a newer release, and is refused before anything is written;
+ *   - an untracked database the caller recognises as already being at some
+ *     version is stamped with that baseline, without running its migrations.
+ */
+export class SchemaTooNewError extends Error {
+    databaseVersion;
+    supportedVersion;
+    code = 'MEMORY_SCHEMA_TOO_NEW';
+    constructor(databaseVersion, supportedVersion) {
+        super(`memory database is at schema version ${databaseVersion}, but this @monoes/memory ` +
+            `supports up to ${supportedVersion}. It was written by a newer monomind; upgrade ` +
+            `monomind to use it. Refusing to open it so this older version cannot damage it.`);
+        this.databaseVersion = databaseVersion;
+        this.supportedVersion = supportedVersion;
+        this.name = 'SchemaTooNewError';
+    }
+}
+const CREATE_TRACKING_TABLE = `
+  CREATE TABLE IF NOT EXISTS schema_migrations (
+    id INTEGER PRIMARY KEY,
+    description TEXT NOT NULL,
+    applied_at INTEGER NOT NULL,
+    baseline INTEGER NOT NULL DEFAULT 0
+  )`;
+const RECORD = 'INSERT OR IGNORE INTO schema_migrations (id, description, applied_at, baseline) VALUES (?, ?, ?, ?)';
+function hasTrackingTable(driver) {
+    return (driver.get("SELECT name FROM sqlite_master WHERE type = 'table' AND name = 'schema_migrations'") !== null);
+}
+/** Highest recorded migration id; 0 for an untracked database. */
+export function schemaMigrationVersion(driver) {
+    if (!hasTrackingTable(driver))
+        return 0;
+    return Number(driver.get('SELECT MAX(id) AS v FROM schema_migrations')?.v ?? 0) || 0;
+}
+function isRecorded(driver, id) {
+    return driver.get('SELECT id FROM schema_migrations WHERE id = ?', [id]) !== null;
+}
+export function runMigrations(driver, migrations, options = {}) {
+    migrations.forEach((m, i) => {
+        if (m.id !== i + 1)
+            throw new Error(`schema migration ids must be 1..n in order; got ${m.id} at position ${i + 1}`);
+    });
+    const latest = migrations.length;
+    // Refuse before writing anything, the tracking table included.
+    const recorded = schemaMigrationVersion(driver);
+    if (recorded > latest)
+        throw new SchemaTooNewError(recorded, latest);
+    driver.exec(CREATE_TRACKING_TABLE);
+    const report = { from: recorded, to: recorded, applied: [], baselined: [] };
+    if (recorded === 0 && options.baseline) {
+        const base = Math.min(Math.max(0, Math.floor(options.baseline(driver))), latest);
+        if (base > 0) {
+            const now = Date.now();
+            driver.transaction(() => {
+                for (const m of migrations.slice(0, base)) {
+                    if (driver.run(RECORD, [m.id, m.description, now, 1]) > 0)
+                        report.baselined.push(m.id);
+                }
+            });
+            report.from = report.to = base;
+        }
+    }
+    for (const m of migrations) {
+        if (m.id <= report.to)
+            continue;
+        driver.transaction(() => {
+            // Re-checked inside the transaction: another process may have applied it meanwhile.
+            if (isRecorded(driver, m.id))
+                return;
+            m.up(driver);
+            driver.run(RECORD, [m.id, m.description, Date.now(), 0]);
+            report.applied.push(m.id);
+        });
+        report.to = m.id;
+    }
+    return report;
+}
+//# sourceMappingURL=schema-migrations.js.map

package/dist/schema-migrations.js.map

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

@@ -23,12 +23,17 @@
  */
 import type { SqlDriver } from './sql-driver.js';
 /**
- * Bumped when the canonical schema changes; stored in PRAGMA user_version.
- * A database below this version gets the one-time repair migrations
- * (namespace+key dedupe, FTS5 row dedupe) on its next open; at or above it
- * they are skipped (issue #426: they full-scanned the table on every open).
- * 4 = the version that started gating those repairs, so every existing store
- * gets them once more under the current code.
+ * The PRAGMA user_version stamp, frozen at 4. Schema changes are now numbered
+ * migrations (memoryMigrations(), recorded in `schema_migrations`); do not bump
+ * this for them.
+ *
+ * It is still written on every open because releases before the migration
+ * runner gate their full-table repairs (namespace+key dedupe, FTS5 row dedupe,
+ * issue #426) on `user_version < 4`, and write their own value back when they
+ * open the file. Here it serves two purposes: a store at 4 with no
+ * `schema_migrations` table was left by that code at the current schema and is
+ * adopted as a baseline; a tracked store found below 4 was opened by an older
+ * release since, so the repairs run again.
  */
 export declare const SCHEMA_VERSION = 4;
 /**
@@ -93,15 +98,22 @@ export declare function hasFTS5Table(driver: SqlDriver): boolean;
  * Returns true if the FTS5 table is usable after this call.
  */
 export declare function createFTS5Index(driver: SqlDriver, repair?: boolean): boolean;
+/** Version of the newest migration this build knows. */
+export declare const LATEST_MEMORY_MIGRATION: number;
 /**
- * Bring a database to the canonical schema: create tables, migrate legacy
- * inline embeddings, enforce uniqueness, build the FTS5 index, and record
- * the version.
+ * Bring a database to the latest schema: refuse one from a newer release,
+ * adopt or migrate it (see memoryMigrations), then re-assert the invariants an
+ * older release that opened the file since may have undone.
+ *
+ * Those invariants are not one-shot migrations on purpose:
+ *   - FTS5 sync triggers are redefined on every open (cheap, no data), since
+ *     an older release reinstalls its own definitions;
+ *   - the FTS5 table is built whenever it is missing, so a store first opened
+ *     where FTS5 was unavailable gains it once a build that has FTS5 opens it;
+ *   - the namespace+key repair re-runs whenever the unique index is missing;
+ *   - both dedupe repairs re-run when user_version has dropped below 4.
  *
- * The dedupe repairs scan every row, so they run only when the stored
- * version is below SCHEMA_VERSION (an older release that opens the file
- * writes its own lower version back, so it gets repaired again next time).
- * The namespace+key repair also re-runs whenever the unique index is missing.
+ * Throws SchemaTooNewError for a store from a newer release.
  */
 export declare function initializeSchema(driver: SqlDriver): MigrationReport;
 //# sourceMappingURL=sql-schema.d.ts.map

package/dist/sql-schema.d.ts.map

@@ -1 +1 @@
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package/dist/sql-schema.js

@@ -21,13 +21,19 @@
  * conservative — it copies before it drops, is idempotent, and leaves the
  * legacy column in place rather than rewriting the table.
  */
+import { runMigrations } from './schema-migrations.js';
 /**
- * Bumped when the canonical schema changes; stored in PRAGMA user_version.
- * A database below this version gets the one-time repair migrations
- * (namespace+key dedupe, FTS5 row dedupe) on its next open; at or above it
- * they are skipped (issue #426: they full-scanned the table on every open).
- * 4 = the version that started gating those repairs, so every existing store
- * gets them once more under the current code.
+ * The PRAGMA user_version stamp, frozen at 4. Schema changes are now numbered
+ * migrations (memoryMigrations(), recorded in `schema_migrations`); do not bump
+ * this for them.
+ *
+ * It is still written on every open because releases before the migration
+ * runner gate their full-table repairs (namespace+key dedupe, FTS5 row dedupe,
+ * issue #426) on `user_version < 4`, and write their own value back when they
+ * open the file. Here it serves two purposes: a store at 4 with no
+ * `schema_migrations` table was left by that code at the current schema and is
+ * adopted as a baseline; a tracked store found below 4 was opened by an older
+ * release since, so the repairs run again.
  */
 export const SCHEMA_VERSION = 4;
 /**
@@ -146,30 +152,30 @@ export function hasLegacyInlineEmbedding(driver) {
  */
 export function migrateLegacyInlineEmbeddings(driver) {
     const report = { legacyColumnFound: false, migrated: 0, skipped: 0 };
+    driver.transaction(() => copyLegacyInlineEmbeddings(driver, report));
+    return report;
+}
+/** Body of migrateLegacyInlineEmbeddings without its transaction, for use inside a migration. */
+function copyLegacyInlineEmbeddings(driver, report) {
     if (!hasLegacyInlineEmbedding(driver))
-        return report;
+        return;
     report.legacyColumnFound = true;
-    driver.transaction(() => {
-        const rows = driver.all(`SELECT e.id AS id, e.embedding AS embedding
-         FROM memory_entries e
-        WHERE e.embedding IS NOT NULL`);
-        for (const row of rows) {
-            const id = String(row.id);
-            const existing = driver.get('SELECT entry_id FROM memory_embeddings WHERE entry_id = ?', [
-                id,
-            ]);
-            if (existing) {
-                report.skipped++;
-                continue;
-            }
-            driver.run('INSERT OR IGNORE INTO memory_embeddings (entry_id, embedding) VALUES (?, ?)', [
-                id,
-                row.embedding,
-            ]);
-            report.migrated++;
+    const rows = driver.all(`SELECT e.id AS id, e.embedding AS embedding
+       FROM memory_entries e
+      WHERE e.embedding IS NOT NULL`);
+    for (const row of rows) {
+        const id = String(row.id);
+        const existing = driver.get('SELECT entry_id FROM memory_embeddings WHERE entry_id = ?', [id]);
+        if (existing) {
+            report.skipped++;
+            continue;
         }
-    });
-    return report;
+        driver.run('INSERT OR IGNORE INTO memory_embeddings (entry_id, embedding) VALUES (?, ?)', [
+            id,
+            row.embedding,
+        ]);
+        report.migrated++;
+    }
 }
 // ===== FTS5 Full-Text Search Index (Issue #66) =============================
 /**
@@ -335,28 +341,89 @@ function hasNamespaceKeyUniqueIndex(driver) {
         return false;
     }
 }
+const CANONICAL_TABLES = [
+    'memory_entries',
+    'memory_embeddings',
+    'memory_entry_tags',
+    'agent_reads',
+];
 /**
- * Bring a database to the canonical schema: create tables, migrate legacy
- * inline embeddings, enforce uniqueness, build the FTS5 index, and record
- * the version.
+ * The memory schema as numbered migrations. 1-4 are the schema the pre-runner
+ * `initializeSchema()` produced, split into the steps it took; a store it
+ * left at user_version 4 is adopted at version 4 without any of them running.
+ * Each is idempotent, because a store below user_version 4 (or an untracked
+ * one in an unknown state) runs all of them.
  *
- * The dedupe repairs scan every row, so they run only when the stored
- * version is below SCHEMA_VERSION (an older release that opens the file
- * writes its own lower version back, so it gets repaired again next time).
- * The namespace+key repair also re-runs whenever the unique index is missing.
+ * Append new migrations at the end; never edit or renumber a shipped one.
+ */
+function memoryMigrations(report) {
+    return [
+        {
+            id: 1,
+            description: 'canonical tables and indexes (memory_entries, memory_embeddings, memory_entry_tags, agent_reads)',
+            up: createCanonicalSchema,
+        },
+        {
+            id: 2,
+            description: 'copy legacy inline memory_entries.embedding into memory_embeddings (column kept)',
+            up: (driver) => copyLegacyInlineEmbeddings(driver, report),
+        },
+        {
+            id: 3,
+            description: 'dedupe namespace+key and add UNIQUE index idx_namespace_key_unique',
+            up: enforceNamespaceKeyUnique,
+        },
+        {
+            id: 4,
+            description: 'FTS5 index memory_entries_fts with sync triggers, deduping stale rows',
+            up: (driver) => void createFTS5Index(driver, true),
+        },
+    ];
+}
+/** Version of the newest migration this build knows. */
+export const LATEST_MEMORY_MIGRATION = memoryMigrations({
+    legacyColumnFound: false,
+    migrated: 0,
+    skipped: 0,
+}).length;
+/** An untracked store left at user_version 4 by the pre-runner code is already at migration 4. */
+function detectBaseline(driver) {
+    const tables = new Set(driver.all("SELECT name FROM sqlite_master WHERE type = 'table'").map((r) => String(r.name)));
+    return readSchemaVersion(driver) >= SCHEMA_VERSION && CANONICAL_TABLES.every((t) => tables.has(t))
+        ? 4
+        : 0;
+}
+/**
+ * Bring a database to the latest schema: refuse one from a newer release,
+ * adopt or migrate it (see memoryMigrations), then re-assert the invariants an
+ * older release that opened the file since may have undone.
+ *
+ * Those invariants are not one-shot migrations on purpose:
+ *   - FTS5 sync triggers are redefined on every open (cheap, no data), since
+ *     an older release reinstalls its own definitions;
+ *   - the FTS5 table is built whenever it is missing, so a store first opened
+ *     where FTS5 was unavailable gains it once a build that has FTS5 opens it;
+ *   - the namespace+key repair re-runs whenever the unique index is missing;
+ *   - both dedupe repairs re-run when user_version has dropped below 4.
+ *
+ * Throws SchemaTooNewError for a store from a newer release.
  */
 export function initializeSchema(driver) {
-    const needsRepair = readSchemaVersion(driver) < SCHEMA_VERSION;
-    createCanonicalSchema(driver);
-    const report = migrateLegacyInlineEmbeddings(driver);
-    if (needsRepair || !hasNamespaceKeyUniqueIndex(driver))
+    const storedUserVersion = readSchemaVersion(driver);
+    const report = { legacyColumnFound: false, migrated: 0, skipped: 0 };
+    const run = runMigrations(driver, memoryMigrations(report), { baseline: detectBaseline });
+    if (!report.legacyColumnFound)
+        report.legacyColumnFound = hasLegacyInlineEmbedding(driver);
+    // run.from >= 4: the repairs did not just run as migrations 3-4.
+    const regressed = storedUserVersion < SCHEMA_VERSION && run.from >= 4;
+    if (regressed || !hasNamespaceKeyUniqueIndex(driver))
         enforceNamespaceKeyUnique(driver);
-    createFTS5Index(driver, needsRepair);
+    createFTS5Index(driver, regressed);
     try {
         driver.exec(`PRAGMA user_version = ${SCHEMA_VERSION}`);
     }
     catch {
-        /* pragma unsupported on this driver — version tracking is advisory */
+        /* pragma unsupported on this driver — the stamp is advisory */
     }
     return report;
 }

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package/package.json

@@ -1,8 +1,9 @@
 {
   "name": "@monoes/memory",
-  "version": "2.24.1",
+  "version": "2.24.4",
   "type": "module",
   "description": "Memory module - JSON pattern store and a SQLite + embeddings backend with a size-gated HNSW ANN fast path built in",
+  "license": "Apache-2.0",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {
@@ -10,16 +11,16 @@
     "./*": "./dist/*.js"
   },
   "engines": {
-    "node": ">=22.12.0"
+    "node": ">=22.22.0"
   },
   "dependencies": {
     "better-sqlite3": "^12.0.0",
-    "sql.js": "^1.10.3"
+    "sql.js": "^1.16.0"
   },
   "devDependencies": {
     "@types/better-sqlite3": "^7.6.11",
     "@types/sql.js": "^1.4.9",
-    "vitest": "^4.1.4"
+    "vitest": "^5.1.0"
   },
   "files": [
     "dist",