@claude-flow/cli 3.41.4 → 3.42.1

package/dist/src/mcp-tools/policy-enforcer.js

@@ -0,0 +1,177 @@
+/**
+ * MCP Governance Policy Enforcer (opt-in).
+ *
+ * `.harness/mcp-policy.json` declares governance intent (defaultDeny,
+ * auditLog, maxToolCallsPerTurn, dangerousPatterns, ...) for the claude-flow
+ * MCP server, but until now nothing in the running server (mcp-server.ts)
+ * ever read it: `harness mcp-scan` grades the file's *posture* offline, the
+ * live `tools/call` dispatch never consulted it. Any connected MCP client
+ * could call every registered tool with no audit trail and no call budget.
+ *
+ * This module wires the two policy fields that are actually in this
+ * server's jurisdiction, per the policy file's own rationale comment
+ * (`dangerousPatterns` / `allowShell` / `allowNetwork` / `allowFileWrite`
+ * describe the native-Claude-Code-tool layer — Bash/Write/Edit/WebFetch —
+ * not this MCP server's memory_-, hooks_-, agentdb_-prefixed tool surface,
+ * so they are intentionally left unenforced here):
+ *   - `auditLog`: append a JSONL record for every `tools/call`.
+ *   - `maxToolCallsPerTurn`: bound calls per MCP *session* (one stdio
+ *     process lifetime), deny once exceeded.
+ *
+ * Fully opt-in via `RUFLO_MCP_ENFORCE_POLICY=1` (or `true`). Unset/false
+ * means every function below is a no-op on the hot path — the pre-existing
+ * `tools/call` behavior is unchanged.
+ *
+ * FAIL-CLOSED once enforcement is enabled (PR #3139 review round 1):
+ * a missing/malformed policy file, or a failed mandatory audit-log write,
+ * denies the call rather than silently degrading to unrestricted execution.
+ * The whole point of opting in is a restriction that actually holds; an
+ * enforcement flag that quietly falls back to "no restriction" on its own
+ * misconfiguration defeats the feature. See `evaluateToolCall()`.
+ *
+ * Known scope limits (disclosed, not fixed here):
+ *   - Only wired into the stdio `tools/call` dispatch
+ *     (`MCPServerManager.handleMCPMessage`). The separate HTTP/websocket
+ *     path (`startHttpServer()`, via `@claude-flow/mcp`) does not call
+ *     this module and is unaffected even when this flag is set.
+ *
+ * `maxToolCallsPerTurn` reset semantics (dream-cycle 2026-09-01, follow-up
+ * to 2026-08-31 review round 1): despite the field's name, the original
+ * implementation enforced a *session-lifetime cumulative* cap that never
+ * reset — a long-lived stdio session could exhaust the budget under
+ * entirely legitimate use and stay locked out until the MCP server process
+ * restarted. Research that night (see the dream-cycle gist) found: (1) the
+ * MCP spec only mandates "rate limit tool invocations" with zero mechanism
+ * guidance, and its 2026-07-28 revision (SEP-2567) is actively removing the
+ * session concept from the protocol entirely; (2) every framework/product
+ * that gets this right (FastMCP's rate-limiting middleware, the PolicyLayer
+ * MCP firewall, Cloudflare's public rate limiter) anchors the reset to
+ * wall-clock time, not to a turn or session counter that never decays —
+ * a turn-count reset is gameable by a chatty loop re-arming its own budget,
+ * which wall-clock time is not. This module now enforces a *sliding
+ * wall-clock window*: `maxToolCallsPerTurn` calls are allowed per rolling
+ * `turnWindowMs` (default 60000) per session, keyed by call timestamp so
+ * calls fall out of the window as time passes rather than accumulating
+ * forever. `now` is an injectable parameter (defaults to `Date.now`) so
+ * production callers need no change and tests stay fully deterministic via
+ * `vi.useFakeTimers()`.
+ */
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+export function isPolicyEnforcementEnabled(env = process.env) {
+    const v = env.RUFLO_MCP_ENFORCE_POLICY;
+    return v === '1' || (v ?? '').toLowerCase() === 'true';
+}
+export function loadMcpPolicy(policyPath = path.join(process.cwd(), '.harness', 'mcp-policy.json')) {
+    try {
+        const raw = fs.readFileSync(policyPath, 'utf-8');
+        const parsed = JSON.parse(raw);
+        if (typeof parsed !== 'object' || parsed === null)
+            return null;
+        return parsed;
+    }
+    catch {
+        return null;
+    }
+}
+const DEFAULT_TURN_WINDOW_MS = 60_000;
+const sessionState = new Map();
+/** Test-only: clear per-session call state between test cases. */
+export function resetPolicyEnforcerState() {
+    sessionState.clear();
+}
+/**
+ * Checks (and, if allowed, records) a tool call against
+ * `policy.maxToolCallsPerTurn`, counted over a sliding window of
+ * `policy.turnWindowMs` (default 60000ms) rather than the session's whole
+ * lifetime. Calls older than the window are pruned before comparing count
+ * to limit, so a session that pauses gets its budget back rather than
+ * staying denied until the process restarts. `now` defaults to `Date.now`
+ * for production callers; tests inject a controlled clock instead.
+ */
+export function checkAndRecordCall(policy, sessionId, now = Date.now()) {
+    const limit = policy.maxToolCallsPerTurn;
+    if (typeof limit !== 'number' || !Number.isFinite(limit) || limit <= 0) {
+        return { allowed: true };
+    }
+    const configuredWindow = policy.turnWindowMs;
+    const windowMs = typeof configuredWindow === 'number' && Number.isFinite(configuredWindow) && configuredWindow > 0
+        ? configuredWindow
+        : DEFAULT_TURN_WINDOW_MS;
+    const state = sessionState.get(sessionId) ?? { callTimes: [] };
+    const cutoff = now - windowMs;
+    state.callTimes = state.callTimes.filter((t) => t > cutoff);
+    if (state.callTimes.length >= limit) {
+        sessionState.set(sessionId, state);
+        return {
+            allowed: false,
+            reason: `maxToolCallsPerTurn (${limit}) exceeded within the last ${windowMs}ms for this session`,
+        };
+    }
+    state.callTimes.push(now);
+    sessionState.set(sessionId, state);
+    return { allowed: true };
+}
+let auditLogPathOverride = null;
+/** Test-only: redirect the audit log to a temp file instead of the default path. */
+export function setAuditLogPathForTesting(p) {
+    auditLogPathOverride = p;
+}
+function defaultAuditLogPath() {
+    return path.join(os.tmpdir(), 'ruflo-mcp-audit.jsonl');
+}
+export function getAuditLogPath() {
+    return auditLogPathOverride ?? defaultAuditLogPath();
+}
+/**
+ * Appends one JSONL audit record. Returns `true` if `policy.auditLog` is not
+ * set (nothing was required) or the write succeeded; `false` only when
+ * `auditLog` is required and the write itself failed (disk full, unwritable
+ * path, etc). Never throws — the caller (`evaluateToolCall`) decides what a
+ * failed *mandatory* write means for the call (fail-closed: deny it).
+ */
+export function appendAuditLog(policy, entry) {
+    if (!policy.auditLog)
+        return true;
+    try {
+        fs.appendFileSync(getAuditLogPath(), `${JSON.stringify(entry)}\n`, 'utf-8');
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Single enforcement entry point for a `tools/call` dispatch. Combines, in
+ * order: fail-closed on a missing/malformed policy, the per-session call
+ * budget, and fail-closed on a failed mandatory audit-log write. `policy`
+ * is the result of `loadMcpPolicy()` — pass `null` straight through when it
+ * failed to load, rather than re-deciding that here.
+ */
+export function evaluateToolCall(policy, sessionId, toolName, now = Date.now()) {
+    if (policy === null) {
+        return {
+            allowed: false,
+            reason: 'RUFLO_MCP_ENFORCE_POLICY is set but .harness/mcp-policy.json is missing or invalid — failing closed',
+        };
+    }
+    const budget = checkAndRecordCall(policy, sessionId, now);
+    const auditOk = appendAuditLog(policy, {
+        timestamp: new Date(now).toISOString(),
+        sessionId,
+        toolName,
+        allowed: budget.allowed,
+        reason: budget.reason,
+    });
+    if (!budget.allowed)
+        return budget;
+    if (!auditOk) {
+        return {
+            allowed: false,
+            reason: 'audit log write failed and policy.auditLog is required — failing closed',
+        };
+    }
+    return { allowed: true };
+}
+//# sourceMappingURL=policy-enforcer.js.map

package/dist/src/mcp-tools/seraphina-tools.js

@@ -1,3 +1,4 @@
+import { relayPayload } from './x-federation-tools.js';
 // ADR-125 precedence: explicit tool args (metaLlmUrl / gatewayUrl) take precedence over the
 // SERAPHINA_METALLM_URL / RUFLO_X_GATEWAY_URL env vars, which precede the defaults.
 const META_LLM = (override) => (override || process.env.SERAPHINA_METALLM_URL || 'https://api.cognitum.one').replace(/\/$/, '');
@@ -14,7 +15,9 @@ async function gatewayRead(uri, gatewayUrl) {
     const text = await res.text();
     const line = text.split('\n').find((l) => l.startsWith('data:'));
     const p = JSON.parse(line ? line.slice(5) : text);
-    return JSON.parse(p.result?.contents?.[0]?.text ?? '{}');
+    // roster and claims are relay-sourced and therefore fenced (#3300). These values
+    // are indexed directly below, so take the payload, not the envelope.
+    return relayPayload(p.result?.contents?.[0]?.text ?? '{}');
 }
 async function gatewaySync(sinceSeconds, limit, gatewayUrl) {
     const res = await fetch(`${GATEWAY(gatewayUrl)}/mcp`, { method: 'POST', headers: { 'content-type': 'application/json', accept: 'application/json, text/event-stream' },
@@ -22,7 +25,9 @@ async function gatewaySync(sinceSeconds, limit, gatewayUrl) {
     const text = await res.text();
     const line = text.split('\n').find((l) => l.startsWith('data:'));
     const p = JSON.parse(line ? line.slice(5) : text);
-    return JSON.parse(p.result?.content?.[0]?.text ?? '{}');
+    // federation_sync is relay-sourced and therefore fenced (#3300); `.messages` is
+    // read directly below, so an envelope here would silently mean "empty swarm".
+    return relayPayload(p.result?.content?.[0]?.text ?? '{}');
 }
 export async function askSeraphina(goal, opts = {}) {
     // Credential: intentionally env-only (never a CLI flag). Registered in audit-env-var-precedence.mjs.

package/dist/src/mcp-tools/x-federation-tools.d.ts

@@ -8,5 +8,17 @@
  * `ruv://federation/registry` resource), not through these gateway-identity tools.
  */
 import type { MCPTool } from './types.js';
+export declare function parseGatewayText(text: string): Record<string, unknown>;
+/**
+ * The payload, for consumers INSIDE this package that immediately index the
+ * value (`recent.messages`, `Object.keys(roster)`).
+ *
+ * At the MCP boundary we return the whole envelope so the caller can see whose
+ * words these are. Internally that shape is a hazard: reading `.messages` off an
+ * envelope yields undefined and `Object.keys()` yields the envelope's own five
+ * keys, so a miscount looks like a real answer. Never do a bare property read on
+ * a parseGatewayText result — come through here.
+ */
+export declare function relayPayload(text: string): Record<string, unknown>;
 export declare const xFederationTools: MCPTool[];
 //# sourceMappingURL=x-federation-tools.d.ts.map

package/dist/src/mcp-tools/x-federation-tools.js

@@ -18,18 +18,100 @@ async function gatewayRpc(method, params, gatewayUrl) {
         throw new Error(`x.ruv.io: ${payload.error.message ?? 'rpc error'}`);
     return payload.result;
 }
+/**
+ * Relay-sourced gateway responses are not bare JSON. Since #3300 the gateway
+ * wraps anything published by other federation members in a provenance envelope
+ * (plugins/ruflo-x-gateway/src/untrusted.mjs): several lines of gateway-authored
+ * prose, then the JSON body between a matched
+ * `<<<UNTRUSTED_RELAY_DATA <uuid>>>>` / `<<<END_UNTRUSTED_RELAY_DATA <uuid>>>>`
+ * pair. `JSON.parse` on the whole string fails on the first prose word, which is
+ * the `Unexpected token 'T', "The block "...` seen from every federation read.
+ *
+ * Three things keep a publisher from closing the block early, and it is worth
+ * being precise about which one is doing the work today:
+ *   1. The body is JSON.stringify'd, so it is a SINGLE line — a publisher's text
+ *      cannot contain a raw newline, and the markers below are newline-anchored.
+ *      This is what actually neutralises forged markers in relay content today.
+ *   2. The token backreference: a forged END carrying any other token does not
+ *      terminate the region. This is the defence that survives (1) — if the body
+ *      is ever pretty-printed, it becomes the only one left. It is tested
+ *      directly rather than incidentally, so it cannot be refactored away quietly.
+ *   3. Exactly one opening marker is permitted. `fenceUntrusted` splices its
+ *      `note` verbatim BEFORE the fence, so a caller that ever interpolates
+ *      relay-derived text into a note could otherwise smuggle in a complete
+ *      earlier envelope; first-match-wins would return it, with untrusted:false.
+ *
+ * We deliberately return the WHOLE envelope (`untrusted`, `provenance`, `relay`,
+ * `retrievedAt`, `data`) rather than lifting `data` out of it. The point of the
+ * envelope is that a caller can tell whose words these are; quietly unwrapping to
+ * the payload would restore valid JSON by discarding the labelling that made it
+ * safe to read. Unfenced responses (the registry resource, gateway-authored
+ * errors) parse unchanged.
+ */
+const UNTRUSTED_FENCE = /<<<UNTRUSTED_RELAY_DATA ([0-9a-fA-F-]{36})>>>\n([\s\S]*?)\n<<<END_UNTRUSTED_RELAY_DATA \1>>>/;
+// Count only NEWLINE-ANCHORED opening markers. A marker inside the body is just
+// characters — the body is one JSON line, so it can never be preceded by a raw
+// newline and can never open a fence. Counting raw occurrences instead would make
+// a publisher able to hard-fail every read simply by typing the marker into a
+// message, which trades a parse bug for a denial of service.
+const OPEN_MARKER_ANCHORED = /(?:^|\n)<<<UNTRUSTED_RELAY_DATA /g;
+export function parseGatewayText(text) {
+    // One response carries exactly one envelope. More than one means something
+    // upstream spliced an envelope-shaped string into the response, and picking
+    // either is a guess — refuse rather than choose.
+    const opens = (text.match(OPEN_MARKER_ANCHORED) ?? []).length;
+    if (opens > 1) {
+        throw new Error('x.ruv.io: response carries more than one untrusted-data envelope (tampered response)');
+    }
+    const fenced = UNTRUSTED_FENCE.exec(text);
+    if (fenced)
+        return JSON.parse(fenced[2]);
+    // An opening marker with no matching close is a truncated or tampered response.
+    // Fail loudly: parsing the remainder would silently drop relay content.
+    if (opens === 1) {
+        throw new Error('x.ruv.io: untrusted-data envelope is unterminated (truncated or tampered response)');
+    }
+    return JSON.parse(text);
+}
+/**
+ * The payload, for consumers INSIDE this package that immediately index the
+ * value (`recent.messages`, `Object.keys(roster)`).
+ *
+ * At the MCP boundary we return the whole envelope so the caller can see whose
+ * words these are. Internally that shape is a hazard: reading `.messages` off an
+ * envelope yields undefined and `Object.keys()` yields the envelope's own five
+ * keys, so a miscount looks like a real answer. Never do a bare property read on
+ * a parseGatewayText result — come through here.
+ */
+export function relayPayload(text) {
+    const parsed = parseGatewayText(text);
+    return (parsed.untrusted === true && parsed.data !== undefined
+        ? parsed.data
+        : parsed);
+}
 async function gatewayTool(name, args) {
     const { gatewayUrl, ...rest } = args;
     const r = (await gatewayRpc('tools/call', { name, arguments: rest }, gatewayUrl));
-    const text = r.content?.[0]?.text ?? '{}';
-    const parsed = JSON.parse(text);
-    if (r.isError || parsed.error)
-        throw new Error(String(parsed.error ?? 'gateway tool error'));
+    const raw = r.content?.[0]?.text ?? '{}';
+    // An isError result is the SDK's createToolError, whose message is raw text and
+    // not JSON. Parsing first turns "private channels cannot be published…" into
+    // "Unexpected token 'p'" — the same class of bug this parser exists to fix.
+    if (r.isError) {
+        let msg = raw;
+        try {
+            msg = String(parseGatewayText(raw).error ?? raw);
+        }
+        catch { /* raw text: use as-is */ }
+        throw new Error(msg || 'gateway tool error');
+    }
+    const parsed = parseGatewayText(raw);
+    if (parsed.error)
+        throw new Error(String(parsed.error));
     return parsed;
 }
 async function gatewayResource(uri, gatewayUrl) {
     const r = (await gatewayRpc('resources/read', { uri }, gatewayUrl));
-    return JSON.parse(r.contents?.[0]?.text ?? '{}');
+    return parseGatewayText(r.contents?.[0]?.text ?? '{}');
 }
 // Credential: intentionally env-only (a secret must never be a CLI flag — it would land in
 // shell history / process lists). Registered in scripts/audit-env-var-precedence.mjs.

package/dist/src/memory/intelligence.d.ts

@@ -178,13 +178,25 @@ declare class LocalReasoningBank {
      */
     store(pattern: Omit<StoredPattern, 'usageCount' | 'createdAt' | 'lastUsedAt'> & Partial<StoredPattern>): void;
     /**
-     * Find similar patterns by embedding
+     * Find similar patterns by embedding.
+     *
+     * `confidence` on each result is the pattern's own learned reliability
+     * (unchanged from storage) — NOT how well it matches this query. The
+     * per-query cosine score is returned separately as `similarity`. Callers
+     * that want "how good a semantic match is this" must read `.similarity`;
+     * callers that want "how reliable has this pattern proven to be" read
+     * `.confidence`. Prior to this fix both were conflated (confidence was
+     * overwritten with the cosine score), which silently broke any consumer
+     * that needed to tell them apart (found during the 2026-09-12 dream-cycle
+     * intelligence-surface review).
      */
     findSimilar(queryEmbedding: number[], options: {
         k?: number;
         threshold?: number;
         type?: string;
-    }): StoredPattern[];
+    }): (StoredPattern & {
+        similarity: number;
+    })[];
     /**
      * Optimized cosine similarity
      */

package/dist/src/memory/intelligence.js

@@ -250,10 +250,20 @@ class LocalSonaCoordinator {
                     const oldConfidence = pattern.confidence;
                     // Check EWC penalty before applying update
                     if (ewcConsolidator) {
-                        const oldWeights = [oldConfidence];
                         const proposedConfidence = Math.min(1.0, oldConfidence + this.config.loraLearningRate * reward);
-                        const newWeights = [proposedConfidence];
-                        const penalty = ewcConsolidator.getPenalty(oldWeights, newWeights);
+                        // Use computeConfidencePenalty (averages the full Fisher diagonal),
+                        // not getPenalty([oldConf],[newConf]) — that call shape collapses
+                        // to fisherDiag[0] only (Math.min(1,1,384) === 1), an arbitrary
+                        // single dimension instead of the full accumulated Fisher signal.
+                        // computeConfidencePenalty exists precisely for this
+                        // scalar-confidence case (see its docstring) but was unwired.
+                        // Note: neither call shape differentiates between patterns — both
+                        // take only a confidence delta, not a per-pattern embedding, so
+                        // two patterns with the same delta under the same consolidator
+                        // state get the same penalty either way. This fix corrects which
+                        // shared Fisher signal informs that penalty; it does not add
+                        // per-pattern discrimination (see ewc-distill-confidence-gate.test.ts).
+                        const penalty = ewcConsolidator.computeConfidencePenalty(oldConfidence, proposedConfidence);
                         totalEwcPenalty += penalty;
                         // If penalty is too high, reduce the update magnitude
                         if (penalty > this.config.ewcLambda) {
@@ -279,13 +289,14 @@ class LocalSonaCoordinator {
                 }
             }
         }
-        // Update EWC Fisher matrix with confidence changes
+        // Update EWC Fisher matrix with confidence changes. updateFisherFromConfidences
+        // takes the full per-pattern embedding + confidence-delta batch directly (it
+        // computes the same squared confidence-delta-scaled-embedding gradient proxy
+        // internally) — replaces the previous per-change recordGradient loop, which
+        // updated the full 384-dim globalFisher but fed a signal that getPenalty's
+        // 1-element call shape then read back only at index 0.
         if (ewcConsolidator && confidenceChanges.length > 0) {
-            for (const change of confidenceChanges) {
-                // Use confidence delta as gradient proxy
-                const gradient = change.embedding.map(e => e * Math.abs(change.newConf - change.oldConf));
-                ewcConsolidator.recordGradient(change.id, gradient, true);
-            }
+            ewcConsolidator.updateFisherFromConfidences(confidenceChanges);
         }
         // Persist updated patterns
         bank.flushToDisk();
@@ -467,7 +478,17 @@ class LocalReasoningBank {
         this.saveToDisk();
     }
     /**
-     * Find similar patterns by embedding
+     * Find similar patterns by embedding.
+     *
+     * `confidence` on each result is the pattern's own learned reliability
+     * (unchanged from storage) — NOT how well it matches this query. The
+     * per-query cosine score is returned separately as `similarity`. Callers
+     * that want "how good a semantic match is this" must read `.similarity`;
+     * callers that want "how reliable has this pattern proven to be" read
+     * `.confidence`. Prior to this fix both were conflated (confidence was
+     * overwritten with the cosine score), which silently broke any consumer
+     * that needed to tell them apart (found during the 2026-09-12 dream-cycle
+     * intelligence-surface review).
      */
     findSimilar(queryEmbedding, options) {
         const { k = 5, threshold = 0.5, type } = options;
@@ -489,7 +510,7 @@ class LocalReasoningBank {
             // Update usage
             s.pattern.usageCount++;
             s.pattern.lastUsedAt = Date.now();
-            return { ...s.pattern, confidence: s.score };
+            return { ...s.pattern, similarity: s.score };
         });
     }
     /**
@@ -985,7 +1006,7 @@ export async function findSimilarPatterns(query, options) {
             usageCount: r.usageCount,
             createdAt: r.createdAt,
             lastUsedAt: r.lastUsedAt,
-            similarity: r.similarity ?? r.confidence ?? 0.5
+            similarity: r.similarity
         }));
     }
     catch {

package/dist/src/memory/memory-bridge.js

@@ -1866,7 +1866,12 @@ export async function bridgeStorePattern(options) {
             }
             catch { /* HNSW is best-effort */ }
         }
-        return { success: true, patternId: result.id, controller: 'bridge-fallback' };
+        // #3324: bridgeStoreEntry's `result.id` is its OWN internally generated
+        // row id (generateId('entry')), a different value from the `key` the row
+        // was actually stored under. getEntry/memory_retrieve look up by `key`,
+        // so returning result.id here handed the caller a handle that can never
+        // be read back — return `patternId` (the real key) instead.
+        return { success: true, patternId, controller: 'bridge-fallback' };
     }
     catch {
         return null;
@@ -1915,10 +1920,13 @@ export async function bridgeSearchPatterns(options) {
                 const qEmb = await generateEmbedding(options.query);
                 if (qEmb && Array.isArray(qEmb.embedding) && qEmb.embedding.length > 0) {
                     const hits = reasoningBank.findSimilar(qEmb.embedding, { k, threshold });
+                    // findSimilar() no longer overwrites confidence with the query-match
+                    // score — prefer similarity (the actual match strength) for search ranking,
+                    // falling back to confidence/score only for older/foreign result shapes.
                     mapped = (Array.isArray(hits) ? hits : []).map((r) => ({
                         id: r.id ?? '',
                         content: r.content ?? '',
-                        score: r.confidence ?? r.score ?? 0,
+                        score: r.similarity ?? r.confidence ?? r.score ?? 0,
                     }));
                 }
             }

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

@@ -1855,12 +1855,15 @@ export async function checkMemoryInitialization(dbPath) {
     if (!fs.existsSync(path_)) {
         return { initialized: false };
     }
+    // #3249: declared outside the try so the handle can be released on the
+    // failure path as well as the success path.
+    let db;
     try {
         // Try to load with sql.js
         const initSqlJs = (await import('sql.js')).default;
         const SQL = await initSqlJs();
         const fileBuffer = fs.readFileSync(path_);
-        const db = new SQL.Database(fileBuffer);
+        db = new SQL.Database(fileBuffer);
         // Check for metadata table
         const tables = db.exec("SELECT name FROM sqlite_master WHERE type='table'");
         const tableNames = tables[0]?.values?.map(v => v[0]) || [];
@@ -1876,7 +1879,6 @@ export async function checkMemoryInitialization(dbPath) {
         catch {
             // Metadata table might not exist
         }
-        db.close();
         return {
             initialized: true,
             version,
@@ -1893,6 +1895,21 @@ export async function checkMemoryInitialization(dbPath) {
         // Could not read database
         return { initialized: false };
     }
+    finally {
+        // #3249: release the handle on every path. An RFE1-encrypted image is not
+        // parseable as SQLite, so the schema query above throws and the catch
+        // returns — which used to skip the inline db.close() entirely, leaving the
+        // sql.js Database and its MEMFS copy open for the life of the process.
+        // Every memory MCP tool call runs this check, so a long session accumulates
+        // one unclosed handle per call. Measured retention is a few hundred KiB per
+        // leaked handle (it does not scale with image size).
+        try {
+            db?.close();
+        }
+        catch {
+            // Already closed, or never successfully constructed.
+        }
+    }
 }
 /**
  * Apply temporal decay to patterns