@claude-flow/cli 3.41.1 → 3.41.3

package/.claude/helpers/helpers.manifest.json

@@ -1,6 +1,6 @@
 {
   "manifest": {
-    "version": "3.41.1",
+    "version": "3.41.3",
     "files": {
       "auto-memory-hook.mjs": "85fe05c757421c52137c0bc8545a0896bab6b4714538c2a11d1d0835bfcc8c1c",
       "hook-handler.cjs": "209d9fafe10e17d1be0866727f6f9cf9ac66f9a0793f1c793a4f58319e8e4583",
@@ -8,6 +8,6 @@
       "statusline.cjs": "4a48353b4f1566fa4379b00fd0321b6676a22b6cc91fbbd8380ac5183d619468"
     }
   },
-  "signature": "6JrRzvJx81mt9GZLoEwVmk8GNxDCaHMrR/8YywbD947dVkjWUFnTBCemqG1LKoRbfubrOlLr5i71BX3v8W98CQ==",
+  "signature": "YKF5dYIr74cL7hG0bQ8z6ygCZF4Atdhj79kRLOoCKLSO+o0pbUvs+4u9qQHN9Jig99FufZYKwvciYrE/85XaBA==",
   "algorithm": "ed25519"
 }

package/catalog-manifest.json

@@ -1,8 +1,8 @@
 {
   "schemaVersion": 1,
   "generation": 6,
-  "generatedAt": "2026-09-10T14:41:32.208Z",
-  "gitSha": "cda8b04f",
+  "generatedAt": "2026-09-14T17:14:45.365Z",
+  "gitSha": "8008bc35",
   "catalog": {
     "agents": 167,
     "tools": 418,

package/dist/src/commands/memory.js

@@ -9,6 +9,23 @@ import { distillCommand } from './memory-distill.js';
 import { backupCommand } from './memory-backup.js';
 import { countSiblingStoreRows } from '../memory/sibling-store.js';
 import { resolveDbPath } from '../memory/memory-initializer.js';
+/**
+ * #3228: a miss in one store is not a miss in the memory.
+ *
+ * 3.41.1 disclosed the sibling AgentDB store from `memory list` only. `retrieve`,
+ * `search` and `stats` kept reporting a clean negative — "Key not found", "No
+ * results" — while the rows sat in the file this interface does not read. On the
+ * reported Windows install that is 31,673 rows in the other store answering
+ * `found:false`. A confident negative is worse than an error, because nothing
+ * prompts anyone to look further.
+ */
+async function warnIfSiblingHasRows(pathFlag) {
+    const unread = await countSiblingStoreRows(resolveDbPath(pathFlag));
+    if (unread && unread.rows > 0) {
+        output.printWarning(`This read covered one store. ${unread.rows} entries are in ${unread.path} and were not searched. ` +
+            `That store is written by the MCP/AgentDB path; read it with --path ${unread.path}.`);
+    }
+}
 // Memory backends
 const BACKENDS = [
     { value: 'agentdb', label: 'AgentDB', hint: 'Vector database with HNSW indexing (150x-12,500x faster)' },
@@ -287,6 +304,7 @@ const retrieveCommand = {
             }
             if (!result.found || !result.entry) {
                 output.printWarning(`Key not found: ${key}`);
+                await warnIfSiblingHasRows(ctx.flags.path);
                 return { success: false, exitCode: 1, data: { key, found: false } };
             }
             const entry = result.entry;
@@ -667,6 +685,7 @@ const searchCommand = {
             output.writeln();
             if (results.length === 0) {
                 output.printWarning('No results found');
+                await warnIfSiblingHasRows(ctx.flags.path);
                 output.writeln(output.dim('Try: claude-flow memory store -k "key" --value "data"'));
                 return { success: true, data: [] };
             }
@@ -746,6 +765,7 @@ const listCommand = {
             output.writeln();
             if (entries.length === 0) {
                 output.printWarning('No entries found');
+                await warnIfSiblingHasRows(ctx.flags.path);
                 output.printInfo('Store data: claude-flow memory store -k "key" --value "data"');
                 return { success: true, data: [] };
             }

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

@@ -88,13 +88,18 @@ function publishEvent(ws, nt, sk, tags, content) {
         ws.send(JSON.stringify(['EVENT', ev]));
     });
 }
-function reqEvents(ws, filter) {
+function reqEvents(ws, nt, filter) {
     const out = [];
     return new Promise((resolve) => {
         const t = setTimeout(() => resolve(out), 12000);
         ws.on('message', (d) => {
             const m = JSON.parse(d.toString());
-            if (m[0] === 'EVENT')
+            // Only a signature-verified event can be trusted as evidence of who sent
+            // it. Without this check an unverified EVENT frame — relay bug, MITM, or
+            // a compromised relay — would reach callers that treat .pubkey/.id as
+            // authenticated (channel_accept's NIP-44 conversation-key derivation,
+            // channel_read's returned identity).
+            if (m[0] === 'EVENT' && nt.verifyEvent(m[2]))
                 out.push(m[2]);
             else if (m[0] === 'EOSE') {
                 clearTimeout(t);
@@ -168,7 +173,7 @@ export const xFederationChannelTools = [
                 return degraded();
             const { sk, pubkey } = loadOrCreateKey(t.nt, KEY_FILE());
             const relay = RELAY_WS(i.relayWs);
-            const evs = await relayCall(relay, sk, t.nt, (ws) => reqEvents(ws, {
+            const evs = await relayCall(relay, sk, t.nt, (ws) => reqEvents(ws, t.nt, {
                 kinds: [1], '#t': ['ruflo-swarm'], '#k': ['ChannelGrant'], '#p': [pubkey],
                 since: Math.floor(Date.now() / 1000) - (i.sinceSeconds ?? 7 * 86400), limit: 200,
             }));
@@ -256,7 +261,7 @@ export const xFederationChannelTools = [
             if (!t)
                 return degraded();
             const { sk } = loadOrCreateKey(t.nt, KEY_FILE());
-            const evs = await relayCall(RELAY_WS(i.relayWs), sk, t.nt, (ws) => reqEvents(ws, {
+            const evs = await relayCall(RELAY_WS(i.relayWs), sk, t.nt, (ws) => reqEvents(ws, t.nt, {
                 kinds: [1], '#t': ['ruflo-swarm'], '#c': [i.channel],
                 since: Math.floor(Date.now() / 1000) - (i.sinceSeconds ?? 3600), limit: i.limit ?? 100,
             }));
@@ -266,9 +271,12 @@ export const xFederationChannelTools = [
                 const ev = e;
                 const k = ev.tags.find((x) => x[0] === 'k')?.[1];
                 const base = { id: ev.id, pubkey: ev.pubkey, created_at: ev.created_at };
+                // base's verified id/pubkey/created_at must win over the parsed/decrypted
+                // body — spread body first so a stray id/pubkey/created_at key in the
+                // publisher's own content can't override the authenticated identity.
                 if (k !== 'enc') {
                     try {
-                        return { ...base, ...JSON.parse(ev.content) };
+                        return { ...JSON.parse(ev.content), ...base };
                     }
                     catch {
                         return { ...base, raw: ev.content };
@@ -277,7 +285,7 @@ export const xFederationChannelTools = [
                 if (!key)
                     return { ...base, encrypted: true, reason: 'no channel key held' };
                 try {
-                    return { ...base, ...JSON.parse(t.nip44.v2.decrypt(ev.content, key)) };
+                    return { ...JSON.parse(t.nip44.v2.decrypt(ev.content, key)), ...base };
                 }
                 catch {
                     return { ...base, encrypted: true, reason: 'held key does not open this message' };

package/dist/src/services/daemon-autostart.js

@@ -54,14 +54,32 @@ export function isDaemonAlive(projectRoot) {
 }
 /** Project-local opt-out: `{ "daemon": { "autostart": false } }` in claude-flow.config.json. */
 function autostartDisabledByProjectConfig(projectRoot) {
-    try {
-        const raw = fs.readFileSync(path.join(projectRoot, 'claude-flow.config.json'), 'utf-8');
-        const cfg = JSON.parse(raw);
-        return cfg?.daemon?.autostart === false;
-    }
-    catch {
-        return false; // absent/malformed config = not disabled
+    // #3278: read BOTH files, and both spellings.
+    //
+    // This used to consult only `claude-flow.config.json` with the key
+    // `daemon.autostart`. But `init` generates `.claude/settings.json` with
+    // `claudeFlow.daemon.autoStart` — a different file and a different capital S —
+    // and writes it `false` under the comment "Opt-in only — prevents unintended
+    // token consumption (#1427, #1330)". So the one setting a fresh project
+    // actually ships was never read, and the runtime spent tokens the generated
+    // config existed to prevent. Accept either spelling in either file: a user who
+    // wrote the word "autostart: false" anywhere sensible meant it.
+    const readsFalse = (v) => v === false;
+    for (const [file, pick] of [
+        ['claude-flow.config.json', (c) => c?.daemon],
+        [path.join('.claude', 'settings.json'), (c) => c?.claudeFlow?.daemon],
+    ]) {
+        try {
+            const cfg = JSON.parse(fs.readFileSync(path.join(projectRoot, file), 'utf-8'));
+            const d = pick(cfg);
+            if (readsFalse(d?.autostart) || readsFalse(d?.autoStart))
+                return true;
+        }
+        catch {
+            // absent/malformed config = this file says nothing; keep checking the others
+        }
     }
+    return false;
 }
 function autostartDisabled(projectRoot) {
     if (/^(0|false|no|off)$/i.test(process.env.RUFLO_DAEMON_AUTOSTART ?? ''))

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@claude-flow/cli",
-  "version": "3.41.1",
+  "version": "3.41.3",
   "type": "module",
   "description": "Ruflo CLI - Enterprise AI agent orchestration with 60+ specialized agents, swarm coordination, MCP server, self-learning hooks, and vector memory for Claude Code",
   "main": "dist/src/index.js",