@claude-flow/cli 3.25.2 → 3.25.4

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

@@ -1,12 +1,12 @@
 {
   "manifest": {
-    "version": "3.23.0",
+    "version": "3.25.4",
     "files": {
       "auto-memory-hook.mjs": "68be7e9a9eba7bf9c4e8a230db7bf61a243b965639f8504842799d6c6ca28762",
       "hook-handler.cjs": "bc4d2d26823d49b3ab1dded2946b66369f1f67bd76b4c30dca9f3b6df3cca8f0",
-      "intelligence.cjs": "760cb82ed2000031abc1ac1fa90a014e7d91d93966e3aa4741b07ab7aff8d066"
+      "intelligence.cjs": "bd1f8e4b034944aee1df0391dc47ac2e8cc4b3aa542c65407a59d49620bbf76b"
     }
   },
-  "signature": "of5l9RP68iPcmcC5dckDv+KIOiENJKifWxYKwQTwAiXiyRNNZuMwQ8y8Bd8+wGviTRxIzBfSuxL1nuJ/rX3xDQ==",
+  "signature": "F3TIRoNcQTCkNeMEk5Isah5CWkV/zddUKR/6pieOlAWoYgI2BEUO7avQj8B8UP4vhvgT9TSgbYsis2UnnnQyBg==",
   "algorithm": "ed25519"
 }

package/README.md

@@ -1,6 +1,8 @@
 <div align="center">
 
 [![Ruflo Banner](ruflo/assets/ruflo-small.jpeg)](https://cognitum.one/agentic-engineering)
+[![Agentics Foundation Banner](docs/assets/sv-summit.png)](https://agentics.org/siliconvalley/?UTM=GH-RuFlo-SV)
+
 
 <!-- Try Ruflo — the 4 badges first-time visitors actually act on -->
 [![Try the UI Beta — flo.ruv.io](https://img.shields.io/badge/_Try_the_UI_Beta-flo.ruv.io-6366f1?style=for-the-badge&logoColor=white&logo=svelte)](https://flo.ruv.io/)

package/dist/src/benchmarks/gaia-agent.js

@@ -537,11 +537,11 @@ export function isAnswerCorrect(modelAnswer, expected) {
     // Exact match
     if (normModel === normExpected)
         return true;
-    // Substring match (expected contained in model answer or vice versa)
+    // Substring match: expected contained in model answer (forward only).
+    // Reverse (normExpected.includes(normModel)) removed — see #2566 / ADR-169 R1:
+    // it scored fragmentary model answers ("a" vs "Paris, France") as correct.
     if (normModel.includes(normExpected))
         return true;
-    if (normExpected.includes(normModel))
-        return true;
     // Numeric match with tolerance
     const numModel = parseFloat(normModel.replace(/[^0-9.\-]/g, ''));
     const numExpected = parseFloat(normExpected.replace(/[^0-9.\-]/g, ''));

package/dist/src/commands/doctor.js

@@ -269,11 +269,24 @@ async function checkLearningBridge() {
             message: `@claude-flow/memory resolvable${version ? ` (v${version})` : ''}`,
         };
     }
+    // #2599: Self-heal on plain `doctor` (not just --fix). The project-side resolver
+    // fails when the sidecar is stale or missing (e.g. npx cache generation rotated),
+    // but the CLI process itself can resolve @claude-flow/memory from its own module
+    // context. Write the sidecar automatically instead of hard-failing the check.
+    const record = recordMemoryPackagePath(cwd, 'doctor-auto');
+    if (record) {
+        const version = readMemoryPackageVersion(record.distPath);
+        return {
+            name: 'Learning Bridge',
+            status: 'pass',
+            message: `@claude-flow/memory resolvable via auto-recorded sidecar${version ? ` (v${version})` : ''}`,
+        };
+    }
     return {
         name: 'Learning Bridge',
         status: 'fail',
         message: '@claude-flow/memory NOT resolvable — SessionStart self-learning imports are a silent no-op',
-        fix: 'npx ruflo@latest doctor --fix   (records resolver sidecar) — or: npm i -D @claude-flow/memory',
+        fix: 'npm i -D @claude-flow/memory   (optional dep appears absent — likely --omit=optional install)',
     };
 }
 // Check API keys

package/dist/src/commands/memory.js

@@ -66,16 +66,19 @@ const storeCommand = {
         {
             name: 'upsert',
             short: 'u',
-            description: 'Update if key exists (insert or replace)',
+            // #2594: default true so `store → delete → store` doesn't hit the UNIQUE
+            // (namespace, key) constraint on the soft-deleted row. Pass --no-upsert
+            // for strict insert semantics.
+            description: 'Update if key exists (default; pass --no-upsert for strict insert)',
             type: 'boolean',
-            default: false
+            default: true
         },
         DB_PATH_OPTION
     ],
     examples: [
         { command: 'claude-flow memory store -k "api/auth" -v "JWT implementation"', description: 'Store text' },
         { command: 'claude-flow memory store -k "pattern/singleton" --vector', description: 'Store vector' },
-        { command: 'claude-flow memory store -k "pattern" -v "updated" --upsert', description: 'Update existing' }
+        { command: 'claude-flow memory store -k "pattern" -v "new" --no-upsert', description: 'Strict insert (fail if key exists)' }
     ],
     action: async (ctx) => {
         const key = ctx.flags.key;

package/dist/src/commands/neural.js

@@ -498,7 +498,9 @@ const statusCommand = {
                     },
                     {
                         component: 'ReasoningBank',
-                        status: stats.reasoningBankSize > 0 ? output.success('Active') : output.dim('Empty'),
+                        status: (stats.patternsLearned > 0 || stats.reasoningBankSize > 0)
+                            ? output.success('Active')
+                            : output.dim('Empty'),
                         details: `${stats.patternsLearned} patterns stored`,
                     },
                     {

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

@@ -2243,11 +2243,11 @@ export async function verifyMemoryInit(dbPath, options) {
                 duration: Date.now() - indexStart
             });
         }
-        // Cleanup test entry
-        db.run(`DELETE FROM memory_entries WHERE id = ?`, [testId]);
-        // Save changes
-        const data = db.export();
-        writeFileRestricted(dbPath, Buffer.from(data), { encrypt: true });
+        // Verification is read-only: sql.js holds an in-memory copy; discarding it on
+        // close() leaves the on-disk DB untouched. Writing back here would race the
+        // still-open better-sqlite3 handle (WAL) owned by ControllerRegistry /
+        // repairVectorIndexes — atomic rename fails with EPERM on Windows (#2596)
+        // and risks clobbering concurrent writes on all platforms.
         db.close();
         const passed = tests.filter(t => t.passed).length;
         const failed = tests.filter(t => !t.passed).length;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@claude-flow/cli",
-  "version": "3.25.2",
+  "version": "3.25.4",
   "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",
@@ -89,7 +89,7 @@
     "test:plugin-store": "npx tsx src/plugins/tests/standalone-test.ts",
     "test:pattern-store": "npx tsx src/transfer/store/tests/standalone-test.ts",
     "postinstall": "node ./scripts/postinstall.cjs",
-    "prepublishOnly": "cp ../../../README.md ./README.md && rm -rf plugins && mkdir -p plugins && cp -r ../../../plugins/ruflo-metaharness plugins/",
+    "prepublishOnly": "cp ../../../README.md ./README.md && rm -rf plugins && mkdir -p plugins && cp -r ../../../plugins/ruflo-metaharness plugins/ && node scripts/sign-helpers.mjs && node scripts/verify-helpers.mjs",
     "release": "npm version prerelease --preid=alpha && npm run publish:all",
     "publish:all": "./scripts/publish.sh"
   },
@@ -108,33 +108,10 @@
     "yaml": "^2.8.0"
   },
   "optionalDependencies": {
-    "@claude-flow/aidefence": "^3.0.2",
-    "@claude-flow/codex": "^3.0.0-alpha.8",
-    "@claude-flow/embeddings": "^3.0.0-alpha.18",
-    "@claude-flow/guidance": "^3.0.0-alpha.1",
     "@claude-flow/memory": "^3.0.0-alpha.21",
-    "@claude-flow/plugin-gastown-bridge": "^0.1.3",
     "@claude-flow/security": "^3.0.0-alpha.10",
-    "@metaharness/darwin": "~0.8.0",
-    "@metaharness/kernel": "~0.1.2",
-    "@metaharness/redblue": "~0.1.4",
-    "@metaharness/router": "~0.3.2",
-    "@metaharness/weight-eft": "~0.1.1",
-    "@ruvector/attention": "^0.1.32",
-    "@ruvector/attention-darwin-arm64": "0.1.32",
-    "@ruvector/diskann": "^0.1.0",
-    "@ruvector/learning-wasm": "^0.1.29",
-    "@ruvector/router": "^0.1.30",
-    "@ruvector/ruvllm-wasm": "^2.0.2",
-    "@ruvector/rvagent-wasm": "^0.1.0",
-    "@ruvector/sona": "^0.1.6",
-    "@ruvector/tiny-dancer": "^0.1.22",
-    "agentbbs": "~0.1.0",
     "agentdb": "^3.0.0-alpha.17",
     "agentic-flow": "^3.0.0-alpha.1",
-    "agenticow": "~0.2.4",
-    "metaharness": "~0.2.8",
-    "page-agent": "~1.11.0",
     "ruvector": "^0.2.27"
   },
   "publishConfig": {