claude-flow 3.5.49 → 3.5.50

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "claude-flow",
-  "version": "3.5.49",
+  "version": "3.5.50",
   "description": "Ruflo - Enterprise AI agent orchestration for Claude Code. Deploy 60+ specialized agents in coordinated swarms with self-learning, fault-tolerant consensus, vector memory, and MCP integration",
   "main": "dist/index.js",
   "type": "module",

package/v3/@claude-flow/cli/dist/src/init/executor.js

@@ -642,12 +642,48 @@ async function createDirectories(targetDir, options, result) {
  */
 async function writeSettings(targetDir, options, result) {
     const settingsPath = path.join(targetDir, '.claude', 'settings.json');
+    const generated = JSON.parse(generateSettingsJson(options));
     if (fs.existsSync(settingsPath) && !options.force) {
-        result.skipped.push('.claude/settings.json');
+        // Merge hooks/env/permissions into existing settings instead of skipping
+        try {
+            const existing = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
+            let merged = false;
+            // Merge hooks (the critical missing piece — #1484)
+            if (generated.hooks && !existing.hooks) {
+                existing.hooks = generated.hooks;
+                merged = true;
+            }
+            // Merge env vars (for CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS etc.)
+            if (generated.env) {
+                existing.env = { ...(existing.env || {}), ...generated.env };
+                merged = true;
+            }
+            // Merge permissions (add ruflo allow rules)
+            if (generated.permissions?.allow) {
+                const existingAllow = existing.permissions?.allow || [];
+                const newRules = generated.permissions.allow.filter((r) => !existingAllow.includes(r));
+                if (newRules.length > 0) {
+                    existing.permissions = existing.permissions || {};
+                    existing.permissions.allow = [...existingAllow, ...newRules];
+                    merged = true;
+                }
+            }
+            if (merged) {
+                fs.writeFileSync(settingsPath, JSON.stringify(existing, null, 2), 'utf-8');
+                result.created.files.push('.claude/settings.json (merged hooks)');
+            }
+            else {
+                result.skipped.push('.claude/settings.json');
+            }
+        }
+        catch {
+            // Existing file is corrupt — overwrite
+            fs.writeFileSync(settingsPath, JSON.stringify(generated, null, 2), 'utf-8');
+            result.created.files.push('.claude/settings.json');
+        }
         return;
     }
-    const content = generateSettingsJson(options);
-    fs.writeFileSync(settingsPath, content, 'utf-8');
+    fs.writeFileSync(settingsPath, JSON.stringify(generated, null, 2), 'utf-8');
     result.created.files.push('.claude/settings.json');
 }
 /**

package/v3/@claude-flow/cli/dist/src/memory/memory-bridge.js

@@ -358,7 +358,8 @@ export async function bridgeSearchEntries(options) {
     if (!ctx)
         return null;
     try {
-        const { query: queryStr, namespace = 'default', limit = 10, threshold = 0.3 } = options;
+        const { query: queryStr, namespace, limit = 10, threshold = 0.3 } = options;
+        const effectiveNamespace = namespace || 'all';
         const startTime = Date.now();
         // Generate query embedding
         let queryEmbedding = null;
@@ -373,7 +374,7 @@ export async function bridgeSearchEntries(options) {
             // Fall back to keyword search
         }
         // better-sqlite3: .prepare().all() returns array of objects
-        const nsFilter = namespace !== 'all'
+        const nsFilter = effectiveNamespace !== 'all'
             ? `AND namespace = ?`
             : '';
         let rows;
@@ -384,7 +385,7 @@ export async function bridgeSearchEntries(options) {
         WHERE status = 'active' ${nsFilter}
         LIMIT 1000
       `);
-            rows = namespace !== 'all' ? stmt.all(namespace) : stmt.all();
+            rows = effectiveNamespace !== 'all' ? stmt.all(effectiveNamespace) : stmt.all();
         }
         catch {
             return null;

package/v3/@claude-flow/cli/dist/src/memory/memory-initializer.js

@@ -356,14 +356,14 @@ export async function getHNSWIndex(options) {
             return null; // VectorDb not found
         }
         const { VectorDb } = ruvectorCore;
-        // Persistent storage paths
-        const swarmDir = path.join(process.cwd(), '.swarm');
+        // Persistent storage paths — resolve to absolute to survive CWD changes
+        const swarmDir = path.resolve(process.cwd(), '.swarm');
         if (!fs.existsSync(swarmDir)) {
             fs.mkdirSync(swarmDir, { recursive: true });
         }
         const hnswPath = path.join(swarmDir, 'hnsw.index');
         const metadataPath = path.join(swarmDir, 'hnsw.metadata.json');
-        const dbPath = options?.dbPath || path.join(swarmDir, 'memory.db');
+        const dbPath = options?.dbPath ? path.resolve(options.dbPath) : path.join(swarmDir, 'memory.db');
         // Create HNSW index with persistent storage
         // @ruvector/core uses string enum for distanceMetric: 'Cosine', 'Euclidean', 'DotProduct', 'Manhattan'
         const db = new VectorDb({
@@ -1694,8 +1694,8 @@ export async function storeEntry(options) {
     }
     // Fallback: raw sql.js
     const { key, value, namespace = 'default', generateEmbeddingFlag = true, tags = [], ttl, dbPath: customPath, upsert = false } = options;
-    const swarmDir = path.join(process.cwd(), '.swarm');
-    const dbPath = customPath || path.join(swarmDir, 'memory.db');
+    const swarmDir = path.resolve(process.cwd(), '.swarm');
+    const dbPath = customPath ? path.resolve(customPath) : path.join(swarmDir, 'memory.db');
     try {
         if (!fs.existsSync(dbPath)) {
             return { success: false, id: '', error: 'Database not initialized. Run: claude-flow memory init' };
@@ -1785,9 +1785,10 @@ export async function searchEntries(options) {
             return bridgeResult;
     }
     // Fallback: raw sql.js
-    const { query, namespace = 'default', limit = 10, threshold = 0.3, dbPath: customPath } = options;
-    const swarmDir = path.join(process.cwd(), '.swarm');
-    const dbPath = customPath || path.join(swarmDir, 'memory.db');
+    const { query, namespace, limit = 10, threshold = 0.3, dbPath: customPath } = options;
+    const effectiveNamespace = namespace || 'all';
+    const swarmDir = path.resolve(process.cwd(), '.swarm');
+    const dbPath = customPath ? path.resolve(customPath) : path.join(swarmDir, 'memory.db');
     const startTime = Date.now();
     try {
         if (!fs.existsSync(dbPath)) {
@@ -1799,7 +1800,7 @@ export async function searchEntries(options) {
         const queryEmb = await generateEmbedding(query);
         const queryEmbedding = queryEmb.embedding;
         // Try HNSW search first (150x faster)
-        const hnswResults = await searchHNSWIndex(queryEmbedding, { k: limit, namespace });
+        const hnswResults = await searchHNSWIndex(queryEmbedding, { k: limit, namespace: effectiveNamespace });
         if (hnswResults && hnswResults.length > 0) {
             // Filter by threshold
             const filtered = hnswResults.filter(r => r.score >= threshold);
@@ -1815,11 +1816,11 @@ export async function searchEntries(options) {
         const fileBuffer = fs.readFileSync(dbPath);
         const db = new SQL.Database(fileBuffer);
         // Get entries with embeddings
-        const searchStmt = db.prepare(namespace !== 'all'
+        const searchStmt = db.prepare(effectiveNamespace !== 'all'
             ? `SELECT id, key, namespace, content, embedding FROM memory_entries WHERE status = 'active' AND namespace = ? LIMIT 1000`
             : `SELECT id, key, namespace, content, embedding FROM memory_entries WHERE status = 'active' LIMIT 1000`);
-        if (namespace !== 'all') {
-            searchStmt.bind([namespace]);
+        if (effectiveNamespace !== 'all') {
+            searchStmt.bind([effectiveNamespace]);
         }
         const searchRows = [];
         while (searchStmt.step()) {

package/v3/@claude-flow/cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@claude-flow/cli",
-  "version": "3.5.49",
+  "version": "3.5.50",
   "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",