From e1cac5dd5010e41a6a400ffaec0c091052ffcf19 Mon Sep 17 00:00:00 2001
From: catlog22 <catlog22@github.com>
Date: Sat, 20 Dec 2025 11:08:34 +0800
Subject: [PATCH] Refactor search modes and optimize embedding generation

- Updated the dashboard template to hide the Code Graph Explorer feature.
- Enhanced the `executeCodexLens` function to use `exec` for better cross-platform compatibility and improved command execution.
- Changed the default `maxResults` and `limit` parameters in the smart search tool to 10 for better performance.
- Introduced a new `priority` search mode in the smart search tool, replacing the previous `parallel` mode, which now follows a fallback strategy: hybrid -> exact -> ripgrep.
- Optimized the embedding generation process in the embedding manager by batching operations and using a cached embedder instance to reduce model loading overhead.
- Implemented a thread-safe singleton pattern for the embedder to improve performance across multiple searches.
---
 .claude/workflows/context-tools.md            |   2 +-
 ccw/src/core/dashboard-generator.ts           |   4 +
 .../dashboard-css/30-core-memory.css          | 176 ++++++++++-
 .../dashboard-js/components/mcp-manager.js    |  16 +-
 ccw/src/templates/dashboard-js/i18n.js        |  46 ++-
 ccw/src/templates/dashboard-js/state.js       |   5 +
 ccw/src/templates/dashboard-js/utils.js       |  31 ++
 .../dashboard-js/views/cli-manager.js         |   3 +-
 .../dashboard-js/views/core-memory.js         | 208 ++++++++++++-
 .../dashboard-js/views/mcp-manager.js         | 122 +++++---
 ccw/src/templates/dashboard.html              |   2 +
 ccw/src/tools/codex-lens.ts                   |  86 +++---
 ccw/src/tools/smart-search.ts                 | 278 +++++++++---------
 .../src/codexlens/cli/embedding_manager.py    | 104 +++++--
 .../src/codexlens/search/hybrid_search.py     |   5 +-
 codex-lens/src/codexlens/semantic/embedder.py |  48 ++-
 16 files changed, 852 insertions(+), 284 deletions(-)

diff --git a/.claude/workflows/context-tools.md b/.claude/workflows/context-tools.md
index 54a36296..e2874696 100644
--- a/.claude/workflows/context-tools.md
+++ b/.claude/workflows/context-tools.md
@@ -10,7 +10,7 @@
 smart_search(query="authentication logic")
 
 // Step 2: Only if search warns "No CodexLens index found", then init
-smart_search(action="init", path=".")                  // Creates FTS index only
+smart_search(action="init", path=".")   // Creates FTS index only
 
 // Note: For semantic/vector search, use "ccw view" dashboard to create vector index
 ```
diff --git a/ccw/src/core/dashboard-generator.ts b/ccw/src/core/dashboard-generator.ts
index 68d33677..cbe798c3 100644
--- a/ccw/src/core/dashboard-generator.ts
+++ b/ccw/src/core/dashboard-generator.ts
@@ -173,6 +173,10 @@ function generateFromUnifiedTemplate(data: unknown): string {
   jsContent = jsContent.replace(/\{\{PROJECT_PATH\}\}/g, projectPath.replace(/\\/g, '/'));
   jsContent = jsContent.replace('{{RECENT_PATHS}}', JSON.stringify(recentPaths));
 
+  // Inject platform information for cross-platform MCP command generation
+  // 'win32' for Windows, 'darwin' for macOS, 'linux' for Linux
+  jsContent = jsContent.replace(/\{\{SERVER_PLATFORM\}\}/g, process.platform);
+
   // Inject JS and CSS into HTML template
   html = html.replace('{{JS_CONTENT}}', jsContent);
   html = html.replace('{{CSS_CONTENT}}', cssContent);
diff --git a/ccw/src/templates/dashboard-css/30-core-memory.css b/ccw/src/templates/dashboard-css/30-core-memory.css
index a3e736b2..a20556a5 100644
--- a/ccw/src/templates/dashboard-css/30-core-memory.css
+++ b/ccw/src/templates/dashboard-css/30-core-memory.css
@@ -224,6 +224,13 @@
   border-radius: 8px;
   padding: 1.25rem;
   transition: all 0.2s ease;
+  cursor: pointer;
+  /* Fixed card dimensions */
+  display: flex;
+  flex-direction: column;
+  height: 280px;
+  min-height: 280px;
+  max-height: 280px;
 }
 
 .memory-card:hover {
@@ -239,8 +246,9 @@
 .memory-card-header {
   display: flex;
   justify-content: space-between;
-  align-items: flex-start;
-  margin-bottom: 1rem;
+  align-items: center;
+  margin-bottom: 0.75rem;
+  flex-shrink: 0;
 }
 
 .memory-id {
@@ -248,7 +256,8 @@
   align-items: center;
   gap: 0.5rem;
   font-size: 0.875rem;
-  color: hsl(var(--muted-foreground));
+  color: hsl(var(--foreground));
+  font-weight: 600;
   flex-wrap: wrap;
 }
 
@@ -257,6 +266,10 @@
   height: 16px;
 }
 
+.memory-id i[data-lucide="star"] {
+  color: hsl(38 92% 50%);
+}
+
 .memory-actions {
   display: flex;
   gap: 0.5rem;
@@ -282,34 +295,83 @@
   color: hsl(var(--destructive));
 }
 
+.icon-btn.favorite-active {
+  color: hsl(38 92% 50%);
+}
+
+.icon-btn.favorite-active:hover {
+  color: hsl(38 92% 40%);
+}
+
 .icon-btn i {
   width: 18px;
   height: 18px;
 }
 
+/* Copy ID Button */
+.copy-id-btn {
+  background: none;
+  border: none;
+  padding: 0.125rem 0.25rem;
+  cursor: pointer;
+  color: hsl(var(--muted-foreground));
+  transition: color 0.2s;
+  display: inline-flex;
+  align-items: center;
+  justify-content: center;
+  margin-left: 0.25rem;
+  border-radius: 4px;
+}
+
+.copy-id-btn:hover {
+  color: hsl(var(--primary));
+  background: hsl(var(--muted));
+}
+
+.copy-id-btn i {
+  width: 14px;
+  height: 14px;
+}
+
+.copy-id-btn.copied {
+  color: hsl(var(--success, 142 76% 36%));
+}
+
 /* Memory Content */
 .memory-content {
-  margin-bottom: 1rem;
-}
-
-.memory-summary {
-  font-size: 0.9375rem;
-  line-height: 1.6;
-  color: hsl(var(--foreground));
+  flex: 1;
+  min-height: 0;
+  overflow: hidden;
+  margin-bottom: 0.75rem;
 }
 
+.memory-summary,
 .memory-preview {
   font-size: 0.875rem;
   line-height: 1.5;
   color: hsl(var(--muted-foreground));
+  /* Fixed height with ellipsis */
+  display: -webkit-box;
+  -webkit-line-clamp: 4;
+  -webkit-box-orient: vertical;
+  overflow: hidden;
+  text-overflow: ellipsis;
+  max-height: 6em;
+}
+
+.memory-summary {
+  color: hsl(var(--foreground));
 }
 
 /* Memory Tags */
 .memory-tags {
   display: flex;
   flex-wrap: wrap;
-  gap: 0.5rem;
-  margin-bottom: 1rem;
+  gap: 0.375rem;
+  margin-bottom: 0.5rem;
+  flex-shrink: 0;
+  max-height: 2rem;
+  overflow: hidden;
 }
 
 .tag {
@@ -321,13 +383,14 @@
   font-weight: 500;
 }
 
-/* Memory Footer */
+/* Memory Footer - Fixed at bottom */
 .memory-footer {
   display: flex;
   flex-direction: column;
-  gap: 0.75rem;
-  padding-top: 1rem;
+  gap: 0.5rem;
+  padding-top: 0.75rem;
   border-top: 1px solid hsl(var(--border));
+  margin-top: auto;
 }
 
 .memory-meta {
@@ -850,6 +913,89 @@
   margin: 0;
 }
 
+/* Relations Detail Styles */
+.relations-detail h4 {
+  font-size: 1rem;
+  font-weight: 600;
+  margin-bottom: 1rem;
+  color: hsl(var(--foreground));
+}
+
+.clusters-list {
+  display: flex;
+  flex-direction: column;
+  gap: 1rem;
+}
+
+.relation-cluster-item {
+  padding: 1rem;
+  background: hsl(var(--muted) / 0.3);
+  border: 1px solid hsl(var(--border));
+  border-radius: 8px;
+}
+
+.relation-cluster-header {
+  display: flex;
+  align-items: center;
+  gap: 0.5rem;
+  margin-bottom: 0.75rem;
+}
+
+.relation-cluster-header i {
+  width: 18px;
+  height: 18px;
+  color: hsl(var(--primary));
+}
+
+.relation-cluster-header .cluster-name {
+  font-weight: 600;
+  color: hsl(var(--foreground));
+}
+
+.cluster-relations-list {
+  display: flex;
+  flex-wrap: wrap;
+  align-items: center;
+  gap: 0.5rem;
+  padding-top: 0.75rem;
+  border-top: 1px solid hsl(var(--border));
+}
+
+.relations-label {
+  font-size: 0.8125rem;
+  color: hsl(var(--muted-foreground));
+}
+
+.relation-tag {
+  display: inline-flex;
+  align-items: center;
+  gap: 0.375rem;
+  padding: 0.25rem 0.625rem;
+  background: hsl(var(--accent));
+  border-radius: 4px;
+  font-size: 0.8125rem;
+}
+
+.relation-tag i {
+  width: 12px;
+  height: 12px;
+  color: hsl(var(--muted-foreground));
+}
+
+.relation-tag .relation-type {
+  font-size: 0.6875rem;
+  padding: 0.125rem 0.375rem;
+  background: hsl(var(--primary) / 0.15);
+  color: hsl(var(--primary));
+  border-radius: 3px;
+  margin-left: 0.25rem;
+}
+
+.text-muted {
+  color: hsl(var(--muted-foreground));
+  font-size: 0.875rem;
+}
+
 /* Dark Mode Adjustments */
 [data-theme="dark"] .memory-card {
   background: #1e293b;
diff --git a/ccw/src/templates/dashboard-js/components/mcp-manager.js b/ccw/src/templates/dashboard-js/components/mcp-manager.js
index 89ef2531..e8486a19 100644
--- a/ccw/src/templates/dashboard-js/components/mcp-manager.js
+++ b/ccw/src/templates/dashboard-js/components/mcp-manager.js
@@ -928,11 +928,19 @@ function selectCcwTools(type) {
 }
 
 // Build CCW Tools config with selected tools
+// Uses isWindowsPlatform from state.js to generate platform-appropriate commands
 function buildCcwToolsConfig(selectedTools) {
-  const config = {
-    command: "cmd",
-    args: ["/c", "npx", "-y", "ccw-mcp"]
-  };
+  // Windows requires 'cmd /c' wrapper to execute npx
+  // Other platforms (macOS, Linux) can run npx directly
+  const config = isWindowsPlatform
+    ? {
+        command: "cmd",
+        args: ["/c", "npx", "-y", "ccw-mcp"]
+      }
+    : {
+        command: "npx",
+        args: ["-y", "ccw-mcp"]
+      };
 
   // Add env if not all tools or not default 4 core tools
   const coreTools = ['write_file', 'edit_file', 'codex_lens', 'smart_search'];
diff --git a/ccw/src/templates/dashboard-js/i18n.js b/ccw/src/templates/dashboard-js/i18n.js
index e596f258..133b14ae 100644
--- a/ccw/src/templates/dashboard-js/i18n.js
+++ b/ccw/src/templates/dashboard-js/i18n.js
@@ -1291,8 +1291,27 @@ const i18n = {
     'coreMemory.clusterUpdateError': 'Failed to update cluster',
     'coreMemory.memberRemoved': 'Member removed',
     'coreMemory.memberRemoveError': 'Failed to remove member',
+    'coreMemory.favorites': 'Favorites',
+    'coreMemory.totalFavorites': 'Total Favorites',
+    'coreMemory.noFavorites': 'No favorites yet',
+    'coreMemory.toggleFavorite': 'Toggle Favorite',
+    'coreMemory.addedToFavorites': 'Added to favorites',
+    'coreMemory.removedFromFavorites': 'Removed from favorites',
+    'coreMemory.favoriteError': 'Failed to update favorite',
+    'coreMemory.relations': 'Relations',
+    'coreMemory.showRelations': 'Show Relations',
+    'coreMemory.relationsFor': 'Relations',
+    'coreMemory.noRelations': 'No cluster relations found',
+    'coreMemory.noRelationsHint': 'Use Auto Cluster in the Clusters tab to create relations',
+    'coreMemory.belongsToClusters': 'Belongs to Clusters',
+    'coreMemory.relationsError': 'Failed to load relations',
+
+    // Common additions
+    'common.copyId': 'Copy ID',
+    'common.copied': 'Copied!',
+    'common.copyError': 'Failed to copy',
   },
-  
+
   zh: {
     // App title and brand
     'app.title': 'CCW 控制面板',
@@ -1589,13 +1608,13 @@ const i18n = {
     'index.projects': '项目数',
     'index.totalSize': '总大小',
     'index.vectorIndexes': '向量',
-    'index.ftsIndexes': '全文',
+    'index.ftsIndexes': 'FTS',
     'index.projectId': '项目 ID',
     'index.size': '大小',
     'index.type': '类型',
     'index.lastModified': '修改时间',
     'index.vector': '向量',
-    'index.fts': '全文',
+    'index.fts': 'FTS',
     'index.noIndexes': '暂无索引',
     'index.notConfigured': '未配置',
     'index.initCurrent': '索引当前项目',
@@ -1608,7 +1627,7 @@ const i18n = {
     'index.cleanAllConfirm': '确定要清理所有索引吗？此操作无法撤销。',
     'index.cleanAllSuccess': '所有索引已清理',
     'index.vectorIndex': '向量索引',
-    'index.normalIndex': '全文索引',
+    'index.normalIndex': 'FTS索引',
     'index.vectorDesc': '语义搜索（含嵌入向量）',
     'index.normalDesc': '快速全文搜索',
 
@@ -2585,6 +2604,25 @@ const i18n = {
     'coreMemory.clusterUpdateError': '更新聚类失败',
     'coreMemory.memberRemoved': '成员已移除',
     'coreMemory.memberRemoveError': '移除成员失败',
+    'coreMemory.favorites': '收藏',
+    'coreMemory.totalFavorites': '收藏总数',
+    'coreMemory.noFavorites': '暂无收藏',
+    'coreMemory.toggleFavorite': '切换收藏',
+    'coreMemory.addedToFavorites': '已添加到收藏',
+    'coreMemory.removedFromFavorites': '已从收藏移除',
+    'coreMemory.favoriteError': '更新收藏失败',
+    'coreMemory.relations': '关联',
+    'coreMemory.showRelations': '显示关联',
+    'coreMemory.relationsFor': '关联关系',
+    'coreMemory.noRelations': '未找到聚类关联',
+    'coreMemory.noRelationsHint': '在聚类 Tab 中使用自动聚类来创建关联',
+    'coreMemory.belongsToClusters': '所属聚类',
+    'coreMemory.relationsError': '加载关联失败',
+
+    // Common additions
+    'common.copyId': '复制 ID',
+    'common.copied': '已复制！',
+    'common.copyError': '复制失败',
   }
 };
 
diff --git a/ccw/src/templates/dashboard-js/state.js b/ccw/src/templates/dashboard-js/state.js
index 68753190..1c6e1316 100644
--- a/ccw/src/templates/dashboard-js/state.js
+++ b/ccw/src/templates/dashboard-js/state.js
@@ -10,6 +10,11 @@ let workflowData = {{WORKFLOW_DATA}};
 let projectPath = '{{PROJECT_PATH}}';
 let recentPaths = {{RECENT_PATHS}};
 
+// Platform detection for cross-platform MCP command generation
+// 'win32' for Windows, 'darwin' for macOS, 'linux' for Linux
+const serverPlatform = '{{SERVER_PLATFORM}}';
+const isWindowsPlatform = serverPlatform === 'win32';
+
 // ========== Application State ==========
 // Current filter for session list view ('all', 'active', 'archived')
 let currentFilter = 'all';
diff --git a/ccw/src/templates/dashboard-js/utils.js b/ccw/src/templates/dashboard-js/utils.js
index 743dcd1e..e1995c1a 100644
--- a/ccw/src/templates/dashboard-js/utils.js
+++ b/ccw/src/templates/dashboard-js/utils.js
@@ -5,6 +5,37 @@
 
 // ========== HTML/Text Processing ==========
 
+/**
+ * Encode JSON config data to Base64 for safe HTML attribute storage
+ * @param {Object} config - Configuration object to encode
+ * @returns {string} Base64 encoded JSON string
+ */
+function encodeConfigData(config) {
+  try {
+    const jsonStr = JSON.stringify(config);
+    return btoa(encodeURIComponent(jsonStr));
+  } catch (err) {
+    console.error('[Utils] Error encoding config data:', err);
+    return '';
+  }
+}
+
+/**
+ * Decode Base64 config data back to JSON object
+ * @param {string} encoded - Base64 encoded string
+ * @returns {Object|null} Decoded configuration object or null on error
+ */
+function decodeConfigData(encoded) {
+  try {
+    if (!encoded) return null;
+    const jsonStr = decodeURIComponent(atob(encoded));
+    return JSON.parse(jsonStr);
+  } catch (err) {
+    console.error('[Utils] Error decoding config data:', err);
+    return null;
+  }
+}
+
 /**
  * Escape HTML special characters to prevent XSS attacks
  * @param {string} str - String to escape
diff --git a/ccw/src/templates/dashboard-js/views/cli-manager.js b/ccw/src/templates/dashboard-js/views/cli-manager.js
index c285e2ab..859c684d 100644
--- a/ccw/src/templates/dashboard-js/views/cli-manager.js
+++ b/ccw/src/templates/dashboard-js/views/cli-manager.js
@@ -392,7 +392,8 @@ function renderToolsSection() {
     '<div class="tool-item-right">' +
       (codexLensStatus.ready
         ? '<span class="tool-status-text success"><i data-lucide="check-circle" class="w-3.5 h-3.5"></i> v' + (codexLensStatus.version || 'installed') + '</span>' +
-          '<button class="btn-sm btn-outline" onclick="event.stopPropagation(); initCodexLensIndex()"><i data-lucide="database" class="w-3 h-3"></i> ' + t('cli.initIndex') + '</button>' +
+          '<button class="btn-sm btn-outline" onclick="event.stopPropagation(); initCodexLensIndex(\'vector\')" title="' + (t('index.vectorDesc') || 'Semantic search with embeddings') + '"><i data-lucide="sparkles" class="w-3 h-3"></i> ' + (t('index.vectorIndex') || 'Vector') + '</button>' +
+          '<button class="btn-sm btn-outline" onclick="event.stopPropagation(); initCodexLensIndex(\'normal\')" title="' + (t('index.normalDesc') || 'Fast full-text search only') + '"><i data-lucide="file-text" class="w-3 h-3"></i> ' + (t('index.normalIndex') || 'FTS') + '</button>' +
           '<button class="btn-sm btn-outline btn-danger" onclick="event.stopPropagation(); uninstallCodexLens()"><i data-lucide="trash-2" class="w-3 h-3"></i> ' + t('cli.uninstall') + '</button>'
         : '<span class="tool-status-text muted"><i data-lucide="circle-dashed" class="w-3.5 h-3.5"></i> ' + t('cli.notInstalled') + '</span>' +
           '<button class="btn-sm btn-primary" onclick="event.stopPropagation(); installCodexLens()"><i data-lucide="download" class="w-3 h-3"></i> ' + t('cli.install') + '</button>') +
diff --git a/ccw/src/templates/dashboard-js/views/core-memory.js b/ccw/src/templates/dashboard-js/views/core-memory.js
index 5caad34f..99fced53 100644
--- a/ccw/src/templates/dashboard-js/views/core-memory.js
+++ b/ccw/src/templates/dashboard-js/views/core-memory.js
@@ -66,6 +66,10 @@ async function renderCoreMemoryView() {
             <i data-lucide="brain"></i>
             ${t('coreMemory.memories')}
           </button>
+          <button class="tab-btn" id="favoritesViewBtn" onclick="showFavoritesView()">
+            <i data-lucide="star"></i>
+            ${t('coreMemory.favorites') || 'Favorites'}
+          </button>
           <button class="tab-btn" id="clustersViewBtn" onclick="showClustersView()">
             <i data-lucide="folder-tree"></i>
             ${t('coreMemory.clusters')}
@@ -106,6 +110,22 @@ async function renderCoreMemoryView() {
         </div>
       </div>
 
+      <!-- Favorites Tab Content (hidden by default) -->
+      <div class="cm-tab-panel" id="favoritesGrid" style="display: none;">
+        <div class="memory-stats">
+          <div class="stat-item">
+            <span class="stat-label">${t('coreMemory.totalFavorites') || 'Total Favorites'}</span>
+            <span class="stat-value" id="totalFavoritesCount">0</span>
+          </div>
+        </div>
+        <div class="memories-grid" id="favoritesGridContent">
+          <div class="empty-state">
+            <i data-lucide="star"></i>
+            <p>${t('coreMemory.noFavorites') || 'No favorites yet'}</p>
+          </div>
+        </div>
+      </div>
+
       <!-- Clusters Tab Content (hidden by default) -->
       <div class="cm-tab-panel clusters-container" id="clustersContainer" style="display: none;">
         <div class="clusters-layout">
@@ -213,21 +233,21 @@ function renderMemoryCard(memory) {
   const priority = metadata.priority || 'medium';
 
   return `
-    <div class="memory-card ${isArchived ? 'archived' : ''}" data-memory-id="${memory.id}">
+    <div class="memory-card ${isArchived ? 'archived' : ''}" data-memory-id="${memory.id}" onclick="viewMemoryDetail('${memory.id}')">
       <div class="memory-card-header">
         <div class="memory-id">
-          <i data-lucide="bookmark"></i>
+          ${metadata.favorite ? '<i data-lucide="star"></i>' : ''}
           <span>${memory.id}</span>
           ${isArchived ? `<span class="badge badge-archived">${t('common.archived')}</span>` : ''}
           ${priority !== 'medium' ? `<span class="badge badge-priority-${priority}">${priority}</span>` : ''}
         </div>
-        <div class="memory-actions">
-          <button class="icon-btn" onclick="viewMemoryDetail('${memory.id}')" title="${t('common.view')}">
-            <i data-lucide="eye"></i>
-          </button>
+        <div class="memory-actions" onclick="event.stopPropagation()">
           <button class="icon-btn" onclick="editMemory('${memory.id}')" title="${t('common.edit')}">
             <i data-lucide="edit"></i>
           </button>
+          <button class="icon-btn ${metadata.favorite ? 'favorite-active' : ''}" onclick="toggleFavorite('${memory.id}')" title="${t('coreMemory.toggleFavorite') || 'Toggle Favorite'}">
+            <i data-lucide="star"></i>
+          </button>
           ${!isArchived
             ? `<button class="icon-btn" onclick="archiveMemory('${memory.id}')" title="${t('common.archive')}">
                  <i data-lucide="archive"></i>
@@ -270,11 +290,19 @@ function renderMemoryCard(memory) {
             : ''
           }
         </div>
-        <div class="memory-features">
+        <div class="memory-features" onclick="event.stopPropagation()">
           <button class="feature-btn" onclick="generateMemorySummary('${memory.id}')" title="${t('coreMemory.generateSummary')}">
             <i data-lucide="sparkles"></i>
             ${t('coreMemory.summary')}
           </button>
+          <button class="feature-btn" onclick="copyMemoryId('${memory.id}')" title="${t('common.copyId') || 'Copy ID'}">
+            <i data-lucide="copy"></i>
+            ${t('common.copyId') || 'Copy ID'}
+          </button>
+          <button class="feature-btn" onclick="showMemoryRelations('${memory.id}')" title="${t('coreMemory.showRelations') || 'Show Relations'}">
+            <i data-lucide="git-branch"></i>
+            ${t('coreMemory.relations') || 'Relations'}
+          </button>
         </div>
       </div>
     </div>
@@ -565,18 +593,44 @@ function escapeHtml(text) {
   return div.innerHTML;
 }
 
+async function copyMemoryId(memoryId) {
+  try {
+    await navigator.clipboard.writeText(memoryId);
+    showNotification(t('common.copied') || 'Copied!', 'success');
+  } catch (error) {
+    console.error('Failed to copy:', error);
+    showNotification(t('common.copyError') || 'Failed to copy', 'error');
+  }
+}
+
 // View Toggle Functions
 function showMemoriesView() {
   document.getElementById('memoriesGrid').style.display = '';
+  document.getElementById('favoritesGrid').style.display = 'none';
   document.getElementById('clustersContainer').style.display = 'none';
   document.getElementById('memoriesViewBtn').classList.add('active');
+  document.getElementById('favoritesViewBtn').classList.remove('active');
   document.getElementById('clustersViewBtn').classList.remove('active');
 }
 
+async function showFavoritesView() {
+  document.getElementById('memoriesGrid').style.display = 'none';
+  document.getElementById('favoritesGrid').style.display = '';
+  document.getElementById('clustersContainer').style.display = 'none';
+  document.getElementById('memoriesViewBtn').classList.remove('active');
+  document.getElementById('favoritesViewBtn').classList.add('active');
+  document.getElementById('clustersViewBtn').classList.remove('active');
+
+  // Load favorites
+  await refreshFavorites();
+}
+
 function showClustersView() {
   document.getElementById('memoriesGrid').style.display = 'none';
+  document.getElementById('favoritesGrid').style.display = 'none';
   document.getElementById('clustersContainer').style.display = '';
   document.getElementById('memoriesViewBtn').classList.remove('active');
+  document.getElementById('favoritesViewBtn').classList.remove('active');
   document.getElementById('clustersViewBtn').classList.add('active');
 
   // Load clusters from core-memory-clusters.js
@@ -586,3 +640,143 @@ function showClustersView() {
     console.error('loadClusters is not available. Make sure core-memory-clusters.js is loaded.');
   }
 }
+
+// Favorites Functions
+async function refreshFavorites() {
+  const allMemories = await fetchCoreMemories(false);
+  const favorites = allMemories.filter(m => m.metadata && m.metadata.favorite);
+
+  const countEl = document.getElementById('totalFavoritesCount');
+  const gridEl = document.getElementById('favoritesGridContent');
+
+  if (countEl) countEl.textContent = favorites.length;
+
+  if (gridEl) {
+    if (favorites.length === 0) {
+      gridEl.innerHTML = `
+        <div class="empty-state">
+          <i data-lucide="star"></i>
+          <p>${t('coreMemory.noFavorites') || 'No favorites yet'}</p>
+        </div>
+      `;
+    } else {
+      gridEl.innerHTML = favorites.map(memory => renderMemoryCard(memory)).join('');
+    }
+  }
+
+  lucide.createIcons();
+}
+
+async function showMemoryRelations(memoryId) {
+  try {
+    // Fetch all clusters
+    const response = await fetch(`/api/core-memory/clusters?path=${encodeURIComponent(projectPath)}`);
+    if (!response.ok) throw new Error(`HTTP ${response.status}`);
+
+    const result = await response.json();
+    const clusters = result.clusters || [];
+
+    // Find clusters containing this memory
+    const relatedClusters = [];
+    for (const cluster of clusters) {
+      const detailRes = await fetch(`/api/core-memory/clusters/${cluster.id}?path=${encodeURIComponent(projectPath)}`);
+      if (detailRes.ok) {
+        const detail = await detailRes.json();
+        const members = detail.members || [];
+        if (members.some(m => m.session_id === memoryId || m.id === memoryId)) {
+          relatedClusters.push({
+            ...cluster,
+            relations: detail.relations || []
+          });
+        }
+      }
+    }
+
+    // Show in modal
+    const modal = document.getElementById('memoryDetailModal');
+    document.getElementById('memoryDetailTitle').textContent = t('coreMemory.relationsFor') || `Relations: ${memoryId}`;
+
+    const body = document.getElementById('memoryDetailBody');
+    if (relatedClusters.length === 0) {
+      body.innerHTML = `
+        <div class="empty-state">
+          <i data-lucide="git-branch"></i>
+          <p>${t('coreMemory.noRelations') || 'No cluster relations found'}</p>
+          <p class="text-muted">${t('coreMemory.noRelationsHint') || 'Use Auto Cluster in the Clusters tab to create relations'}</p>
+        </div>
+      `;
+    } else {
+      body.innerHTML = `
+        <div class="relations-detail">
+          <h4>${t('coreMemory.belongsToClusters') || 'Belongs to Clusters'}</h4>
+          <div class="clusters-list">
+            ${relatedClusters.map(cluster => `
+              <div class="relation-cluster-item">
+                <div class="relation-cluster-header">
+                  <i data-lucide="folder"></i>
+                  <span class="cluster-name">${escapeHtml(cluster.name)}</span>
+                  <span class="badge badge-${cluster.status}">${cluster.status}</span>
+                </div>
+                ${cluster.relations && cluster.relations.length > 0 ? `
+                  <div class="cluster-relations-list">
+                    <span class="relations-label">${t('coreMemory.relatedClusters')}:</span>
+                    ${cluster.relations.map(rel => `
+                      <span class="relation-tag">
+                        <i data-lucide="link"></i>
+                        ${escapeHtml(rel.target_name || rel.target_id)}
+                        <span class="relation-type">${rel.relation_type}</span>
+                      </span>
+                    `).join('')}
+                  </div>
+                ` : ''}
+              </div>
+            `).join('')}
+          </div>
+        </div>
+      `;
+    }
+
+    modal.style.display = 'flex';
+    lucide.createIcons();
+  } catch (error) {
+    console.error('Failed to load relations:', error);
+    showNotification(t('coreMemory.relationsError') || 'Failed to load relations', 'error');
+  }
+}
+
+async function toggleFavorite(memoryId) {
+  try {
+    const memory = await fetchMemoryById(memoryId);
+    if (!memory) return;
+
+    const metadata = memory.metadata || {};
+    metadata.favorite = !metadata.favorite;
+
+    const response = await fetch('/api/core-memory/memories', {
+      method: 'POST',
+      headers: { 'Content-Type': 'application/json' },
+      body: JSON.stringify({ ...memory, metadata, path: projectPath })
+    });
+
+    if (!response.ok) throw new Error(`HTTP ${response.status}`);
+
+    showNotification(
+      metadata.favorite
+        ? (t('coreMemory.addedToFavorites') || 'Added to favorites')
+        : (t('coreMemory.removedFromFavorites') || 'Removed from favorites'),
+      'success'
+    );
+
+    // Refresh current view
+    await refreshCoreMemories();
+
+    // Also refresh favorites if visible
+    const favoritesGrid = document.getElementById('favoritesGrid');
+    if (favoritesGrid && favoritesGrid.style.display !== 'none') {
+      await refreshFavorites();
+    }
+  } catch (error) {
+    console.error('Failed to toggle favorite:', error);
+    showNotification(t('coreMemory.favoriteError') || 'Failed to update favorite', 'error');
+  }
+}
diff --git a/ccw/src/templates/dashboard-js/views/mcp-manager.js b/ccw/src/templates/dashboard-js/views/mcp-manager.js
index 1e92cf48..1d966836 100644
--- a/ccw/src/templates/dashboard-js/views/mcp-manager.js
+++ b/ccw/src/templates/dashboard-js/views/mcp-manager.js
@@ -324,7 +324,7 @@ async function renderMcpManager() {
                     <button class="px-3 py-1 text-xs bg-primary text-primary-foreground rounded hover:opacity-90 transition-opacity"
                             data-action="copy-to-codex"
                             data-server-name="${escapeHtml(serverName)}"
-                            data-server-config="${escapeHtml(JSON.stringify(serverConfig))}"
+                            data-server-config="${encodeConfigData(serverConfig)}"
                             title="${t('mcp.codex.copyToCodex')}">
                       <i data-lucide="arrow-right" class="w-3.5 h-3.5 inline"></i> Codex
                     </button>
@@ -684,7 +684,7 @@ async function renderMcpManager() {
                     <button class="px-3 py-1 text-xs bg-primary text-primary-foreground rounded hover:opacity-90 transition-opacity"
                             data-action="copy-codex-to-claude"
                             data-server-name="${escapeHtml(serverName)}"
-                            data-server-config='${JSON.stringify(serverConfig).replace(/'/g, "&#39;")}'
+                            data-server-config="${encodeConfigData(serverConfig)}"
                             title="${t('mcp.claude.copyToClaude')}">
                       <i data-lucide="arrow-right" class="w-3.5 h-3.5 inline"></i> Claude
                     </button>
@@ -823,7 +823,7 @@ function renderProjectAvailableServerCard(entry) {
   return `
     <div class="mcp-server-card bg-card border border-border rounded-lg p-4 hover:shadow-md transition-all cursor-pointer ${canToggle && !isEnabled ? 'opacity-60' : ''}"
          data-server-name="${escapeHtml(name)}"
-         data-server-config="${escapeHtml(JSON.stringify(config))}"
+         data-server-config="${encodeConfigData(config)}"
          data-server-source="${source}"
          data-action="view-details"
          title="${t('mcp.clickToViewDetails')}">
@@ -867,7 +867,7 @@ function renderProjectAvailableServerCard(entry) {
         <div class="flex items-center gap-2">
           <button class="text-xs text-success hover:text-success/80 transition-colors flex items-center gap-1"
                   data-server-name="${escapeHtml(name)}"
-                  data-server-config="${escapeHtml(JSON.stringify(config))}"
+                  data-server-config="${encodeConfigData(config)}"
                   data-action="save-as-template"
                   onclick="event.stopPropagation()"
                   title="${t('mcp.saveAsTemplate')}">
@@ -898,7 +898,7 @@ function renderGlobalManagementCard(serverName, serverConfig) {
   return `
     <div class="mcp-server-card mcp-server-global bg-card border border-success/30 rounded-lg p-4 hover:shadow-md transition-all cursor-pointer"
          data-server-name="${escapeHtml(serverName)}"
-         data-server-config="${escapeHtml(JSON.stringify(serverConfig))}"
+         data-server-config="${encodeConfigData(serverConfig)}"
          data-server-source="global"
          data-action="view-details"
          title="${t('mcp.clickToEdit')}">
@@ -976,7 +976,7 @@ function renderAvailableServerCard(serverName, serverInfo) {
           <button class="px-3 py-1 text-xs bg-primary text-primary-foreground rounded hover:opacity-90 transition-opacity"
                   data-server-name="${escapeHtml(originalName)}"
                   data-server-key="${escapeHtml(serverName)}"
-                  data-server-config='${JSON.stringify(serverConfig).replace(/'/g, "&#39;")}'
+                  data-server-config="${encodeConfigData(serverConfig)}"
                   data-scope="project"
                   data-action="add-from-other"
                   title="${t('mcp.installToProject')}">
@@ -985,7 +985,7 @@ function renderAvailableServerCard(serverName, serverInfo) {
           <button class="px-3 py-1 text-xs bg-success text-success-foreground rounded hover:opacity-90 transition-opacity"
                   data-server-name="${escapeHtml(originalName)}"
                   data-server-key="${escapeHtml(serverName)}"
-                  data-server-config='${JSON.stringify(serverConfig).replace(/'/g, "&#39;")}'
+                  data-server-config="${encodeConfigData(serverConfig)}"
                   data-scope="global"
                   data-action="add-from-other"
                   title="${t('mcp.installToGlobal')}">
@@ -1014,7 +1014,7 @@ function renderAvailableServerCard(serverName, serverInfo) {
       <div class="mt-3 pt-3 border-t border-border flex items-center gap-2">
         <button class="text-xs text-primary hover:text-primary/80 transition-colors flex items-center gap-1"
                 data-server-name="${escapeHtml(originalName)}"
-                data-server-config="${escapeHtml(JSON.stringify(serverConfig))}"
+                data-server-config="${encodeConfigData(serverConfig)}"
                 data-action="install-to-project"
                 title="${t('mcp.installToProject')}">
           <i data-lucide="download" class="w-3 h-3"></i>
@@ -1022,7 +1022,7 @@ function renderAvailableServerCard(serverName, serverInfo) {
         </button>
         <button class="text-xs text-success hover:text-success/80 transition-colors flex items-center gap-1"
                 data-server-name="${escapeHtml(originalName)}"
-                data-server-config="${escapeHtml(JSON.stringify(serverConfig))}"
+                data-server-config="${encodeConfigData(serverConfig)}"
                 data-action="install-to-global"
                 title="${t('mcp.installToGlobal')}">
           <i data-lucide="globe" class="w-3 h-3"></i>
@@ -1072,7 +1072,7 @@ function renderAvailableServerCardForCodex(serverName, serverInfo) {
           <button class="px-3 py-1 text-xs bg-primary text-primary-foreground rounded hover:opacity-90 transition-opacity"
                   data-action="copy-to-codex"
                   data-server-name="${escapeHtml(originalName)}"
-                  data-server-config="${escapeHtml(JSON.stringify(serverConfig))}"
+                  data-server-config="${encodeConfigData(serverConfig)}"
                   title="${t('mcp.codex.copyToCodex')}">
             <i data-lucide="arrow-right" class="w-3.5 h-3.5 inline"></i> Codex
           </button>
@@ -1100,7 +1100,7 @@ function renderAvailableServerCardForCodex(serverName, serverInfo) {
         <button class="text-xs text-primary hover:text-primary/80 transition-colors flex items-center gap-1"
                 data-action="copy-to-codex"
                 data-server-name="${escapeHtml(originalName)}"
-                data-server-config="${escapeHtml(JSON.stringify(serverConfig))}"
+                data-server-config="${encodeConfigData(serverConfig)}"
                 title="${t('mcp.codex.copyToCodex')}">
           <i data-lucide="download" class="w-3 h-3"></i>
           ${t('mcp.codex.install')}
@@ -1130,7 +1130,7 @@ function renderCodexServerCard(serverName, serverConfig) {
   return `
     <div class="mcp-server-card bg-card border border-primary/20 rounded-lg p-4 hover:shadow-md transition-all cursor-pointer ${!isEnabled ? 'opacity-60' : ''}"
          data-server-name="${escapeHtml(serverName)}"
-         data-server-config="${escapeHtml(JSON.stringify(serverConfig))}"
+         data-server-config="${encodeConfigData(serverConfig)}"
          data-cli-type="codex"
          data-action="view-details-codex"
          title="${t('mcp.clickToEdit')}">
@@ -1180,7 +1180,7 @@ function renderCodexServerCard(serverName, serverConfig) {
           <button class="text-xs text-primary hover:text-primary/80 transition-colors flex items-center gap-1"
                   data-action="copy-codex-to-claude"
                   data-server-name="${escapeHtml(serverName)}"
-                  data-server-config='${JSON.stringify(serverConfig).replace(/'/g, "&#39;")}'
+                  data-server-config="${encodeConfigData(serverConfig)}"
                   title="${t('mcp.codex.copyToClaude')}">
             <i data-lucide="copy" class="w-3 h-3"></i>
             ${t('mcp.codex.copyToClaude')}
@@ -1250,7 +1250,7 @@ function renderCrossCliServerCard(server, isClaude) {
         <button class="w-full px-3 py-2 text-sm font-medium bg-primary hover:bg-primary/90 text-primary-foreground rounded-lg transition-colors flex items-center justify-center gap-1.5"
                 data-action="copy-cross-cli"
                 data-server-name="${escapeHtml(name)}"
-                data-server-config='${JSON.stringify(config).replace(/'/g, "&#39;")}'
+                data-server-config="${encodeConfigData(config)}"
                 data-from-cli="${fromCli}"
                 data-target-cli="${targetCli}">
           <i data-lucide="copy" class="w-4 h-4"></i>
@@ -1357,14 +1357,18 @@ function attachMcpEventListeners() {
   // Add from other projects (with scope selection)
   document.querySelectorAll('.mcp-server-card button[data-action="add-from-other"]').forEach(btn => {
     btn.addEventListener('click', async (e) => {
-      const serverName = btn.dataset.serverName;
-      const serverConfig = JSON.parse(btn.dataset.serverConfig);
-      const scope = btn.dataset.scope; // 'project' or 'global'
+      try {
+        const serverName = btn.dataset.serverName;
+        const serverConfig = decodeConfigData(btn.dataset.serverConfig);
+        const scope = btn.dataset.scope; // 'project' or 'global'
 
-      if (scope === 'global') {
-        await addGlobalMcpServer(serverName, serverConfig);
-      } else {
-        await copyMcpServerToProject(serverName, serverConfig);
+        if (scope === 'global') {
+          await addGlobalMcpServer(serverName, serverConfig);
+        } else {
+          await copyMcpServerToProject(serverName, serverConfig);
+        }
+      } catch (err) {
+        console.error('[MCP] Error adding server from other project:', err);
       }
     });
   });
@@ -1392,27 +1396,39 @@ function attachMcpEventListeners() {
   // Install to project buttons
   document.querySelectorAll('.mcp-server-card button[data-action="install-to-project"]').forEach(btn => {
     btn.addEventListener('click', async (e) => {
-      const serverName = btn.dataset.serverName;
-      const serverConfig = JSON.parse(btn.dataset.serverConfig);
-      await copyMcpServerToProject(serverName, serverConfig);
+      try {
+        const serverName = btn.dataset.serverName;
+        const serverConfig = decodeConfigData(btn.dataset.serverConfig);
+        await copyMcpServerToProject(serverName, serverConfig);
+      } catch (err) {
+        console.error('[MCP] Error installing to project:', err);
+      }
     });
   });
 
   // Install to global buttons
   document.querySelectorAll('.mcp-server-card button[data-action="install-to-global"]').forEach(btn => {
     btn.addEventListener('click', async (e) => {
-      const serverName = btn.dataset.serverName;
-      const serverConfig = JSON.parse(btn.dataset.serverConfig);
-      await addGlobalMcpServer(serverName, serverConfig);
+      try {
+        const serverName = btn.dataset.serverName;
+        const serverConfig = decodeConfigData(btn.dataset.serverConfig);
+        await addGlobalMcpServer(serverName, serverConfig);
+      } catch (err) {
+        console.error('[MCP] Error installing to global:', err);
+      }
     });
   });
 
   // Save as template buttons
   document.querySelectorAll('.mcp-server-card button[data-action="save-as-template"]').forEach(btn => {
     btn.addEventListener('click', async (e) => {
-      const serverName = btn.dataset.serverName;
-      const serverConfig = JSON.parse(btn.dataset.serverConfig);
-      await saveMcpAsTemplate(serverName, serverConfig);
+      try {
+        const serverName = btn.dataset.serverName;
+        const serverConfig = decodeConfigData(btn.dataset.serverConfig);
+        await saveMcpAsTemplate(serverName, serverConfig);
+      } catch (err) {
+        console.error('[MCP] Error saving as template:', err);
+      }
     });
   });
 
@@ -1507,10 +1523,14 @@ function attachMcpEventListeners() {
   document.querySelectorAll('button[data-action="copy-to-codex"]').forEach(btn => {
     btn.addEventListener('click', async (e) => {
       e.preventDefault();
-      const serverName = btn.dataset.serverName;
-      const serverConfig = JSON.parse(btn.dataset.serverConfig);
-      console.log('[MCP] Copying to Codex:', serverName);
-      await copyClaudeServerToCodex(serverName, serverConfig);
+      try {
+        const serverName = btn.dataset.serverName;
+        const serverConfig = decodeConfigData(btn.dataset.serverConfig);
+        console.log('[MCP] Copying to Codex:', serverName);
+        await copyClaudeServerToCodex(serverName, serverConfig);
+      } catch (err) {
+        console.error('[MCP] Error copying to Codex:', err);
+      }
     });
   });
 
@@ -1522,7 +1542,7 @@ function attachMcpEventListeners() {
       const serverName = btn.dataset.serverName;
       let serverConfig;
       try {
-        serverConfig = JSON.parse(btn.dataset.serverConfig);
+        serverConfig = decodeConfigData(btn.dataset.serverConfig);
       } catch (err) {
         console.error('[MCP] JSON Parse Error:', err);
         if (typeof showRefreshToast === 'function') {
@@ -1543,7 +1563,7 @@ function attachMcpEventListeners() {
       const serverName = btn.dataset.serverName;
       let serverConfig;
       try {
-        serverConfig = JSON.parse(btn.dataset.serverConfig);
+        serverConfig = decodeConfigData(btn.dataset.serverConfig);
       } catch (err) {
         console.error('[MCP] JSON Parse Error:', err);
         if (typeof showRefreshToast === 'function') {
@@ -1567,14 +1587,21 @@ function attachMcpEventListeners() {
       }
       try {
         const serverName = card.dataset.serverName;
-        // Decode HTML entities before parsing JSON
-        const configStr = unescapeHtml(card.dataset.serverConfig);
-        const serverConfig = JSON.parse(configStr);
+        const configData = card.dataset.serverConfig;
+        if (!configData) {
+          console.error('[MCP] Missing server config for:', serverName);
+          return;
+        }
+        const serverConfig = decodeConfigData(configData);
+        if (!serverConfig) {
+          console.error('[MCP] Failed to decode server config for:', serverName);
+          return;
+        }
         const serverSource = card.dataset.serverSource;
         console.log('[MCP] Card clicked:', serverName, serverSource);
         showMcpEditModal(serverName, serverConfig, serverSource, 'claude');
       } catch (err) {
-        console.error('[MCP] Error handling card click:', err, card.dataset.serverConfig);
+        console.error('[MCP] Error handling card click:', err);
       }
     });
   });
@@ -1588,13 +1615,20 @@ function attachMcpEventListeners() {
       }
       try {
         const serverName = card.dataset.serverName;
-        // Decode HTML entities before parsing JSON
-        const configStr = unescapeHtml(card.dataset.serverConfig);
-        const serverConfig = JSON.parse(configStr);
+        const configData = card.dataset.serverConfig;
+        if (!configData) {
+          console.error('[MCP] Missing server config for:', serverName);
+          return;
+        }
+        const serverConfig = decodeConfigData(configData);
+        if (!serverConfig) {
+          console.error('[MCP] Failed to decode server config for:', serverName);
+          return;
+        }
         console.log('[MCP] Codex card clicked:', serverName);
         showMcpEditModal(serverName, serverConfig, 'codex', 'codex');
       } catch (err) {
-        console.error('[MCP] Error handling Codex card click:', err, card.dataset.serverConfig);
+        console.error('[MCP] Error handling Codex card click:', err);
       }
     });
   });
diff --git a/ccw/src/templates/dashboard.html b/ccw/src/templates/dashboard.html
index 208bb4d9..5ba38df9 100644
--- a/ccw/src/templates/dashboard.html
+++ b/ccw/src/templates/dashboard.html
@@ -331,10 +331,12 @@
                 <i data-lucide="history" class="nav-icon"></i>
                 <span class="nav-text flex-1" data-i18n="nav.history">History</span>
               </li>
+              <!-- Hidden: Code Graph Explorer (feature disabled)
               <li class="nav-item flex items-center gap-2 mx-2 px-3 py-2.5 text-sm text-muted-foreground hover:bg-hover hover:text-foreground rounded cursor-pointer transition-colors" data-view="graph-explorer" data-tooltip="Code Graph Explorer">
                 <i data-lucide="git-branch" class="nav-icon"></i>
                 <span class="nav-text flex-1" data-i18n="nav.graphExplorer">Graph</span>
               </li>
+              -->
             </ul>
           </div>
 
diff --git a/ccw/src/tools/codex-lens.ts b/ccw/src/tools/codex-lens.ts
index 7fca02dd..383d15a8 100644
--- a/ccw/src/tools/codex-lens.ts
+++ b/ccw/src/tools/codex-lens.ts
@@ -11,7 +11,7 @@
 
 import { z } from 'zod';
 import type { ToolSchema, ToolResult } from '../types/tool.js';
-import { spawn, execSync } from 'child_process';
+import { spawn, execSync, exec } from 'child_process';
 import { existsSync, mkdirSync } from 'fs';
 import { join, dirname } from 'path';
 import { homedir } from 'os';
@@ -443,22 +443,44 @@ async function executeCodexLens(args: string[], options: ExecuteOptions = {}): P
   }
 
   return new Promise((resolve) => {
-    const child = spawn(VENV_PYTHON, ['-m', 'codexlens', ...args], {
-      cwd,
-      stdio: ['ignore', 'pipe', 'pipe'],
+    // Build command string - quote paths for shell execution
+    const quotedPython = `"${VENV_PYTHON}"`;
+    const cmdArgs = args.map(arg => {
+      // Quote arguments that contain spaces or special characters
+      if (arg.includes(' ') || arg.includes('\\')) {
+        return `"${arg}"`;
+      }
+      return arg;
     });
 
-    let stdout = '';
-    let stderr = '';
-    let timedOut = false;
+    // Build full command - on Windows, prepend cd to handle different drives
+    let fullCmd: string;
+    if (process.platform === 'win32' && cwd) {
+      // Use cd /d to change drive and directory, then run command
+      fullCmd = `cd /d "${cwd}" && ${quotedPython} -m codexlens ${cmdArgs.join(' ')}`;
+    } else {
+      fullCmd = `${quotedPython} -m codexlens ${cmdArgs.join(' ')}`;
+    }
 
-    child.stdout.on('data', (data) => {
-      const chunk = data.toString();
-      stdout += chunk;
+    // Use exec with shell option for cross-platform compatibility
+    exec(fullCmd, {
+      cwd: process.platform === 'win32' ? undefined : cwd, // Don't use cwd on Windows, use cd command instead
+      timeout,
+      maxBuffer: 50 * 1024 * 1024, // 50MB buffer for large outputs
+      shell: process.platform === 'win32' ? process.env.ComSpec : undefined,
+    }, (error, stdout, stderr) => {
+      if (error) {
+        if (error.killed) {
+          resolve({ success: false, error: 'Command timed out' });
+        } else {
+          resolve({ success: false, error: stderr || error.message });
+        }
+        return;
+      }
 
-      // Report progress if callback provided
-      if (onProgress) {
-        const lines = chunk.split('\n');
+      // Report final progress if callback provided
+      if (onProgress && stdout) {
+        const lines = stdout.split('\n');
         for (const line of lines) {
           const progress = parseProgressLine(line.trim());
           if (progress) {
@@ -466,44 +488,8 @@ async function executeCodexLens(args: string[], options: ExecuteOptions = {}): P
           }
         }
       }
-    });
 
-    child.stderr.on('data', (data) => {
-      const chunk = data.toString();
-      stderr += chunk;
-
-      // Also check stderr for progress (some tools output there)
-      if (onProgress) {
-        const lines = chunk.split('\n');
-        for (const line of lines) {
-          const progress = parseProgressLine(line.trim());
-          if (progress) {
-            onProgress(progress);
-          }
-        }
-      }
-    });
-
-    const timeoutId = setTimeout(() => {
-      timedOut = true;
-      child.kill('SIGTERM');
-    }, timeout);
-
-    child.on('close', (code) => {
-      clearTimeout(timeoutId);
-
-      if (timedOut) {
-        resolve({ success: false, error: 'Command timed out' });
-      } else if (code === 0) {
-        resolve({ success: true, output: stdout.trim() });
-      } else {
-        resolve({ success: false, error: stderr || `Exit code: ${code}` });
-      }
-    });
-
-    child.on('error', (err) => {
-      clearTimeout(timeoutId);
-      resolve({ success: false, error: `Spawn failed: ${err.message}` });
+      resolve({ success: true, output: stdout.trim() });
     });
   });
 }
diff --git a/ccw/src/tools/smart-search.ts b/ccw/src/tools/smart-search.ts
index e728eedc..7736c920 100644
--- a/ccw/src/tools/smart-search.ts
+++ b/ccw/src/tools/smart-search.ts
@@ -27,26 +27,21 @@ import type { ProgressInfo } from './codex-lens.js';
 const ParamsSchema = z.object({
   action: z.enum(['init', 'search', 'search_files', 'status']).default('search'),
   query: z.string().optional(),
-  mode: z.enum(['auto', 'hybrid', 'exact', 'ripgrep', 'parallel']).default('auto'),
+  mode: z.enum(['auto', 'hybrid', 'exact', 'ripgrep', 'priority']).default('auto'),
   output_mode: z.enum(['full', 'files_only', 'count']).default('full'),
   path: z.string().optional(),
   paths: z.array(z.string()).default([]),
   contextLines: z.number().default(0),
-  maxResults: z.number().default(100),
+  maxResults: z.number().default(10),
   includeHidden: z.boolean().default(false),
   languages: z.array(z.string()).optional(),
-  limit: z.number().default(100),
-  parallelWeights: z.object({
-    hybrid: z.number().default(0.5),
-    exact: z.number().default(0.3),
-    ripgrep: z.number().default(0.2),
-  }).optional(),
+  limit: z.number().default(10),
 });
 
 type Params = z.infer<typeof ParamsSchema>;
 
 // Search mode constants
-const SEARCH_MODES = ['auto', 'hybrid', 'exact', 'ripgrep', 'parallel'] as const;
+const SEARCH_MODES = ['auto', 'hybrid', 'exact', 'ripgrep', 'priority'] as const;
 
 // Classification confidence threshold
 const CONFIDENCE_THRESHOLD = 0.7;
@@ -89,6 +84,7 @@ interface SearchMetadata {
   warning?: string;
   note?: string;
   index_status?: 'indexed' | 'not_indexed' | 'partial';
+  fallback_history?: string[];
   // Init action specific
   action?: string;
   path?: string;
@@ -120,6 +116,13 @@ interface IndexStatus {
   warning?: string;
 }
 
+/**
+ * Strip ANSI color codes from string (for JSON parsing)
+ */
+function stripAnsi(str: string): string {
+  return str.replace(/\x1b\[[0-9;]*m/g, '');
+}
+
 /**
  * Check if CodexLens index exists for current directory
  * @param path - Directory path to check
@@ -140,7 +143,7 @@ async function checkIndexStatus(path: string = '.'): Promise<IndexStatus> {
     // Parse status output
     try {
       // Strip ANSI color codes from JSON output
-      const cleanOutput = (result.output || '{}').replace(/\x1b\[[0-9;]*m/g, '');
+      const cleanOutput = stripAnsi(result.output || '{}');
       const parsed = JSON.parse(cleanOutput);
       // Handle both direct and nested response formats (status returns {success, result: {...}})
       const status = parsed.result || parsed;
@@ -293,7 +296,7 @@ function buildRipgrepCommand(params: {
   maxResults: number;
   includeHidden: boolean;
 }): { command: string; args: string[] } {
-  const { query, paths = ['.'], contextLines = 0, maxResults = 100, includeHidden = false } = params;
+  const { query, paths = ['.'], contextLines = 0, maxResults = 10, includeHidden = false } = params;
 
   const args = [
     '-n', // Show line numbers
@@ -478,7 +481,7 @@ async function executeAutoMode(params: Params): Promise<SearchResult> {
  * No index required, fallback to CodexLens if ripgrep unavailable
  */
 async function executeRipgrepMode(params: Params): Promise<SearchResult> {
-  const { query, paths = [], contextLines = 0, maxResults = 100, includeHidden = false, path = '.' } = params;
+  const { query, paths = [], contextLines = 0, maxResults = 10, includeHidden = false, path = '.' } = params;
 
   if (!query) {
     return {
@@ -520,8 +523,8 @@ async function executeRipgrepMode(params: Params): Promise<SearchResult> {
     // Parse results
     let results: SemanticMatch[] = [];
     try {
-      const parsed = JSON.parse(result.output || '{}');
-      const data = parsed.results || parsed;
+      const parsed = JSON.parse(stripAnsi(result.output || '{}'));
+      const data = parsed.result?.results || parsed.results || parsed;
       results = (Array.isArray(data) ? data : []).map((item: any) => ({
         file: item.path || item.file,
         score: item.score || 0,
@@ -632,7 +635,7 @@ async function executeRipgrepMode(params: Params): Promise<SearchResult> {
  * Requires index
  */
 async function executeCodexLensExactMode(params: Params): Promise<SearchResult> {
-  const { query, path = '.', limit = 100 } = params;
+  const { query, path = '.', maxResults = 10 } = params;
 
   if (!query) {
     return {
@@ -653,7 +656,7 @@ async function executeCodexLensExactMode(params: Params): Promise<SearchResult>
   // Check index status
   const indexStatus = await checkIndexStatus(path);
 
-  const args = ['search', query, '--limit', limit.toString(), '--mode', 'exact', '--json'];
+  const args = ['search', query, '--limit', maxResults.toString(), '--mode', 'exact', '--json'];
   const result = await executeCodexLens(args, { cwd: path });
 
   if (!result.success) {
@@ -673,8 +676,8 @@ async function executeCodexLensExactMode(params: Params): Promise<SearchResult>
   // Parse results
   let results: SemanticMatch[] = [];
   try {
-    const parsed = JSON.parse(result.output || '{}');
-    const data = parsed.results || parsed;
+    const parsed = JSON.parse(stripAnsi(result.output || '{}'));
+    const data = parsed.result?.results || parsed.results || parsed;
     results = (Array.isArray(data) ? data : []).map((item: any) => ({
       file: item.path || item.file,
       score: item.score || 0,
@@ -704,7 +707,7 @@ async function executeCodexLensExactMode(params: Params): Promise<SearchResult>
  * Requires index with embeddings
  */
 async function executeHybridMode(params: Params): Promise<SearchResult> {
-  const { query, path = '.', limit = 100 } = params;
+  const { query, path = '.', maxResults = 10 } = params;
 
   if (!query) {
     return {
@@ -725,7 +728,7 @@ async function executeHybridMode(params: Params): Promise<SearchResult> {
   // Check index status
   const indexStatus = await checkIndexStatus(path);
 
-  const args = ['search', query, '--limit', limit.toString(), '--mode', 'hybrid', '--json'];
+  const args = ['search', query, '--limit', maxResults.toString(), '--mode', 'hybrid', '--json'];
   const result = await executeCodexLens(args, { cwd: path });
 
   if (!result.success) {
@@ -745,8 +748,8 @@ async function executeHybridMode(params: Params): Promise<SearchResult> {
   // Parse results
   let results: SemanticMatch[] = [];
   try {
-    const parsed = JSON.parse(result.output || '{}');
-    const data = parsed.results || parsed;
+    const parsed = JSON.parse(stripAnsi(result.output || '{}'));
+    const data = parsed.result?.results || parsed.results || parsed;
     results = (Array.isArray(data) ? data : []).map((item: any) => ({
       file: item.path || item.file,
       score: item.score || 0,
@@ -828,94 +831,114 @@ function applyRRFFusion(
 }
 
 /**
- * Mode: parallel - Run all backends simultaneously with RRF fusion
- * Returns best results from hybrid + exact + ripgrep combined
+ * Promise wrapper with timeout support
+ * @param promise - The promise to wrap
+ * @param ms - Timeout in milliseconds
+ * @param modeName - Name of the mode for error message
+ * @returns A new promise that rejects on timeout
  */
-async function executeParallelMode(params: Params): Promise<SearchResult> {
-  const { query, path = '.', limit = 100, parallelWeights } = params;
+function withTimeout<T>(promise: Promise<T>, ms: number, modeName: string): Promise<T> {
+  return new Promise((resolve, reject) => {
+    const timer = setTimeout(() => {
+      reject(new Error(`'${modeName}' search timed out after ${ms}ms`));
+    }, ms);
+
+    promise
+      .then(resolve)
+      .catch(reject)
+      .finally(() => clearTimeout(timer));
+  });
+}
+
+/**
+ * Mode: priority - Fallback search strategy: hybrid -> exact -> ripgrep
+ * Returns results from the first backend that succeeds and provides results.
+ * More efficient than parallel mode - stops as soon as valid results are found.
+ */
+async function executePriorityFallbackMode(params: Params): Promise<SearchResult> {
+  const { query, path = '.' } = params;
+  const fallbackHistory: string[] = [];
 
   if (!query) {
+    return { success: false, error: 'Query is required for search' };
+  }
+
+  // Check index status first
+  const indexStatus = await checkIndexStatus(path);
+
+  // 1. Try Hybrid search (highest priority) - 90s timeout for large indexes
+  if (indexStatus.indexed && indexStatus.has_embeddings) {
+    try {
+      const hybridResult = await withTimeout(executeHybridMode(params), 90000, 'hybrid');
+      if (hybridResult.success && hybridResult.results && (hybridResult.results as any[]).length > 0) {
+        fallbackHistory.push('hybrid: success');
+        return {
+          ...hybridResult,
+          metadata: {
+            ...hybridResult.metadata,
+            mode: 'priority',
+            note: 'Result from hybrid search (semantic + vector).',
+            fallback_history: fallbackHistory,
+          },
+        };
+      }
+      fallbackHistory.push('hybrid: no results');
+    } catch (error) {
+      fallbackHistory.push(`hybrid: ${(error as Error).message}`);
+    }
+  } else {
+    fallbackHistory.push(`hybrid: skipped (${!indexStatus.indexed ? 'no index' : 'no embeddings'})`);
+  }
+
+  // 2. Fallback to Exact search - 10s timeout
+  if (indexStatus.indexed) {
+    try {
+      const exactResult = await withTimeout(executeCodexLensExactMode(params), 10000, 'exact');
+      if (exactResult.success && exactResult.results && (exactResult.results as any[]).length > 0) {
+        fallbackHistory.push('exact: success');
+        return {
+          ...exactResult,
+          metadata: {
+            ...exactResult.metadata,
+            mode: 'priority',
+            note: 'Result from exact/FTS search (fallback from hybrid).',
+            fallback_history: fallbackHistory,
+          },
+        };
+      }
+      fallbackHistory.push('exact: no results');
+    } catch (error) {
+      fallbackHistory.push(`exact: ${(error as Error).message}`);
+    }
+  } else {
+    fallbackHistory.push('exact: skipped (no index)');
+  }
+
+  // 3. Final fallback to Ripgrep - 5s timeout
+  try {
+    const ripgrepResult = await withTimeout(executeRipgrepMode(params), 5000, 'ripgrep');
+    fallbackHistory.push(ripgrepResult.success ? 'ripgrep: success' : 'ripgrep: failed');
     return {
-      success: false,
-      error: 'Query is required for search',
-    };
-  }
-
-  // Default weights if not provided
-  const weights = parallelWeights || {
-    hybrid: 0.5,
-    exact: 0.3,
-    ripgrep: 0.2,
-  };
-
-  // Run all backends in parallel
-  const [hybridResult, exactResult, ripgrepResult] = await Promise.allSettled([
-    executeHybridMode(params),
-    executeCodexLensExactMode(params),
-    executeRipgrepMode(params),
-  ]);
-
-  // Collect successful results
-  const resultsMap = new Map<string, any[]>();
-  const backendStatus: Record<string, string> = {};
-
-  if (hybridResult.status === 'fulfilled' && hybridResult.value.success) {
-    resultsMap.set('hybrid', hybridResult.value.results as any[]);
-    backendStatus.hybrid = 'success';
-  } else {
-    backendStatus.hybrid = hybridResult.status === 'rejected'
-      ? `error: ${hybridResult.reason}`
-      : `failed: ${(hybridResult as PromiseFulfilledResult<SearchResult>).value.error}`;
-  }
-
-  if (exactResult.status === 'fulfilled' && exactResult.value.success) {
-    resultsMap.set('exact', exactResult.value.results as any[]);
-    backendStatus.exact = 'success';
-  } else {
-    backendStatus.exact = exactResult.status === 'rejected'
-      ? `error: ${exactResult.reason}`
-      : `failed: ${(exactResult as PromiseFulfilledResult<SearchResult>).value.error}`;
-  }
-
-  if (ripgrepResult.status === 'fulfilled' && ripgrepResult.value.success) {
-    resultsMap.set('ripgrep', ripgrepResult.value.results as any[]);
-    backendStatus.ripgrep = 'success';
-  } else {
-    backendStatus.ripgrep = ripgrepResult.status === 'rejected'
-      ? `error: ${ripgrepResult.reason}`
-      : `failed: ${(ripgrepResult as PromiseFulfilledResult<SearchResult>).value.error}`;
-  }
-
-  // If no results from any backend
-  if (resultsMap.size === 0) {
-    return {
-      success: false,
-      error: 'All search backends failed',
+      ...ripgrepResult,
       metadata: {
-        mode: 'parallel',
-        backend: 'multi-backend',
-        count: 0,
-        query,
-        backend_status: backendStatus,
-      } as any,
+        ...ripgrepResult.metadata,
+        mode: 'priority',
+        note: 'Result from ripgrep search (final fallback).',
+        fallback_history: fallbackHistory,
+      },
     };
+  } catch (error) {
+    fallbackHistory.push(`ripgrep: ${(error as Error).message}`);
   }
 
-  // Apply RRF fusion
-  const fusedResults = applyRRFFusion(resultsMap, weights, limit);
-
+  // All modes failed
   return {
-    success: true,
-    results: fusedResults,
+    success: false,
+    error: 'All search backends in priority mode failed or returned no results.',
     metadata: {
-      mode: 'parallel',
-      backend: 'multi-backend',
-      count: fusedResults.length,
+      mode: 'priority',
       query,
-      backends_used: Array.from(resultsMap.keys()),
-      backend_status: backendStatus,
-      weights,
-      note: 'Parallel mode runs hybrid + exact + ripgrep simultaneously with RRF fusion',
+      fallback_history: fallbackHistory,
     } as any,
   };
 }
@@ -923,11 +946,11 @@ async function executeParallelMode(params: Params): Promise<SearchResult> {
 // Tool schema for MCP
 export const schema: ToolSchema = {
   name: 'smart_search',
-  description: `Intelligent code search with five modes: auto, hybrid, exact, ripgrep, parallel.
+  description: `Intelligent code search with five modes: auto, hybrid, exact, ripgrep, priority.
 
 **Quick Start:**
   smart_search(query="authentication logic")           # Auto mode (intelligent routing)
-  smart_search(action="init", path=".")                # Initialize FTS index (fast, no embeddings)
+  smart_search(action="init", path=".")                # Initialize index (required for hybrid)
   smart_search(action="status")                        # Check index status
 
 **Five Modes:**
@@ -938,7 +961,7 @@ export const schema: ToolSchema = {
 
   2. hybrid: CodexLens RRF fusion (exact + fuzzy + vector)
      - Best quality, semantic understanding
-     - Requires index with embeddings (create via "ccw view" dashboard)
+     - Requires index with embeddings
 
   3. exact: CodexLens FTS (full-text search)
      - Precise keyword matching
@@ -948,20 +971,21 @@ export const schema: ToolSchema = {
      - Fast, no index required
      - Literal string matching
 
-  5. parallel: Run all backends simultaneously
-     - Highest recall, runs hybrid + exact + ripgrep in parallel
-     - Results merged using RRF fusion with configurable weights
+  5. priority: Fallback strategy for best balance of speed and recall
+     - Tries searches in order: hybrid -> exact -> ripgrep
+     - Returns results from the first successful search with results
+     - More efficient than running all backends in parallel
 
 **Actions:**
   - search (default): Intelligent search with auto routing
-  - init: Create FTS index only (no embeddings, faster). For vector/semantic search, use "ccw view" dashboard
+  - init: Create CodexLens index
   - status: Check index and embedding availability
   - search_files: Return file paths only
 
 **Workflow:**
-  1. Run action="init" to create FTS index (fast)
-  2. For semantic search: create vector index via "ccw view" dashboard or "codexlens init <path>"
-  3. Use auto mode - it routes to hybrid for NL queries, exact for simple queries`,
+  1. Run action="init" to create index
+  2. Use auto mode - it routes to hybrid for NL queries, exact for simple queries
+  3. Use priority mode for comprehensive fallback search`,
   inputSchema: {
     type: 'object',
     properties: {
@@ -978,7 +1002,7 @@ export const schema: ToolSchema = {
       mode: {
         type: 'string',
         enum: SEARCH_MODES,
-        description: 'Search mode: auto (default), hybrid (best quality), exact (CodexLens FTS), ripgrep (fast, no index), parallel (all backends with RRF fusion)',
+        description: 'Search mode: auto (default), hybrid (best quality), exact (CodexLens FTS), ripgrep (fast, no index), priority (fallback: hybrid->exact->ripgrep)',
         default: 'auto',
       },
       output_mode: {
@@ -1006,13 +1030,13 @@ export const schema: ToolSchema = {
       },
       maxResults: {
         type: 'number',
-        description: 'Maximum number of results (default: 100)',
-        default: 100,
+        description: 'Maximum number of results (default: 10)',
+        default: 10,
       },
       limit: {
         type: 'number',
         description: 'Alias for maxResults',
-        default: 100,
+        default: 10,
       },
       includeHidden: {
         type: 'boolean',
@@ -1024,15 +1048,6 @@ export const schema: ToolSchema = {
         items: { type: 'string' },
         description: 'Languages to index (for init action). Example: ["javascript", "typescript"]',
       },
-      parallelWeights: {
-        type: 'object',
-        properties: {
-          hybrid: { type: 'number', default: 0.5 },
-          exact: { type: 'number', default: 0.3 },
-          ripgrep: { type: 'number', default: 0.2 },
-        },
-        description: 'RRF weights for parallel mode. Weights should sum to 1.0. Default: {hybrid: 0.5, exact: 0.3, ripgrep: 0.2}',
-      },
     },
     required: [],
   },
@@ -1082,12 +1097,13 @@ export async function handler(params: Record<string, unknown>): Promise<ToolResu
     return { success: false, error: `Invalid params: ${parsed.error.message}` };
   }
 
-  const { action, mode, output_mode, limit, maxResults } = parsed.data;
+  const { action, mode, output_mode } = parsed.data;
 
-  // Use limit if maxResults not provided
-  if (limit && !maxResults) {
-    parsed.data.maxResults = limit;
-  }
+  // Sync limit and maxResults - use the larger of the two if both provided
+  // This ensures user-provided values take precedence over defaults
+  const effectiveLimit = Math.max(parsed.data.limit || 10, parsed.data.maxResults || 10);
+  parsed.data.maxResults = effectiveLimit;
+  parsed.data.limit = effectiveLimit;
 
   try {
     let result: SearchResult;
@@ -1109,7 +1125,7 @@ export async function handler(params: Record<string, unknown>): Promise<ToolResu
 
       case 'search':
       default:
-        // Handle search modes: auto | hybrid | exact | ripgrep | parallel
+        // Handle search modes: auto | hybrid | exact | ripgrep | priority
         switch (mode) {
           case 'auto':
             result = await executeAutoMode(parsed.data);
@@ -1123,11 +1139,11 @@ export async function handler(params: Record<string, unknown>): Promise<ToolResu
           case 'ripgrep':
             result = await executeRipgrepMode(parsed.data);
             break;
-          case 'parallel':
-            result = await executeParallelMode(parsed.data);
+          case 'priority':
+            result = await executePriorityFallbackMode(parsed.data);
             break;
           default:
-            throw new Error(`Unsupported mode: ${mode}. Use: auto, hybrid, exact, ripgrep, or parallel`);
+            throw new Error(`Unsupported mode: ${mode}. Use: auto, hybrid, exact, ripgrep, or priority`);
         }
         break;
     }
diff --git a/codex-lens/src/codexlens/cli/embedding_manager.py b/codex-lens/src/codexlens/cli/embedding_manager.py
index 6fed8ec4..5adb3ca9 100644
--- a/codex-lens/src/codexlens/cli/embedding_manager.py
+++ b/codex-lens/src/codexlens/cli/embedding_manager.py
@@ -9,7 +9,7 @@ from typing import Dict, List, Optional
 try:
     from codexlens.semantic import SEMANTIC_AVAILABLE
     if SEMANTIC_AVAILABLE:
-        from codexlens.semantic.embedder import Embedder
+        from codexlens.semantic.embedder import Embedder, get_embedder
         from codexlens.semantic.vector_store import VectorStore
         from codexlens.semantic.chunker import Chunker, ChunkConfig
 except ImportError:
@@ -167,7 +167,8 @@ def generate_embeddings(
 
     # Initialize components
     try:
-        embedder = Embedder(profile=model_profile)
+        # Use cached embedder (singleton) for performance
+        embedder = get_embedder(profile=model_profile)
         vector_store = VectorStore(index_path)
         chunker = Chunker(config=ChunkConfig(max_chunk_size=chunk_size))
 
@@ -201,10 +202,16 @@ def generate_embeddings(
     if progress_callback:
         progress_callback(f"Processing {len(files)} files...")
 
-    # Process each file
-    total_chunks = 0
-    failed_files = []
+    # Process all files using batch operations for optimal performance
     start_time = time.time()
+    failed_files = []
+
+    # --- OPTIMIZATION Step 1: Collect all chunks from all files ---
+    if progress_callback:
+        progress_callback(f"Step 1/4: Chunking {len(files)} files...")
+
+    all_chunks_with_paths = []  # List of (chunk, file_path) tuples
+    files_with_chunks = set()
 
     for idx, file_row in enumerate(files, 1):
         file_path = file_row["full_path"]
@@ -212,39 +219,88 @@ def generate_embeddings(
         language = file_row["language"] or "python"
 
         try:
-            # Create chunks
             chunks = chunker.chunk_sliding_window(
                 content,
                 file_path=file_path,
                 language=language
             )
-
-            if not chunks:
-                continue
-
-            # Generate embeddings
-            for chunk in chunks:
-                embedding = embedder.embed_single(chunk.content)
-                chunk.embedding = embedding
-
-            # Store chunks
-            vector_store.add_chunks(chunks, file_path)
-            total_chunks += len(chunks)
-
-            if progress_callback:
-                progress_callback(f"[{idx}/{len(files)}] {file_path}: {len(chunks)} chunks")
-
+            if chunks:
+                for chunk in chunks:
+                    all_chunks_with_paths.append((chunk, file_path))
+                files_with_chunks.add(file_path)
         except Exception as e:
-            logger.error(f"Failed to process {file_path}: {e}")
+            logger.error(f"Failed to chunk {file_path}: {e}")
             failed_files.append((file_path, str(e)))
 
+    if not all_chunks_with_paths:
+        elapsed_time = time.time() - start_time
+        return {
+            "success": True,
+            "result": {
+                "chunks_created": 0,
+                "files_processed": len(files) - len(failed_files),
+                "files_failed": len(failed_files),
+                "elapsed_time": elapsed_time,
+                "model_profile": model_profile,
+                "model_name": embedder.model_name,
+                "failed_files": failed_files[:5],
+                "index_path": str(index_path),
+            },
+        }
+
+    total_chunks = len(all_chunks_with_paths)
+
+    # --- OPTIMIZATION Step 2: Batch generate embeddings with memory-safe batching ---
+    # Use smaller batches to avoid OOM errors while still benefiting from batch processing
+    # jina-embeddings-v2-base-code with long chunks needs small batches
+    BATCH_SIZE = 8  # Conservative batch size for memory efficiency
+
+    if progress_callback:
+        num_batches = (total_chunks + BATCH_SIZE - 1) // BATCH_SIZE
+        progress_callback(f"Step 2/4: Generating embeddings for {total_chunks} chunks ({num_batches} batches)...")
+
+    try:
+        all_embeddings = []
+        for batch_start in range(0, total_chunks, BATCH_SIZE):
+            batch_end = min(batch_start + BATCH_SIZE, total_chunks)
+            batch_contents = [chunk.content for chunk, _ in all_chunks_with_paths[batch_start:batch_end]]
+            batch_embeddings = embedder.embed(batch_contents)
+            all_embeddings.extend(batch_embeddings)
+
+            if progress_callback and total_chunks > BATCH_SIZE:
+                progress_callback(f"  Batch {batch_start // BATCH_SIZE + 1}/{(total_chunks + BATCH_SIZE - 1) // BATCH_SIZE}: {len(batch_embeddings)} embeddings")
+    except Exception as e:
+        return {
+            "success": False,
+            "error": f"Failed to generate embeddings: {str(e)}",
+        }
+
+    # --- OPTIMIZATION Step 3: Assign embeddings back to chunks ---
+    if progress_callback:
+        progress_callback(f"Step 3/4: Assigning {len(all_embeddings)} embeddings...")
+
+    for (chunk, _), embedding in zip(all_chunks_with_paths, all_embeddings):
+        chunk.embedding = embedding
+
+    # --- OPTIMIZATION Step 4: Batch store all chunks in single transaction ---
+    if progress_callback:
+        progress_callback(f"Step 4/4: Storing {total_chunks} chunks to database...")
+
+    try:
+        vector_store.add_chunks_batch(all_chunks_with_paths)
+    except Exception as e:
+        return {
+            "success": False,
+            "error": f"Failed to store chunks: {str(e)}",
+        }
+
     elapsed_time = time.time() - start_time
 
     return {
         "success": True,
         "result": {
             "chunks_created": total_chunks,
-            "files_processed": len(files) - len(failed_files),
+            "files_processed": len(files_with_chunks),
             "files_failed": len(failed_files),
             "elapsed_time": elapsed_time,
             "model_profile": model_profile,
diff --git a/codex-lens/src/codexlens/search/hybrid_search.py b/codex-lens/src/codexlens/search/hybrid_search.py
index 40d081be..532e4cfd 100644
--- a/codex-lens/src/codexlens/search/hybrid_search.py
+++ b/codex-lens/src/codexlens/search/hybrid_search.py
@@ -257,7 +257,7 @@ class HybridSearchEngine:
                 return []
 
             # Initialize embedder and vector store
-            from codexlens.semantic.embedder import Embedder
+            from codexlens.semantic.embedder import get_embedder
             from codexlens.semantic.vector_store import VectorStore
 
             vector_store = VectorStore(index_path)
@@ -285,7 +285,8 @@ class HybridSearchEngine:
             else:
                 profile = "code"  # Default fallback
 
-            embedder = Embedder(profile=profile)
+            # Use cached embedder (singleton) for performance
+            embedder = get_embedder(profile=profile)
 
             # Generate query embedding
             query_embedding = embedder.embed_single(query)
diff --git a/codex-lens/src/codexlens/semantic/embedder.py b/codex-lens/src/codexlens/semantic/embedder.py
index 4366b0a8..bd3a903c 100644
--- a/codex-lens/src/codexlens/semantic/embedder.py
+++ b/codex-lens/src/codexlens/semantic/embedder.py
@@ -2,11 +2,57 @@
 
 from __future__ import annotations
 
-from typing import Iterable, List
+import threading
+from typing import Dict, Iterable, List, Optional
 
 from . import SEMANTIC_AVAILABLE
 
 
+# Global embedder cache for singleton pattern
+_embedder_cache: Dict[str, "Embedder"] = {}
+_cache_lock = threading.Lock()
+
+
+def get_embedder(profile: str = "code") -> "Embedder":
+    """Get or create a cached Embedder instance (thread-safe singleton).
+
+    This function provides significant performance improvement by reusing
+    Embedder instances across multiple searches, avoiding repeated model
+    loading overhead (~0.8s per load).
+
+    Args:
+        profile: Model profile ("fast", "code", "multilingual", "balanced")
+
+    Returns:
+        Cached Embedder instance for the given profile
+    """
+    global _embedder_cache
+
+    # Fast path: check cache without lock
+    if profile in _embedder_cache:
+        return _embedder_cache[profile]
+
+    # Slow path: acquire lock for initialization
+    with _cache_lock:
+        # Double-check after acquiring lock
+        if profile in _embedder_cache:
+            return _embedder_cache[profile]
+
+        # Create new embedder and cache it
+        embedder = Embedder(profile=profile)
+        # Pre-load model to ensure it's ready
+        embedder._load_model()
+        _embedder_cache[profile] = embedder
+        return embedder
+
+
+def clear_embedder_cache() -> None:
+    """Clear the embedder cache (useful for testing or memory management)."""
+    global _embedder_cache
+    with _cache_lock:
+        _embedder_cache.clear()
+
+
 class Embedder:
     """Generate embeddings for code chunks using fastembed (ONNX-based).