Add comprehensive tests for schema cleanup migration and search comparison

- Implement tests for migration 005 to verify removal of deprecated fields in the database schema.
- Ensure that new databases are created with a clean schema.
- Validate that keywords are correctly extracted from the normalized file_keywords table.
- Test symbol insertion without deprecated fields and subdir operations without direct_files.
- Create a detailed search comparison test to evaluate vector search vs hybrid search performance.
- Add a script for reindexing projects to extract code relationships and verify GraphAnalyzer functionality.
- Include a test script to check TreeSitter parser availability and relationship extraction from sample files.

ccw/src/templates/dashboard-js/components/cli-status.js

@@ -15,6 +15,9 @@ let smartContextMaxFiles = parseInt(localStorage.getItem('ccw-smart-context-max-
 // Native Resume settings
 let nativeResumeEnabled = localStorage.getItem('ccw-native-resume') !== 'false'; // default true
 
+// Recursive Query settings (for hierarchical storage aggregation)
+let recursiveQueryEnabled = localStorage.getItem('ccw-recursive-query') !== 'false'; // default true
+
 // LLM Enhancement settings for Semantic Search
 let llmEnhancementSettings = {
   enabled: localStorage.getItem('ccw-llm-enhancement-enabled') === 'true',
@@ -26,12 +29,51 @@ let llmEnhancementSettings = {
 
 // ========== Initialization ==========
 function initCliStatus() {
-  // Load CLI status on init
-  loadCliToolStatus();
-  loadCodexLensStatus();
+  // Load all statuses in one call using aggregated endpoint
+  loadAllStatuses();
 }
 
 // ========== Data Loading ==========
+/**
+ * Load all statuses using aggregated endpoint (single API call)
+ */
+async function loadAllStatuses() {
+  try {
+    const response = await fetch('/api/status/all');
+    if (!response.ok) throw new Error('Failed to load status');
+    const data = await response.json();
+
+    // Update all status data
+    cliToolStatus = data.cli || { gemini: {}, qwen: {}, codex: {}, claude: {} };
+    codexLensStatus = data.codexLens || { ready: false };
+    semanticStatus = data.semantic || { available: false };
+
+    // Update badges
+    updateCliBadge();
+    updateCodexLensBadge();
+
+    return data;
+  } catch (err) {
+    console.error('Failed to load aggregated status:', err);
+    // Fallback to individual calls if aggregated endpoint fails
+    return await loadAllStatusesFallback();
+  }
+}
+
+/**
+ * Fallback: Load statuses individually if aggregated endpoint fails
+ */
+async function loadAllStatusesFallback() {
+  console.warn('[CLI Status] Using fallback individual API calls');
+  await Promise.all([
+    loadCliToolStatus(),
+    loadCodexLensStatus()
+  ]);
+}
+
+/**
+ * Legacy: Load CLI tool status individually
+ */
 async function loadCliToolStatus() {
   try {
     const response = await fetch('/api/cli/status');
@@ -49,6 +91,9 @@ async function loadCliToolStatus() {
   }
 }
 
+/**
+ * Legacy: Load CodexLens status individually
+ */
 async function loadCodexLensStatus() {
   try {
     const response = await fetch('/api/codexlens/status');
@@ -71,6 +116,9 @@ async function loadCodexLensStatus() {
   }
 }
 
+/**
+ * Legacy: Load semantic status individually
+ */
 async function loadSemanticStatus() {
   try {
     const response = await fetch('/api/codexlens/semantic/status');
@@ -223,7 +271,7 @@ function renderCliStatus() {
           <div class="flex items-center justify-between w-full mt-1">
             <div class="flex items-center gap-1 text-xs text-muted-foreground">
               <i data-lucide="hard-drive" class="w-3 h-3"></i>
-              <span>~500MB</span>
+              <span>~130MB</span>
             </div>
             <button class="btn-sm btn-outline flex items-center gap-1" onclick="event.stopPropagation(); openSemanticSettingsModal()">
               <i data-lucide="settings" class="w-3 h-3"></i>
@@ -377,8 +425,14 @@ function setNativeResumeEnabled(enabled) {
   showRefreshToast(`Native Resume ${enabled ? 'enabled' : 'disabled'}`, 'success');
 }
 
+function setRecursiveQueryEnabled(enabled) {
+  recursiveQueryEnabled = enabled;
+  localStorage.setItem('ccw-recursive-query', enabled.toString());
+  showRefreshToast(`Recursive Query ${enabled ? 'enabled' : 'disabled'}`, 'success');
+}
+
 async function refreshAllCliStatus() {
-  await Promise.all([loadCliToolStatus(), loadCodexLensStatus()]);
+  await loadAllStatuses();
   renderCliStatus();
 }
 
@@ -779,6 +833,9 @@ async function initCodexLensIndex() {
       } else {
         showRefreshToast(`Index created: ${files} files, ${dirs} directories`, 'success');
         console.log('[CodexLens] Index created successfully');
+
+        // Reload CodexLens status and refresh the view
+        loadCodexLensStatus().then(() => renderCliStatus());
       }
     } else {
       showRefreshToast(`Init failed: ${result.error}`, 'error');
@@ -820,19 +877,15 @@ function openSemanticInstallWizard() {
                 <i data-lucide="check" class="w-4 h-4 text-success mt-0.5"></i>
                 <span><strong>bge-small-en-v1.5</strong> - Embedding model (~130MB)</span>
               </li>
-              <li class="flex items-start gap-2">
-                <i data-lucide="check" class="w-4 h-4 text-success mt-0.5"></i>
-                <span><strong>PyTorch</strong> - Deep learning backend (~300MB)</span>
-              </li>
             </ul>
           </div>
 
-          <div class="bg-warning/10 border border-warning/20 rounded-lg p-3">
+          <div class="bg-primary/10 border border-primary/20 rounded-lg p-3">
             <div class="flex items-start gap-2">
-              <i data-lucide="alert-triangle" class="w-4 h-4 text-warning mt-0.5"></i>
+              <i data-lucide="info" class="w-4 h-4 text-primary mt-0.5"></i>
               <div class="text-sm">
-                <p class="font-medium text-warning">Large Download</p>
-                <p class="text-muted-foreground">Total size: ~500MB. First-time model loading may take a few minutes.</p>
+                <p class="font-medium text-primary">Download Size</p>
+                <p class="text-muted-foreground">Total size: ~130MB. First-time model loading may take a few minutes.</p>
               </div>
             </div>
           </div>
@@ -887,11 +940,10 @@ async function startSemanticInstall() {
 
   // Simulate progress stages
   const stages = [
-    { progress: 10, text: 'Installing numpy...' },
-    { progress: 30, text: 'Installing sentence-transformers...' },
-    { progress: 50, text: 'Installing PyTorch dependencies...' },
-    { progress: 70, text: 'Downloading embedding model...' },
-    { progress: 90, text: 'Finalizing installation...' }
+    { progress: 20, text: 'Installing sentence-transformers...' },
+    { progress: 50, text: 'Downloading embedding model...' },
+    { progress: 80, text: 'Setting up model cache...' },
+    { progress: 95, text: 'Finalizing installation...' }
   ];
 
   let currentStage = 0;

ccw/src/templates/dashboard-js/components/hook-manager.js

@@ -235,6 +235,35 @@ async function loadHookConfig() {
   }
 }
 
+async function loadAvailableSkills() {
+  try {
+    const response = await fetch('/api/skills?path=' + encodeURIComponent(projectPath));
+    if (!response.ok) throw new Error('Failed to load skills');
+    const data = await response.json();
+
+    // Combine project and user skills
+    const projectSkills = (data.projectSkills || []).map(s => ({
+      name: s.name,
+      path: s.path,
+      scope: 'project'
+    }));
+    const userSkills = (data.userSkills || []).map(s => ({
+      name: s.name,
+      path: s.path,
+      scope: 'user'
+    }));
+
+    // Store in window for access by wizard
+    window.availableSkills = [...projectSkills, ...userSkills];
+
+    return window.availableSkills;
+  } catch (err) {
+    console.error('Failed to load available skills:', err);
+    window.availableSkills = [];
+    return [];
+  }
+}
+
 /**
  * Convert internal hook format to Claude Code format
  * Internal: { command, args, matcher, timeout }
@@ -510,7 +539,7 @@ function getHookEventIconLucide(event) {
 let currentWizardTemplate = null;
 let wizardConfig = {};
 
-function openHookWizardModal(wizardId) {
+async function openHookWizardModal(wizardId) {
   const wizard = WIZARD_TEMPLATES[wizardId];
   if (!wizard) {
     showRefreshToast('Wizard template not found', 'error');
@@ -530,6 +559,11 @@ function openHookWizardModal(wizardId) {
     wizardConfig.selectedOptions = [];
   }
 
+  // Ensure available skills are loaded for SKILL context wizard
+  if (wizardId === 'skill-context' && typeof window.availableSkills === 'undefined') {
+    await loadAvailableSkills();
+  }
+
   const modal = document.getElementById('hookWizardModal');
   if (modal) {
     renderWizardModalContent();
@@ -792,9 +826,19 @@ function renderSkillContextConfig() {
   const availableSkills = window.availableSkills || [];
 
   if (selectedOption === 'auto') {
-    const skillBadges = availableSkills.map(function(s) {
-      return '<span class="px-1.5 py-0.5 bg-emerald-500/10 text-emerald-500 rounded text-xs">' + escapeHtml(s.name) + '</span>';
-    }).join(' ');
+    let skillBadges = '';
+    if (typeof window.availableSkills === 'undefined') {
+      // Still loading
+      skillBadges = '<span class="px-1.5 py-0.5 bg-muted text-muted-foreground rounded text-xs">' + t('common.loading') + '...</span>';
+    } else if (availableSkills.length === 0) {
+      // No skills found
+      skillBadges = '<span class="px-1.5 py-0.5 bg-warning/10 text-warning rounded text-xs">' + t('hook.wizard.noSkillsFound') + '</span>';
+    } else {
+      // Skills found
+      skillBadges = availableSkills.map(function(s) {
+        return '<span class="px-1.5 py-0.5 bg-emerald-500/10 text-emerald-500 rounded text-xs">' + escapeHtml(s.name) + '</span>';
+      }).join(' ');
+    }
     return '<div class="bg-muted/30 rounded-lg p-4 text-sm text-muted-foreground">' +
       '<div class="flex items-center gap-2 mb-2">' +
         '<i data-lucide="info" class="w-4 h-4"></i>' +
@@ -814,10 +858,15 @@ function renderSkillContextConfig() {
     '</div>';
   } else {
     configListHtml = skillConfigs.map(function(config, idx) {
-      var skillOptions = availableSkills.map(function(s) {
-        var selected = config.skill === s.id ? 'selected' : '';
-        return '<option value="' + s.id + '" ' + selected + '>' + escapeHtml(s.name) + '</option>';
-      }).join('');
+      var skillOptions = '';
+      if (availableSkills.length === 0) {
+        skillOptions = '<option value="" disabled>' + t('hook.wizard.noSkillsFound') + '</option>';
+      } else {
+        skillOptions = availableSkills.map(function(s) {
+          var selected = config.skill === s.name ? 'selected' : '';
+          return '<option value="' + escapeHtml(s.name) + '" ' + selected + '>' + escapeHtml(s.name) + '</option>';
+        }).join('');
+      }
       return '<div class="border border-border rounded-lg p-3 bg-card">' +
         '<div class="flex items-center justify-between mb-2">' +
           '<select onchange="updateSkillConfig(' + idx + ', \'skill\', this.value)" ' +

ccw/src/templates/dashboard-js/components/mcp-manager.js

@@ -1113,6 +1113,10 @@ async function installCcwToolsMcpToCodex() {
 
     await addCodexMcpServer('ccw-tools', ccwToolsConfig);
 
+    // Reload MCP configuration and refresh the view
+    await loadMcpConfig();
+    renderMcpManager();
+
     const resultLabel = isUpdate ? 'updated in' : 'installed to';
     showRefreshToast(`CCW Tools ${resultLabel} Codex (${selectedTools.length} tools)`, 'success');
   } catch (err) {

ccw/src/templates/dashboard-js/components/navigation.js

@@ -293,8 +293,9 @@ function showRefreshToast(message, type) {
   toast.textContent = message;
   document.body.appendChild(toast);
 
+  // Increase display time to 3.5 seconds for better visibility
   setTimeout(() => {
     toast.classList.add('fade-out');
     setTimeout(() => toast.remove(), 300);
-  }, 2000);
+  }, 3500);
 }