diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 2ebe165..36aff72 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -40,14 +40,12 @@ The following instructions are only to be applied when performing a code review.
 * [ ] Encourage the use of `tools`, but it's not required.
 * [ ] Strongly encourage the use of `model` to specify the model that the chat mode is optimised for.
 
-
 ## Branching Policy
 
-- Always create a new branch for each task, feature, or fix.
-- Use the following naming conventions:
-	- `feature/<short-description>`
-	- `bugfix/<short-description>`
-	- `task/<short-description>`
-- Never commit changes directly to the `main` or default branch.
-- After completing changes, push the branch and open a pull request for review and merging.
+* [ ] Always create a new branch for each task or issue you are working on.
+* [ ] Use descriptive branch names following the convention: `feature/description`, `fix/description`, or `docs/description`.
+* [ ] Never commit directly to the `main` branch.
+* [ ] Always open a pull request for code changes, even for small updates.
+* [ ] Ensure your branch is up to date with `main` before opening a pull request.
+* [ ] Delete the branch after the pull request is merged.
 
diff --git a/.vscode/settings.json b/.vscode/settings.json
index c01085e..95e8122 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,11 +1,14 @@
 {
   "chat.modeFilesLocations": {
-    "chatmodes": true
+    "chatmodes": true,
+    ".github/chatmodes": true
   },
   "chat.promptFilesLocations": {
-    "prompts": true
+    "prompts": true,
+    ".github/prompts": true
   },
   "chat.instructionsFilesLocations": {
-    "instructions": true
+    "instructions": true,
+    ".github/instructions": true
   }
-}
+}
\ No newline at end of file
diff --git a/apply-config.js b/apply-config.js
index b1e5c65..8465d51 100755
--- a/apply-config.js
+++ b/apply-config.js
@@ -101,36 +101,40 @@ async function applyConfig(configPath = "awesome-copilot.config.yml") {
   };
 
   // Import config manager for effective state computation
-  const { computeEffectiveItemStates } = require("./config-manager");
+  const { getEffectivelyEnabledItems } = require("./config-manager");
 
-  // Compute effective states using precedence rules
-  const effectiveStates = computeEffectiveItemStates(config);
+  // Get precomputed sets of effectively enabled items for O(1) performance
+  const effectivelyEnabledSets = getEffectivelyEnabledItems(config);
 
-  // Create sets of effectively enabled items for performance
-  const effectivelyEnabledSets = {
-    prompts: new Set(),
-    instructions: new Set(),
-    chatmodes: new Set()
-  };
-
-  for (const section of ["prompts", "instructions", "chatmodes"]) {
-    for (const [itemName, state] of Object.entries(effectiveStates[section])) {
-      if (state.enabled) {
-        effectivelyEnabledSets[section].add(itemName);
-      }
-    }
-  }
-
-  // Count enabled collections for summary
+  // Count effectively enabled collections for summary
+  // A collection is effectively enabled if it contributes any enabled items
   if (config.collections) {
-    for (const [collectionName, enabled] of Object.entries(config.collections)) {
-      if (enabled) {
+    for (const [collectionName, configEnabled] of Object.entries(config.collections)) {
+      if (configEnabled) {
         const collectionPath = path.join(rootDir, "collections", `${collectionName}.collection.yml`);
         if (fs.existsSync(collectionPath)) {
           const collection = parseCollectionYaml(collectionPath);
           if (collection && collection.items) {
-            summary.collections++;
-            console.log(`✓ Enabled collection: ${collectionName} (${collection.items.length} items)`);
+            // Check if this collection contributes any effectively enabled items
+            let hasEnabledItems = false;
+            for (const item of collection.items) {
+              const itemName = path.basename(item.path).replace(/\.(prompt|instructions|chatmode)\.md$/, '');
+              if (item.kind === "prompt" && effectivelyEnabledSets.prompts.has(itemName)) {
+                hasEnabledItems = true;
+                break;
+              } else if (item.kind === "instruction" && effectivelyEnabledSets.instructions.has(itemName)) {
+                hasEnabledItems = true;
+                break;
+              } else if (item.kind === "chat-mode" && effectivelyEnabledSets.chatmodes.has(itemName)) {
+                hasEnabledItems = true;
+                break;
+              }
+            }
+            
+            if (hasEnabledItems) {
+              summary.collections++;
+              console.log(`✓ Enabled collection: ${collectionName} (${collection.items.length} items)`);
+            }
           }
         }
       }
diff --git a/awesome-copilot.js b/awesome-copilot.js
index 15580e7..4784e95 100755
--- a/awesome-copilot.js
+++ b/awesome-copilot.js
@@ -149,8 +149,16 @@ function handleListCommand(rawArgs) {
     const availableItems = getAllAvailableItems(section);
     
     // Count effectively enabled items
-    const effectivelyEnabled = Object.values(effectiveStates[section] || {})
-      .filter(state => state.enabled).length;
+    let effectivelyEnabled;
+    if (section === "collections") {
+      // For collections, count explicitly enabled ones
+      effectivelyEnabled = Object.values(sanitizedConfig[section] || {})
+        .filter(value => value === true).length;
+    } else {
+      // For other sections, count effectively enabled items
+      effectivelyEnabled = Object.values(effectiveStates[section] || {})
+        .filter(state => state.enabled).length;
+    }
     
     const { totalCharacters } = calculateSectionFootprint(section, sanitizedConfig[section]);
     const headingParts = [
@@ -170,20 +178,40 @@ function handleListCommand(rawArgs) {
 
     // Show items with effective state and reason
     if (section === "collections") {
-      // Collections show simple enabled/disabled
+      // Collections show simple enabled/disabled with count of effectively enabled items
       availableItems.forEach(itemName => {
         const isEnabled = Boolean(sanitizedConfig[section]?.[itemName]);
-        console.log(`  [${isEnabled ? "✓" : " "}] ${itemName}`);
+        
+        // Count how many items this collection would enable
+        let enabledCount = 0;
+        if (isEnabled) {
+          // Simulate what would happen if only this collection was enabled
+          const testConfig = { collections: { [itemName]: true } };
+          const testEffectiveStates = computeEffectiveItemStates(testConfig);
+          
+          for (const sectionName of ["prompts", "instructions", "chatmodes"]) {
+            enabledCount += Object.values(testEffectiveStates[sectionName] || {})
+              .filter(state => state.enabled && state.reason === "collection").length;
+          }
+        }
+        
+        const countText = isEnabled ? ` (${enabledCount} items effectively enabled)` : "";
+        console.log(`  [${isEnabled ? "✓" : " "}] ${itemName}${countText}`);
       });
     } else {
-      // Other sections show effective state with reason
+      // Other sections show effective state with detailed reason
       availableItems.forEach(itemName => {
         const effectiveState = effectiveStates[section]?.[itemName];
         if (effectiveState) {
           const symbol = effectiveState.enabled ? "✓" : " ";
-          const reasonText = effectiveState.reason === "explicit" 
-            ? ` (${effectiveState.reason})`
-            : effectiveState.enabled ? ` (${effectiveState.reason})` : "";
+          let reasonText = "";
+          
+          if (effectiveState.reason === "explicit") {
+            reasonText = ` (explicit:${effectiveState.enabled})`;
+          } else if (effectiveState.reason === "collection" && effectiveState.collections && effectiveState.collections.length > 0) {
+            reasonText = ` (via:[${effectiveState.collections.join(',')}])`;
+          }
+          
           console.log(`  [${symbol}] ${itemName}${reasonText}`);
         } else {
           console.log(`  [ ] ${itemName}`);
diff --git a/config-manager.js b/config-manager.js
index d1b6a10..fbc2cb7 100644
--- a/config-manager.js
+++ b/config-manager.js
@@ -101,6 +101,11 @@ function toBoolean(value) {
     if (normalized === "false") return false;
   }
 
+  // Preserve undefined as undefined for "no explicit override"
+  if (value === undefined) {
+    return undefined;
+  }
+
   return Boolean(value);
 }
 
@@ -185,11 +190,17 @@ function generateConfigHash(config) {
  * Compute effective item states respecting explicit overrides over collections
  * 
  * This function builds membership maps per section and returns effectively enabled items with reasons.
- * It uses the following precedence rules:
- * 1. Explicit true/false overrides everything (highest priority)
+ * It uses strict comparisons to ensure undefined values are never treated as explicitly disabled.
+ * 
+ * Precedence rules with strict undefined handling:
+ * 1. Explicit true/false overrides everything (highest priority) - uses strict === comparisons
  * 2. If undefined and enabled by collection, use true
  * 3. Otherwise, use false (disabled)
  * 
+ * CRITICAL: Only values that are strictly === false are treated as explicitly disabled.
+ * undefined, null, 0, '', or other falsy values are NOT treated as explicit disabling.
+ * This allows collections to enable items that are not explicitly configured.
+ * 
  * @param {Object} config - Configuration object with sections
  * @returns {Object} Effective states for each section with { itemName: { enabled: boolean, reason: string } }
  *                   Reason can be: 'explicit', 'collection', or 'disabled'
@@ -203,14 +214,21 @@ function computeEffectiveItemStates(config) {
     chatmodes: {}
   };
 
-  // Build membership maps: Map<itemName, Set<collectionName>> per section for O(1) lookups
+  // Build detailed membership maps: Map<itemName, Set<collectionName>> per section
+  const collectionMemberships = {
+    prompts: new Map(),
+    instructions: new Map(),
+    chatmodes: new Map()
+  };
+
+  // Build simple enabled sets for O(1) lookups
   const collectionEnabledItems = {
     prompts: new Set(),
     instructions: new Set(),
     chatmodes: new Set()
   };
 
-  // Identify enabled collections per section
+  // Identify enabled collections per section and track memberships
   if (config.collections) {
     for (const [collectionName, enabled] of Object.entries(config.collections)) {
       if (enabled === true) {
@@ -222,12 +240,24 @@ function computeEffectiveItemStates(config) {
               // Extract item name from path - remove directory and all extensions
               const itemName = path.basename(item.path).replace(/\.(prompt|instructions|chatmode)\.md$/, '');
 
+              let sectionName;
               if (item.kind === "prompt") {
-                collectionEnabledItems.prompts.add(itemName);
+                sectionName = "prompts";
               } else if (item.kind === "instruction") {
-                collectionEnabledItems.instructions.add(itemName);
+                sectionName = "instructions";
               } else if (item.kind === "chat-mode") {
-                collectionEnabledItems.chatmodes.add(itemName);
+                sectionName = "chatmodes";
+              }
+
+              if (sectionName) {
+                // Track which collections enable this item
+                if (!collectionMemberships[sectionName].has(itemName)) {
+                  collectionMemberships[sectionName].set(itemName, new Set());
+                }
+                collectionMemberships[sectionName].get(itemName).add(collectionName);
+                
+                // Add to enabled set for O(1) lookups
+                collectionEnabledItems[sectionName].add(itemName);
               }
             });
           }
@@ -247,27 +277,35 @@ function computeEffectiveItemStates(config) {
     for (const itemName of availableItems) {
       const explicitValue = sectionConfig[itemName];
       const isEnabledByCollection = collectionEnabled.has(itemName);
+      const enablingCollections = collectionMemberships[section].get(itemName) || new Set();
 
-      // Precedence rules:
-      // 1. If explicitly set to true or false, use that value
+      // Precedence rules with strict undefined handling:
+      // 1. If explicitly set to true or false, use that value (highest priority)
       // 2. If undefined and enabled by collection, use true
-      // 3. Otherwise, use false
+      // 3. Otherwise, use false (disabled)
+      //
+      // IMPORTANT: Only strict === false comparisons are used to determine explicit disabling.
+      // undefined values are NEVER treated as explicitly disabled, allowing collections to enable them.
 
       let enabled = false;
       let reason = "disabled";
+      let collections = [];
 
       if (explicitValue === true) {
         enabled = true;
         reason = "explicit";
       } else if (explicitValue === false) {
+        // Strict comparison ensures only explicit false disables items
         enabled = false;
         reason = "explicit";
       } else if (explicitValue === undefined && isEnabledByCollection) {
+        // undefined values can be enabled by collections (not treated as disabled)
         enabled = true;
         reason = "collection";
+        collections = Array.from(enablingCollections).sort();
       }
 
-      effectiveStates[section][itemName] = { enabled, reason };
+      effectiveStates[section][itemName] = { enabled, reason, collections };
     }
   }
 
@@ -303,6 +341,93 @@ function getEffectivelyEnabledItems(config) {
   return result;
 }
 
+/**
+ * Toggle a collection's enabled state without modifying individual item flags
+ * 
+ * This function implements the core requirement from TASK-003:
+ * - Only modifies the collection's enabled flag
+ * - Never writes to per-item flags (e.g., config.prompts[item] = enabled)  
+ * - Returns summary information for CLI feedback
+ * - Preserves all existing explicit per-item overrides
+ * 
+ * @param {Object} config - Configuration object with collections section
+ * @param {string} name - Collection name to toggle
+ * @param {boolean} enabled - Desired enabled state for the collection
+ * @returns {Object} Summary object with delta information for CLI feedback
+ */
+function toggleCollection(config, name, enabled) {
+  // Validate inputs
+  if (!config || typeof config !== 'object') {
+    throw new Error('Config object is required');
+  }
+  if (!name || typeof name !== 'string') {
+    throw new Error('Collection name is required');
+  }
+  if (typeof enabled !== 'boolean') {
+    throw new Error('Enabled state must be a boolean');
+  }
+
+  // Ensure collections section exists
+  if (!config.collections) {
+    config.collections = {};
+  }
+
+  // Get current state
+  const currentState = Boolean(config.collections[name]);
+  
+  // Check if collection exists (has a .collection.yml file)
+  const collectionPath = path.join(__dirname, "collections", `${name}.collection.yml`);
+  if (!fs.existsSync(collectionPath)) {
+    throw new Error(`Collection '${name}' does not exist`);
+  }
+
+  // If state is already the desired state, return early
+  if (currentState === enabled) {
+    return {
+      changed: false,
+      collectionName: name,
+      currentState: currentState,
+      newState: enabled,
+      delta: { enabled: [], disabled: [] },
+      message: `Collection '${name}' is already ${enabled ? 'enabled' : 'disabled'}.`
+    };
+  }
+
+  // Compute effective states before the change
+  const effectiveStatesBefore = computeEffectiveItemStates(config);
+
+  // CORE REQUIREMENT: Only modify the collection's enabled flag
+  // Never write to per-item flags (config.prompts[item] = enabled)
+  config.collections[name] = enabled;
+
+  // Compute effective states after the change
+  const effectiveStatesAfter = computeEffectiveItemStates(config);
+
+  // Calculate delta summary for CLI feedback
+  const delta = { enabled: [], disabled: [] };
+  for (const sectionName of ["prompts", "instructions", "chatmodes"]) {
+    for (const item of getAllAvailableItems(sectionName)) {
+      const beforeState = effectiveStatesBefore[sectionName]?.[item]?.enabled || false;
+      const afterState = effectiveStatesAfter[sectionName]?.[item]?.enabled || false;
+      
+      if (!beforeState && afterState) {
+        delta.enabled.push(`${sectionName}/${item}`);
+      } else if (beforeState && !afterState) {
+        delta.disabled.push(`${sectionName}/${item}`);
+      }
+    }
+  }
+
+  return {
+    changed: true,
+    collectionName: name,
+    currentState: currentState,
+    newState: enabled,
+    delta,
+    message: `${enabled ? 'Enabled' : 'Disabled'} collection '${name}'.`
+  };
+}
+
 module.exports = {
   DEFAULT_CONFIG_PATH,
   CONFIG_SECTIONS,
@@ -316,5 +441,6 @@ module.exports = {
   getAllAvailableItems,
   computeEffectiveItemStates,
   getEffectivelyEnabledItems,
-  generateConfigHash
+  generateConfigHash,
+  toggleCollection
 };
diff --git a/test-all.js b/test-all.js
index 8c4ead0..5431778 100644
--- a/test-all.js
+++ b/test-all.js
@@ -8,6 +8,7 @@ const { runTests: runUnitTests } = require('./test-effective-states');
 const { runTests: runIntegrationTests } = require('./test-integration');
 const { runTests: runCliTests } = require('./test-cli');
 const { runTests: runApplyTests } = require('./test-apply-effective');
+const { runTests: runToggleCollectionTests } = require('./test-toggle-collection');
 
 async function runAllTests() {
   console.log('🧪 Running Awesome Copilot Comprehensive Test Suite\n');
@@ -17,7 +18,8 @@ async function runAllTests() {
     unit: false,
     integration: false,
     cli: false,
-    apply: false
+    apply: false,
+    toggleCollection: false
   };
 
   try {
@@ -52,6 +54,14 @@ async function runAllTests() {
     console.error('Apply tests failed with error:', error.message);
   }
 
+  try {
+    console.log('\n🔧 Toggle Collection Tests (TASK-003)');
+    console.log('-'.repeat(36));
+    results.toggleCollection = await runToggleCollectionTests();
+  } catch (error) {
+    console.error('Toggle collection tests failed with error:', error.message);
+  }
+
   try {
     console.log('\n🤖 Repository Instructions Tests');
     console.log('-'.repeat(33));
@@ -71,6 +81,7 @@ async function runAllTests() {
     { name: 'Integration Tests', result: results.integration, emoji: '🔄' },
     { name: 'CLI Tests', result: results.cli, emoji: '⌨️' },
     { name: 'Apply Tests', result: results.apply, emoji: '🎯' },
+    { name: 'Toggle Collection', result: results.toggleCollection, emoji: '🔧' },
     { name: 'Repo Instructions', result: results.repoInstructions, emoji: '🤖' }
   ];
 
diff --git a/test-cli.js b/test-cli.js
index 58a62f2..a3cfd90 100644
--- a/test-cli.js
+++ b/test-cli.js
@@ -92,7 +92,7 @@ async function runTests() {
     
     const result = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
     assert(result.success, 'List should succeed');
-    assert(result.stdout.includes('(collection)'), 'Should show collection reason');
+    assert(result.stdout.includes('(via:[testing-automation])'), 'Should show collection reason');
     assert(result.stdout.includes('[✓]'), 'Should show enabled items');
   });
 
@@ -105,7 +105,7 @@ async function runTests() {
     assert(result.success, 'Individual toggle should succeed');
     
     const listResult = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
-    assert(listResult.stdout.includes('playwright-generate-test (explicit)'), 
+    assert(listResult.stdout.includes('playwright-generate-test (explicit:false)'), 
            'Explicitly disabled item should show explicit reason');
   });
 
@@ -128,6 +128,209 @@ async function runTests() {
     assert(result.stdout.includes('already enabled'), 'Should indicate no change needed');
   });
 
+  // Test 8: Multiple collections effective states
+  await test("Multiple collections effective states", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    
+    // Enable two collections with potential overlap
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle collections csharp-dotnet-development on --config ${TEST_CONFIG}`);
+    
+    const result = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
+    assert(result.success, 'List should succeed');
+    
+    // Should show collection reason for items enabled by collection
+    assert(result.stdout.includes('(collection)'), 'Should show collection reason');
+    assert(result.stdout.includes('[✓]'), 'Should show enabled items');
+    
+    // Count should reflect enabled items from both collections
+    const enabledMatch = result.stdout.match(/Prompts \((\d+)\/\d+ enabled\)/);
+    assert(enabledMatch && parseInt(enabledMatch[1]) > 5, 'Should have multiple enabled prompts from collections');
+  });
+
+  // Test 9: Explicit overrides with collection conflicts
+  await test("Explicit overrides with collection conflicts", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    
+    // Override a collection item explicitly to off
+    await runCommand(`node awesome-copilot.js toggle prompts playwright-generate-test off --config ${TEST_CONFIG}`);
+    
+    const listResult = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
+    assert(listResult.success, 'List should succeed');
+    
+    // Should show explicit reason and disabled state
+    assert(listResult.stdout.includes('playwright-generate-test (explicit)'), 'Should show explicit reason');
+    assert(listResult.stdout.includes('[ ] playwright-generate-test'), 'Should show as disabled despite collection');
+    
+    // Other collection items should still show as enabled
+    assert(listResult.stdout.includes('[✓] playwright-explore-website (collection)'), 'Other collection items should remain enabled');
+  });
+
+  // Test 10: Delta summary accuracy with conflicts
+  await test("Delta summary accuracy with conflicts", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    
+    // Enable collection
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    
+    // Add explicit override to disable one item
+    await runCommand(`node awesome-copilot.js toggle prompts playwright-generate-test off --config ${TEST_CONFIG}`);
+    
+    // Disable the collection - should show accurate delta excluding explicit override
+    const result = await runCommand(`node awesome-copilot.js toggle collections testing-automation off --config ${TEST_CONFIG}`);
+    assert(result.success, 'Toggle should succeed');
+    assert(result.stdout.includes('Delta summary'), 'Should show delta summary');
+    assert(result.stdout.includes('items will be disabled'), 'Should show disabled items count');
+    
+    // Should not include the explicitly disabled item in the delta
+    const lines = result.stdout.split('\n');
+    const disabledItems = lines.filter(line => line.includes('    - prompts/'));
+    assert(!disabledItems.some(line => line.includes('playwright-generate-test')), 
+           'Should not show explicitly disabled item in delta');
+  });
+
+  // Test 11: Instructions and chatmodes effective states
+  await test("Instructions and chatmodes effective states", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    
+    // Test instructions
+    const instructionsResult = await runCommand(`node awesome-copilot.js list instructions --config ${TEST_CONFIG}`);
+    assert(instructionsResult.success, 'Instructions list should succeed');
+    assert(instructionsResult.stdout.includes('[✓] playwright-typescript (collection)'), 
+           'Instructions should show collection reason');
+    
+    // Test chatmodes
+    const chatmodesResult = await runCommand(`node awesome-copilot.js list chatmodes --config ${TEST_CONFIG}`);
+    assert(chatmodesResult.success, 'Chatmodes list should succeed');
+    assert(chatmodesResult.stdout.includes('[✓] tdd-red (collection)'), 
+           'Chatmodes should show collection reason');
+  });
+
+  // Test 12: Collections section display
+  await test("Collections section shows simple enabled/disabled", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    
+    const result = await runCommand(`node awesome-copilot.js list collections --config ${TEST_CONFIG}`);
+    assert(result.success, 'Collections list should succeed');
+    assert(result.stdout.includes('[✓] testing-automation'), 'Should show enabled collection');
+    assert(result.stdout.includes('[ ] csharp-dotnet-development'), 'Should show disabled collection');
+    
+    // Collections should not show reasons (unlike other sections)
+    assert(!result.stdout.includes('(explicit)'), 'Collections should not show reason text');
+    assert(!result.stdout.includes('(collection)'), 'Collections should not show reason text');
+  });
+
+  // Test 13: Output clarity and user-friendliness
+  await test("Output clarity and user-friendliness", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    
+    const result = await runCommand(`node awesome-copilot.js list --config ${TEST_CONFIG}`);
+    assert(result.success, 'List should succeed');
+    
+    // Should show counts (character estimates may or may not appear depending on content)
+    assert(result.stdout.includes('enabled'), 'Should show enabled counts');
+    
+    // Should show helpful usage message
+    assert(result.stdout.includes("Use 'awesome-copilot toggle'"), 'Should show usage instructions');
+    
+    // Should show clear section headers
+    assert(result.stdout.includes('Prompts'), 'Should show Prompts section');
+    assert(result.stdout.includes('Instructions'), 'Should show Instructions section');
+    assert(result.stdout.includes('Chat Modes'), 'Should show Chat Modes section');
+    assert(result.stdout.includes('Collections'), 'Should show Collections section');
+    
+    // Should show configuration path
+    assert(result.stdout.includes('Configuration:'), 'Should show configuration file path');
+  });
+
+  // Test 14: Complex scenario with multiple overrides
+  await test("Complex scenario with multiple overrides", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    
+    // Enable multiple collections
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle collections csharp-dotnet-development on --config ${TEST_CONFIG}`);
+    
+    // Add explicit overrides
+    await runCommand(`node awesome-copilot.js toggle prompts playwright-generate-test off --config ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle prompts create-readme on --config ${TEST_CONFIG}`);
+    
+    const result = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
+    assert(result.success, 'List should succeed');
+    
+    // Should show mixed states with correct reasons
+    assert(result.stdout.includes('[ ] playwright-generate-test (explicit)'), 'Should show explicit disable');
+    assert(result.stdout.includes('[✓] create-readme (explicit)'), 'Should show explicit enable');
+    assert(result.stdout.includes('(collection)'), 'Should show collection-enabled items');
+    
+    // Count should be accurate
+    const enabledMatch = result.stdout.match(/Prompts \((\d+)\/\d+ enabled\)/);
+    assert(enabledMatch, 'Should show enabled count');
+    
+    const enabledCount = parseInt(enabledMatch[1]);
+    assert(enabledCount > 8, 'Should have multiple items enabled from collections and explicit');
+  });
+
+  // Test 15: No misleading disabled messages for shared items
+  await test("No misleading disabled messages for shared items", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    
+    // Enable a collection that has items potentially shared with other collections
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    
+    // Toggle collection off and check delta summary
+    const result = await runCommand(`node awesome-copilot.js toggle collections testing-automation off --config ${TEST_CONFIG}`);
+    assert(result.success, 'Toggle should succeed');
+    
+    // Should show accurate delta - items should be listed as will be disabled
+    // since they're not enabled by other collections in this test
+    assert(result.stdout.includes('Delta summary'), 'Should show delta summary');
+    assert(result.stdout.includes('items will be disabled'), 'Should show disabled items count');
+    
+    // Verify the messaging is clear and not misleading
+    const lines = result.stdout.split('\n');
+    const deltaLines = lines.filter(line => line.includes('+ ') || line.includes('- '));
+    assert(deltaLines.length > 0, 'Should show specific items in delta');
+  });
+
+  // Test 16: Membership and counts verification
+  await test("Membership and counts verification", async () => {
+    await runCommand(`node awesome-copilot.js init ${TEST_CONFIG}`);
+    
+    // Enable collection and add explicit overrides
+    await runCommand(`node awesome-copilot.js toggle collections testing-automation on --config ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle prompts playwright-generate-test off --config ${TEST_CONFIG}`);
+    await runCommand(`node awesome-copilot.js toggle prompts create-readme on --config ${TEST_CONFIG}`);
+    
+    // Get all section results
+    const promptsResult = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
+    const instructionsResult = await runCommand(`node awesome-copilot.js list instructions --config ${TEST_CONFIG}`);
+    const chatmodesResult = await runCommand(`node awesome-copilot.js list chatmodes --config ${TEST_CONFIG}`);
+    
+    // Verify counts are accurate and consistent
+    const promptsMatch = promptsResult.stdout.match(/Prompts \((\d+)\/(\d+) enabled\)/);
+    const instructionsMatch = instructionsResult.stdout.match(/Instructions \((\d+)\/(\d+) enabled\)/);
+    const chatmodesMatch = chatmodesResult.stdout.match(/Chat Modes \((\d+)\/(\d+) enabled\)/);
+    
+    assert(promptsMatch, 'Should show prompts count');
+    assert(instructionsMatch, 'Should show instructions count');  
+    assert(chatmodesMatch, 'Should show chatmodes count');
+    
+    // Counts should be reasonable for testing-automation collection
+    assert(parseInt(promptsMatch[1]) >= 4, 'Should have reasonable prompts enabled');
+    assert(parseInt(instructionsMatch[1]) >= 2, 'Should have reasonable instructions enabled');
+    assert(parseInt(chatmodesMatch[1]) >= 3, 'Should have reasonable chatmodes enabled');
+    
+    // Total items should be consistent
+    assert(parseInt(promptsMatch[2]) > 80, 'Should show total prompts available');
+    assert(parseInt(instructionsMatch[2]) > 70, 'Should show total instructions available');
+    assert(parseInt(chatmodesMatch[2]) > 50, 'Should show total chatmodes available');
+  });
+
   console.log(`\nCLI Test Results: ${passedTests}/${totalTests} passed`);
   
   cleanup(); // Final cleanup
diff --git a/test-effective-config.yml b/test-effective-config.yml
deleted file mode 100644
index 3187a8d..0000000
--- a/test-effective-config.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-# Awesome Copilot Configuration File
-# Manual test for effective state computation
-#
-# Testing precedence rules with undefined values
-
-version: "1.0"
-project:
-  name: "Test Project"
-  description: "Testing effective state precedence"
-  output_directory: ".github"
-collections:
-  testing-automation: false
-prompts:
-  ai-prompt-engineering-safety-review: false
-  playwright-generate-test: true
-instructions:
-chatmodes:
diff --git a/test-effective-states.js b/test-effective-states.js
index 621f04b..4755d7c 100644
--- a/test-effective-states.js
+++ b/test-effective-states.js
@@ -164,7 +164,50 @@ function runTests() {
            'Chat mode should be enabled by collection');
   });
 
-  // Test 8: getEffectivelyEnabledItems returns Sets format
+  // Test 9: TASK-006 - Strict false checks prevent undefined treated as disabled
+  test("TASK-006: Strict false checks prevent undefined treated as disabled", () => {
+    const config = {
+      prompts: {
+        'explicit-false-item': false,
+        'explicit-true-item': true,
+        // 'undefined-item' is undefined (not set)
+      },
+      collections: {
+        'testing-automation': true
+      }
+    };
+    const result = computeEffectiveItemStates(config);
+    
+    // Explicit false should be disabled with reason 'explicit'
+    const explicitFalse = result.prompts['explicit-false-item'];
+    if (explicitFalse) {
+      assert(explicitFalse.reason === 'explicit' && !explicitFalse.enabled,
+             'Items with explicit false should be disabled with reason explicit');
+    }
+    
+    // Explicit true should be enabled with reason 'explicit'  
+    const explicitTrue = result.prompts['explicit-true-item'];
+    if (explicitTrue) {
+      assert(explicitTrue.reason === 'explicit' && explicitTrue.enabled,
+             'Items with explicit true should be enabled with reason explicit');
+    }
+    
+    // Undefined item in collection should be enabled with reason 'collection'
+    const undefinedInCollection = result.prompts['playwright-generate-test'];
+    if (undefinedInCollection) {
+      assert(undefinedInCollection.reason === 'collection' && undefinedInCollection.enabled,
+             'Undefined items should be enabled by collections, not treated as explicitly disabled');
+    }
+    
+    // Undefined item NOT in collection should be disabled with reason 'disabled' (not 'explicit')
+    const undefinedNotInCollection = result.prompts['some-random-item-not-in-any-collection'];
+    if (undefinedNotInCollection) {
+      assert(undefinedNotInCollection.reason === 'disabled' && !undefinedNotInCollection.enabled,
+             'Undefined items not in collections should have reason disabled, not explicit');
+    }
+  });
+
+  // Test 10: getEffectivelyEnabledItems returns Sets format
   test("getEffectivelyEnabledItems returns Sets format", () => {
     const config = {
       prompts: {
@@ -214,6 +257,37 @@ function runTests() {
     assert(result.prompts.size > 0, 'Should have enabled prompts');
   });
 
+  // Test 10: Undefined values are not treated as explicitly disabled (TASK-004)
+  test("Undefined values are not treated as explicitly disabled", () => {
+    const config = {
+      prompts: {
+        'playwright-generate-test': true,   // explicit true
+        'csharp-nunit': false,             // explicit false
+        // 'playwright-explore-website' is undefined (not mentioned)
+      },
+      collections: {
+        'testing-automation': true
+      }
+    };
+    
+    const result = computeEffectiveItemStates(config);
+    
+    // Explicit true should be explicit
+    const explicitTrue = result.prompts['playwright-generate-test'];
+    assert(explicitTrue && explicitTrue.enabled && explicitTrue.reason === 'explicit',
+           'Explicit true should be enabled with explicit reason');
+    
+    // Explicit false should be explicit (strict === false comparison)
+    const explicitFalse = result.prompts['csharp-nunit'];
+    assert(explicitFalse && !explicitFalse.enabled && explicitFalse.reason === 'explicit',
+           'Explicit false should be disabled with explicit reason');
+    
+    // Undefined should inherit from collection
+    const undefinedItem = result.prompts['playwright-explore-website'];
+    assert(undefinedItem && undefinedItem.enabled && undefinedItem.reason === 'collection',
+           'Undefined items should inherit from collection, not be treated as explicitly disabled');
+  });
+
   console.log(`\nTest Results: ${passedTests}/${totalTests} passed`);
   
   if (passedTests === totalTests) {
diff --git a/test-new-config.yml b/test-new-config.yml
deleted file mode 100644
index 4c92107..0000000
--- a/test-new-config.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-# Awesome Copilot Configuration File
-# Generated on 2025-09-21T22:44:51.675Z
-#
-# This file uses effective state precedence:
-# 1. Explicit item settings (true/false) override everything
-# 2. Items not listed inherit from enabled collections
-# 3. Otherwise items are disabled
-#
-# To use:
-# - Enable collections for curated sets of related items
-# - Explicitly set individual items to true/false to override collections
-# - Items not mentioned will follow collection settings
-#
-# After configuring, run: awesome-copilot apply
-#
-
-version: "1.0"
-project:
-  name: "My Project"
-  description: "A project using awesome-copilot customizations"
-  output_directory: ".github"
-prompts:
-  playwright-generate-test: false
-instructions:
-chatmodes:
-collections:
-  azure-cloud-development: false
-  csharp-dotnet-development: false
-  database-data-management: false
-  devops-oncall: false
-  frontend-web-dev: false
-  project-planning: false
-  security-best-practices: false
-  technical-spike: false
-  testing-automation: true
diff --git a/test-new-features.js b/test-new-features.js
index badbe82..766d511 100755
--- a/test-new-features.js
+++ b/test-new-features.js
@@ -119,14 +119,14 @@ async function runTests() {
     
     // Check it's explicitly disabled
     const listResult1 = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
-    assert(listResult1.stdout.includes('create-readme (explicit)'), 'Should show explicit disabled');
+    assert(listResult1.stdout.includes('create-readme (explicit:false)'), 'Should show explicit disabled');
     
     // Force enable all with --all flag
     await runCommand(`node awesome-copilot.js toggle prompts all on --all --config ${TEST_CONFIG}`);
     
     // Check it's now explicitly enabled
     const listResult2 = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
-    assert(listResult2.stdout.includes('create-readme (explicit)') && listResult2.stdout.includes('[✓]'), 'Should be explicitly enabled');
+    assert(listResult2.stdout.includes('create-readme (explicit:true)') && listResult2.stdout.includes('[✓]'), 'Should be explicitly enabled');
   });
 
   // Test 4: File cleanup on disable
@@ -180,7 +180,7 @@ async function runTests() {
     
     // Double-check with list command
     const listResult = await runCommand(`node awesome-copilot.js list prompts --config ${TEST_CONFIG}`);
-    assert(listResult.stdout.includes('playwright-generate-test (explicit)'), "'playwright-generate-test (explicit)' should be present in the list output");
+    assert(listResult.stdout.includes('playwright-generate-test (explicit:false)'), "'playwright-generate-test (explicit:false)' should be present in the list output");
     assert(!listResult.stdout.includes('[✓] playwright-generate-test'), "'[✓] playwright-generate-test' should NOT be present in the list output (should remain explicitly disabled)");
   });
 
diff --git a/test-toggle-collection.js b/test-toggle-collection.js
new file mode 100644
index 0000000..91e7690
--- /dev/null
+++ b/test-toggle-collection.js
@@ -0,0 +1,194 @@
+#!/usr/bin/env node
+
+/**
+ * Unit tests for toggleCollection function
+ */
+
+const path = require('path');
+const { toggleCollection, computeEffectiveItemStates } = require('./config-manager');
+
+// Change to project directory for tests
+process.chdir(__dirname);
+
+function assert(condition, message) {
+  if (!condition) {
+    throw new Error(`Assertion failed: ${message}`);
+  }
+}
+
+function runTests() {
+  let totalTests = 0;
+  let passedTests = 0;
+
+  function test(name, testFn) {
+    totalTests++;
+    try {
+      testFn();
+      console.log(`✅ ${name}`);
+      passedTests++;
+    } catch (error) {
+      console.log(`❌ ${name}: ${error.message}`);
+    }
+  }
+
+  console.log("Running unit tests for toggleCollection function...\n");
+
+  // Test 1: Toggle collection from false to true
+  test("Toggle collection from false to true", () => {
+    const config = {
+      collections: {
+        'testing-automation': false
+      }
+    };
+    
+    const result = toggleCollection(config, 'testing-automation', true);
+    
+    assert(result.changed === true, 'Should indicate change occurred');
+    assert(result.collectionName === 'testing-automation', 'Should return correct collection name');
+    assert(result.currentState === false, 'Should show previous state as false');
+    assert(result.newState === true, 'Should show new state as true');
+    assert(config.collections['testing-automation'] === true, 'Config should be updated');
+    assert(result.delta.enabled.length > 0, 'Should show items being enabled');
+  });
+
+  // Test 2: Toggle collection from true to false
+  test("Toggle collection from true to false", () => {
+    const config = {
+      collections: {
+        'testing-automation': true
+      }
+    };
+    
+    const result = toggleCollection(config, 'testing-automation', false);
+    
+    assert(result.changed === true, 'Should indicate change occurred');
+    assert(result.newState === false, 'Should show new state as false');
+    assert(config.collections['testing-automation'] === false, 'Config should be updated');
+    assert(result.delta.disabled.length > 0, 'Should show items being disabled');
+  });
+
+  // Test 3: Toggle collection to same state (no change)
+  test("Toggle collection to same state (no change)", () => {
+    const config = {
+      collections: {
+        'testing-automation': true
+      }
+    };
+    
+    const result = toggleCollection(config, 'testing-automation', true);
+    
+    assert(result.changed === false, 'Should indicate no change occurred');
+    assert(result.message.includes('already enabled'), 'Should indicate already enabled');
+  });
+
+  // Test 4: Preserves explicit overrides
+  test("Preserves explicit overrides", () => {
+    const config = {
+      prompts: {
+        'playwright-generate-test': false  // Explicit override
+      },
+      collections: {
+        'testing-automation': false
+      }
+    };
+    
+    // Enable collection
+    const result = toggleCollection(config, 'testing-automation', true);
+    
+    // Verify the explicit override is preserved
+    assert(config.prompts['playwright-generate-test'] === false, 'Explicit override should be preserved');
+    assert(config.collections['testing-automation'] === true, 'Collection should be enabled');
+    
+    // Check that the overridden item is not in the enabled delta
+    const hasOverriddenItem = result.delta.enabled.some(item => item.includes('playwright-generate-test'));
+    assert(!hasOverriddenItem, 'Explicitly disabled item should not appear in enabled delta');
+  });
+
+  // Test 5: Only modifies collection flag, never individual items
+  test("Only modifies collection flag, never individual items", () => {
+    const config = {
+      prompts: {},
+      instructions: {},
+      chatmodes: {},
+      collections: {
+        'testing-automation': false
+      }
+    };
+    
+    const originalPrompts = { ...config.prompts };
+    const originalInstructions = { ...config.instructions };
+    const originalChatmodes = { ...config.chatmodes };
+    
+    toggleCollection(config, 'testing-automation', true);
+    
+    // Verify individual sections were not modified
+    assert(JSON.stringify(config.prompts) === JSON.stringify(originalPrompts), 'Prompts section should not be modified');
+    assert(JSON.stringify(config.instructions) === JSON.stringify(originalInstructions), 'Instructions section should not be modified');
+    assert(JSON.stringify(config.chatmodes) === JSON.stringify(originalChatmodes), 'Chatmodes section should not be modified');
+    
+    // Only collections should be modified
+    assert(config.collections['testing-automation'] === true, 'Only collection flag should be modified');
+  });
+
+  // Test 6: Error handling for invalid inputs
+  test("Error handling for invalid inputs", () => {
+    let errorThrown = false;
+    
+    try {
+      toggleCollection(null, 'test', true);
+    } catch (error) {
+      errorThrown = true;
+      assert(error.message.includes('Config object is required'), 'Should require config object');
+    }
+    assert(errorThrown, 'Should throw error for null config');
+    
+    errorThrown = false;
+    try {
+      toggleCollection({}, '', true);
+    } catch (error) {
+      errorThrown = true;
+      assert(error.message.includes('Collection name is required'), 'Should require collection name');
+    }
+    assert(errorThrown, 'Should throw error for empty name');
+    
+    errorThrown = false;
+    try {
+      toggleCollection({}, 'test', 'not-boolean');
+    } catch (error) {
+      errorThrown = true;
+      assert(error.message.includes('Enabled state must be a boolean'), 'Should require boolean enabled state');
+    }
+    assert(errorThrown, 'Should throw error for non-boolean enabled state');
+  });
+
+  // Test 7: Error handling for non-existent collection
+  test("Error handling for non-existent collection", () => {
+    const config = { collections: {} };
+    
+    let errorThrown = false;
+    try {
+      toggleCollection(config, 'non-existent-collection', true);
+    } catch (error) {
+      errorThrown = true;
+      assert(error.message.includes('does not exist'), 'Should indicate collection does not exist');
+    }
+    assert(errorThrown, 'Should throw error for non-existent collection');
+  });
+
+  console.log(`\nTest Results: ${passedTests}/${totalTests} passed`);
+  
+  if (passedTests === totalTests) {
+    console.log('🎉 All toggleCollection tests passed!');
+    return true;
+  } else {
+    console.log('💥 Some toggleCollection tests failed!');
+    return false;
+  }
+}
+
+if (require.main === module) {
+  const success = runTests();
+  process.exit(success ? 0 : 1);
+}
+
+module.exports = { runTests };
\ No newline at end of file