diff --git a/apply-config.js b/apply-config.js
index 675acfd..d36a1e1 100755
--- a/apply-config.js
+++ b/apply-config.js
@@ -5,61 +5,134 @@ const path = require("path");
 const { parseCollectionYaml } = require("./yaml-parser");
 
 /**
- * Simple YAML parser for configuration files
+ * Simple YAML parser for configuration files with enhanced error handling
  */
 function parseConfigYamlContent(content) {
   const lines = content.split("\n");
   const result = {};
   let currentSection = null;
+  let lineNumber = 0;
 
-  for (const line of lines) {
-    const trimmed = line.trim();
+  try {
+    for (const line of lines) {
+      lineNumber++;
+      const trimmed = line.trim();
 
-    // Skip comments and empty lines
-    if (!trimmed || trimmed.startsWith("#")) continue;
+      // Skip comments and empty lines
+      if (!trimmed || trimmed.startsWith("#")) continue;
 
-    if (!trimmed.includes(":")) {
-      continue;
-    }
-
-    const colonIndex = trimmed.indexOf(":");
-    const key = trimmed.substring(0, colonIndex).trim();
-    let value = trimmed.substring(colonIndex + 1).trim();
-
-    // Remove quotes if present
-    if ((value.startsWith('"') && value.endsWith('"')) ||
-        (value.startsWith("'") && value.endsWith("'"))) {
-      value = value.slice(1, -1);
-    }
-
-    // Handle sections (no value)
-    if (!value) {
-      currentSection = key;
-      if (!result[currentSection]) {
-        result[currentSection] = {};
+      if (!trimmed.includes(":")) {
+        continue;
+      }
+
+      const colonIndex = trimmed.indexOf(":");
+      const key = trimmed.substring(0, colonIndex).trim();
+      let value = trimmed.substring(colonIndex + 1).trim();
+
+      // Validate key format
+      if (!key || key.includes(" ") && !currentSection) {
+        throw new Error(`Invalid key format on line ${lineNumber}: "${key}"`);
+      }
+
+      // Remove quotes if present
+      if ((value.startsWith('"') && value.endsWith('"')) ||
+          (value.startsWith("'") && value.endsWith("'"))) {
+        value = value.slice(1, -1);
+      }
+
+      // Handle sections (no value)
+      if (!value) {
+        currentSection = key;
+        if (!result[currentSection]) {
+          result[currentSection] = {};
+        }
+        continue;
+      }
+
+      // Handle boolean values
+      if (value === "true") value = true;
+      else if (value === "false") value = false;
+
+      if (currentSection) {
+        result[currentSection][key] = value;
+      } else {
+        result[key] = value;
       }
-      continue;
     }
 
-    // Handle boolean values
-    if (value === "true") value = true;
-    else if (value === "false") value = false;
+    return result;
+  } catch (error) {
+    throw new Error(`YAML parsing error: ${error.message}`);
+  }
+}
 
-    if (currentSection) {
-      result[currentSection][key] = value;
-    } else {
-      result[key] = value;
-    }
+/**
+ * Validate configuration structure and content
+ */
+function validateConfig(config) {
+  const errors = [];
+  
+  if (!config || typeof config !== 'object') {
+    errors.push("Configuration must be a valid object");
+    return errors;
   }
 
-  return result;
+  // Check version
+  if (!config.version) {
+    errors.push("Configuration must have a 'version' field");
+  }
+
+  // Check project structure
+  if (config.project && typeof config.project !== 'object') {
+    errors.push("'project' field must be an object");
+  }
+
+  // Validate sections
+  const validSections = ['prompts', 'instructions', 'chatmodes', 'collections'];
+  validSections.forEach(section => {
+    if (config[section] && typeof config[section] !== 'object') {
+      errors.push(`'${section}' field must be an object`);
+    } else if (config[section]) {
+      // Validate section items
+      Object.entries(config[section]).forEach(([key, value]) => {
+        if (typeof value !== 'boolean') {
+          errors.push(`${section}.${key} must be a boolean value (true/false)`);
+        }
+      });
+    }
+  });
+
+  // Check for unknown top-level fields
+  const knownFields = ['version', 'project', ...validSections];
+  Object.keys(config).forEach(key => {
+    if (!knownFields.includes(key)) {
+      errors.push(`Unknown configuration field: '${key}'`);
+    }
+  });
+
+  return errors;
 }
 
 function parseConfigYaml(filePath) {
   try {
     const content = fs.readFileSync(filePath, "utf8");
-    return parseConfigYamlContent(content);
+    const config = parseConfigYamlContent(content);
+    
+    // Validate the parsed configuration
+    const validationErrors = validateConfig(config);
+    if (validationErrors.length > 0) {
+      console.error(`Configuration validation errors in ${filePath}:`);
+      validationErrors.forEach(error => {
+        console.error(`  ❌ ${error}`);
+      });
+      throw new Error("Configuration validation failed");
+    }
+    
+    return config;
   } catch (error) {
+    if (error.message === "Configuration validation failed") {
+      throw error;
+    }
     console.error(`Error parsing config file ${filePath}: ${error.message}`);
     return null;
   }
@@ -93,6 +166,7 @@ async function applyConfig(configPath = "awesome-copilot.config.yml") {
   ensureDirectoryExists(path.join(outputDir, "chatmodes"));
   
   let copiedCount = 0;
+  let removedCount = 0;
   const summary = {
     prompts: 0,
     instructions: 0,
@@ -120,67 +194,90 @@ async function applyConfig(configPath = "awesome-copilot.config.yml") {
     }
   }
 
-  // Process prompts
-  if (config.prompts) {
-    for (const [promptName, enabled] of Object.entries(config.prompts)) {
-      if (enabled) {
-        const sourcePath = path.join(rootDir, "prompts", `${promptName}.prompt.md`);
-        if (fs.existsSync(sourcePath)) {
-          const destPath = path.join(outputDir, "prompts", `${promptName}.prompt.md`);
+  // Helper function to process section files
+  function processSection(sectionName, sourceDir, destDir, fileExtension) {
+    const enabledInSection = new Set();
+    
+    if (config[sectionName]) {
+      for (const [itemName, enabled] of Object.entries(config[sectionName])) {
+        const sourcePath = path.join(rootDir, sourceDir, `${itemName}${fileExtension}`);
+        const destPath = path.join(outputDir, destDir, `${itemName}${fileExtension}`);
+        
+        if (enabled && fs.existsSync(sourcePath)) {
           copyFile(sourcePath, destPath);
           copiedCount++;
-          summary.prompts++;
+          summary[sectionName]++;
+          enabledInSection.add(itemName);
+        } else if (!enabled && fs.existsSync(destPath)) {
+          // Remove file if it's disabled
+          fs.unlinkSync(destPath);
+          console.log(`✗ Removed: ${itemName}${fileExtension}`);
+          removedCount++;
         }
       }
     }
+
+    // Remove any files in destination that are not enabled
+    const destDirPath = path.join(outputDir, destDir);
+    if (fs.existsSync(destDirPath)) {
+      const existingFiles = fs.readdirSync(destDirPath)
+        .filter(file => file.endsWith(fileExtension));
+      
+      existingFiles.forEach(file => {
+        const itemName = file.replace(fileExtension, '');
+        if (!enabledInSection.has(itemName) && !isItemInEnabledCollection(file, enabledItems)) {
+          const filePath = path.join(destDirPath, file);
+          fs.unlinkSync(filePath);
+          console.log(`✗ Removed orphaned: ${file}`);
+          removedCount++;
+        }
+      });
+    }
   }
 
+  // Helper function to check if an item is in an enabled collection
+  function isItemInEnabledCollection(filename, enabledItems) {
+    for (const itemPath of enabledItems) {
+      if (path.basename(itemPath) === filename) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  // Process prompts
+  processSection("prompts", "prompts", "prompts", ".prompt.md");
+
   // Process instructions
-  if (config.instructions) {
-    for (const [instructionName, enabled] of Object.entries(config.instructions)) {
-      if (enabled) {
-        const sourcePath = path.join(rootDir, "instructions", `${instructionName}.instructions.md`);
-        if (fs.existsSync(sourcePath)) {
-          const destPath = path.join(outputDir, "instructions", `${instructionName}.instructions.md`);
-          copyFile(sourcePath, destPath);
-          copiedCount++;
-          summary.instructions++;
-        }
-      }
-    }
-  }
+  processSection("instructions", "instructions", "instructions", ".instructions.md");
 
   // Process chat modes
-  if (config.chatmodes) {
-    for (const [chatmodeName, enabled] of Object.entries(config.chatmodes)) {
-      if (enabled) {
-        const sourcePath = path.join(rootDir, "chatmodes", `${chatmodeName}.chatmode.md`);
-        if (fs.existsSync(sourcePath)) {
-          const destPath = path.join(outputDir, "chatmodes", `${chatmodeName}.chatmode.md`);
-          copyFile(sourcePath, destPath);
-          copiedCount++;
-          summary.chatmodes++;
-        }
-      }
-    }
-  }
+  processSection("chatmodes", "chatmodes", "chatmodes", ".chatmode.md");
 
-  // Process items from enabled collections
+  // Process items from enabled collections, but respect individual overrides
   for (const itemPath of enabledItems) {
     const sourcePath = path.join(rootDir, itemPath);
     if (fs.existsSync(sourcePath)) {
       const fileName = path.basename(itemPath);
+      const itemName = fileName.replace(/\.(prompt|instructions|chatmode)\.md$/, '');
       let destPath;
+      let section;
       
       if (fileName.endsWith('.prompt.md')) {
         destPath = path.join(outputDir, "prompts", fileName);
+        section = "prompts";
       } else if (fileName.endsWith('.chatmode.md')) {
         destPath = path.join(outputDir, "chatmodes", fileName);
+        section = "chatmodes";
       } else if (fileName.endsWith('.instructions.md')) {
         destPath = path.join(outputDir, "instructions", fileName);
+        section = "instructions";
       }
       
-      if (destPath && !fs.existsSync(destPath)) {
+      // Only copy if not explicitly disabled in individual settings
+      const isExplicitlyDisabled = config[section] && config[section][itemName] === false;
+      
+      if (destPath && !fs.existsSync(destPath) && !isExplicitlyDisabled) {
         copyFile(sourcePath, destPath);
         copiedCount++;
       }
@@ -193,6 +290,9 @@ async function applyConfig(configPath = "awesome-copilot.config.yml") {
   console.log("=".repeat(50));
   console.log(`📂 Output directory: ${outputDir}`);
   console.log(`📝 Total files copied: ${copiedCount}`);
+  if (removedCount > 0) {
+    console.log(`🗑️  Total files removed: ${removedCount}`);
+  }
   console.log(`🎯 Prompts: ${summary.prompts}`);
   console.log(`📋 Instructions: ${summary.instructions}`);
   console.log(`💭 Chat modes: ${summary.chatmodes}`);
diff --git a/awesome-copilot.js b/awesome-copilot.js
index a64eed5..a2bb7f2 100755
--- a/awesome-copilot.js
+++ b/awesome-copilot.js
@@ -12,7 +12,10 @@ const {
   saveConfig,
   ensureConfigStructure,
   countEnabledItems,
-  getAllAvailableItems
+  getAllAvailableItems,
+  getCollectionItems,
+  updateCollectionItems,
+  getItemToCollectionsMap
 } = require("./config-manager");
 
 const CONFIG_FLAG_ALIASES = ["--config", "-c"];
@@ -115,10 +118,22 @@ function handleListCommand(rawArgs) {
 
   const { config } = loadConfig(configPath);
   const sanitizedConfig = ensureConfigStructure(config);
+  const itemToCollectionsMap = getItemToCollectionsMap();
 
   console.log(`📄 Configuration: ${configPath}`);
 
+  // Always show collections first if they're in the sections to show
+  const orderedSections = [];
+  if (sectionsToShow.includes('collections')) {
+    orderedSections.push('collections');
+  }
   sectionsToShow.forEach(section => {
+    if (section !== 'collections') {
+      orderedSections.push(section);
+    }
+  });
+
+  orderedSections.forEach(section => {
     const availableItems = getAllAvailableItems(section);
     const enabledCount = countEnabledItems(sanitizedConfig[section]);
     const { totalCharacters } = calculateSectionFootprint(section, sanitizedConfig[section]);
@@ -139,11 +154,27 @@ function handleListCommand(rawArgs) {
 
     availableItems.forEach(itemName => {
       const isEnabled = Boolean(sanitizedConfig[section]?.[itemName]);
-      console.log(`  [${isEnabled ? "✓" : " "}] ${itemName}`);
+      let itemDisplay = `  [${isEnabled ? "✓" : " "}] ${itemName}`;
+      
+      // Add collection indicators for non-collection items
+      if (section !== 'collections' && itemToCollectionsMap[itemName]) {
+        const collections = itemToCollectionsMap[itemName].collections;
+        itemDisplay += ` ${collections.map(c => `📦${c}`).join(' ')}`;
+      }
+      
+      // For collections, show how many items they contain
+      if (section === 'collections') {
+        const collectionItems = getCollectionItems(itemName);
+        const totalItems = collectionItems.prompts.length + collectionItems.instructions.length + collectionItems.chatmodes.length;
+        itemDisplay += ` (${totalItems} items)`;
+      }
+      
+      console.log(itemDisplay);
     });
   });
 
   console.log("\nUse 'awesome-copilot toggle' to enable or disable specific items.");
+  console.log("📦 indicates items that are part of collections.");
 }
 
 function handleToggleCommand(rawArgs) {
@@ -165,7 +196,7 @@ function handleToggleCommand(rawArgs) {
   }
 
   const { config, header } = loadConfig(configPath);
-  const configCopy = {
+  let configCopy = {
     ...config,
     [section]: { ...config[section] }
   };
@@ -195,7 +226,32 @@ function handleToggleCommand(rawArgs) {
     const currentState = Boolean(sectionState[itemName]);
     const newState = desiredState === null ? !currentState : desiredState;
     sectionState[itemName] = newState;
-    console.log(`${newState ? "Enabled" : "Disabled"} ${SECTION_METADATA[section].singular} '${itemName}'.`);
+    
+    // Special handling for collections - also toggle individual items
+    if (section === "collections") {
+      console.log(`${newState ? "Enabled" : "Disabled"} ${SECTION_METADATA[section].singular} '${itemName}'.`);
+      
+      // Update individual items in the collection
+      configCopy = updateCollectionItems(configCopy, itemName, newState);
+      
+      const collectionItems = getCollectionItems(itemName);
+      const totalItems = collectionItems.prompts.length + collectionItems.instructions.length + collectionItems.chatmodes.length;
+      
+      if (totalItems > 0) {
+        console.log(`${newState ? "Enabled" : "Disabled"} ${totalItems} individual items from collection '${itemName}'.`);
+        if (collectionItems.prompts.length > 0) {
+          console.log(`  Prompts: ${collectionItems.prompts.join(", ")}`);
+        }
+        if (collectionItems.instructions.length > 0) {
+          console.log(`  Instructions: ${collectionItems.instructions.join(", ")}`);
+        }
+        if (collectionItems.chatmodes.length > 0) {
+          console.log(`  Chat modes: ${collectionItems.chatmodes.join(", ")}`);
+        }
+      }
+    } else {
+      console.log(`${newState ? "Enabled" : "Disabled"} ${SECTION_METADATA[section].singular} '${itemName}'.`);
+    }
   }
 
   const sanitizedConfig = ensureConfigStructure(configCopy);
@@ -210,7 +266,12 @@ function handleToggleCommand(rawArgs) {
     console.log(`Estimated ${SECTION_METADATA[section].label.toLowerCase()} context size: ${formatNumber(totalCharacters)} characters.`);
   }
   maybeWarnAboutContext(section, totalCharacters);
-  console.log("Run 'awesome-copilot apply' to copy updated selections into your project.");
+  
+  // Auto-apply functionality - automatically run apply after toggle
+  console.log("Applying configuration automatically...");
+  applyConfig(configPath).catch(error => {
+    console.error("Error during auto-apply:", error.message);
+  });
 }
 
 function extractConfigOption(rawArgs) {
diff --git a/config-manager.js b/config-manager.js
index 628837f..bd28fbe 100644
--- a/config-manager.js
+++ b/config-manager.js
@@ -3,6 +3,7 @@ const path = require("path");
 
 const { parseConfigYamlContent } = require("./apply-config");
 const { objectToYaml, generateConfigHeader, getAvailableItems } = require("./generate-config");
+const { parseCollectionYaml } = require("./yaml-parser");
 
 const DEFAULT_CONFIG_PATH = "awesome-copilot.config.yml";
 const SECTION_METADATA = {
@@ -158,6 +159,115 @@ function getAllAvailableItems(type) {
   return getAvailableItems(path.join(__dirname, meta.dir), meta.ext);
 }
 
+/**
+ * Get individual items from a collection
+ */
+function getCollectionItems(collectionName) {
+  const collectionPath = path.join(__dirname, "collections", `${collectionName}.collection.yml`);
+  if (!fs.existsSync(collectionPath)) {
+    return { prompts: [], instructions: [], chatmodes: [] };
+  }
+
+  const collection = parseCollectionYaml(collectionPath);
+  if (!collection || !collection.items) {
+    return { prompts: [], instructions: [], chatmodes: [] };
+  }
+
+  const result = { prompts: [], instructions: [], chatmodes: [] };
+  
+  collection.items.forEach(item => {
+    const filePath = item.path;
+    const filename = path.basename(filePath);
+    
+    if (filename.endsWith('.prompt.md')) {
+      const name = filename.replace('.prompt.md', '');
+      result.prompts.push(name);
+    } else if (filename.endsWith('.instructions.md')) {
+      const name = filename.replace('.instructions.md', '');
+      result.instructions.push(name);
+    } else if (filename.endsWith('.chatmode.md')) {
+      const name = filename.replace('.chatmode.md', '');
+      result.chatmodes.push(name);
+    }
+  });
+
+  return result;
+}
+
+/**
+ * Update individual items when a collection is toggled
+ */
+function updateCollectionItems(config, collectionName, enabled) {
+  const items = getCollectionItems(collectionName);
+  const configCopy = { ...config };
+  
+  // Ensure sections exist
+  CONFIG_SECTIONS.forEach(section => {
+    if (!configCopy[section]) {
+      configCopy[section] = {};
+    }
+  });
+
+  // Update individual items
+  items.prompts.forEach(prompt => {
+    configCopy.prompts[prompt] = enabled;
+  });
+  
+  items.instructions.forEach(instruction => {
+    configCopy.instructions[instruction] = enabled;
+  });
+  
+  items.chatmodes.forEach(chatmode => {
+    configCopy.chatmodes[chatmode] = enabled;
+  });
+
+  return configCopy;
+}
+
+/**
+ * Get which collections contain specific items
+ */
+function getItemToCollectionsMap() {
+  const map = {};
+  const collectionsDir = path.join(__dirname, "collections");
+  
+  if (!fs.existsSync(collectionsDir)) {
+    return map;
+  }
+
+  const collectionFiles = fs.readdirSync(collectionsDir)
+    .filter(file => file.endsWith('.collection.yml'));
+
+  collectionFiles.forEach(file => {
+    const collectionName = file.replace('.collection.yml', '');
+    const collectionPath = path.join(collectionsDir, file);
+    const collection = parseCollectionYaml(collectionPath);
+    
+    if (collection && collection.items) {
+      collection.items.forEach(item => {
+        const filename = path.basename(item.path);
+        let itemName;
+        
+        if (filename.endsWith('.prompt.md')) {
+          itemName = filename.replace('.prompt.md', '');
+          if (!map[itemName]) map[itemName] = { section: 'prompts', collections: [] };
+          map[itemName].collections.push(collectionName);
+        } else if (filename.endsWith('.instructions.md')) {
+          itemName = filename.replace('.instructions.md', '');
+          if (!map[itemName]) map[itemName] = { section: 'instructions', collections: [] };
+          map[itemName].collections.push(collectionName);
+        } else if (filename.endsWith('.chatmode.md')) {
+          itemName = filename.replace('.chatmode.md', '');
+          if (!map[itemName]) map[itemName] = { section: 'chatmodes', collections: [] };
+          map[itemName].collections.push(collectionName);
+        }
+      });
+    }
+  });
+
+  return map;
+}
+
 module.exports = {
   DEFAULT_CONFIG_PATH,
   CONFIG_SECTIONS,
@@ -168,5 +278,8 @@ module.exports = {
   ensureConfigStructure,
   sortObjectKeys,
   countEnabledItems,
-  getAllAvailableItems
+  getAllAvailableItems,
+  getCollectionItems,
+  updateCollectionItems,
+  getItemToCollectionsMap
 };
diff --git a/test-invalid.yml b/test-invalid.yml
new file mode 100644
index 0000000..05084e7
--- /dev/null
+++ b/test-invalid.yml
@@ -0,0 +1,16 @@
+# Invalid config for testing
+version: 1.0
+
+project:
+  name: "Test Project"
+  output_directory: ".awesome-copilot"
+
+prompts:
+  breakdown-epic-arch: invalid_value  # This should be boolean
+  breakdown-epic-pm: true
+
+invalid_section:
+  some_key: true
+
+instructions:
+  task-implementation: "yes"  # This should be boolean
\ No newline at end of file