diff --git a/tools/cli/commands/install.js b/tools/cli/commands/install.js
index 64bf7a54..714b45ae 100644
--- a/tools/cli/commands/install.js
+++ b/tools/cli/commands/install.js
@@ -26,14 +26,23 @@ module.exports = {
       // Regular install/update flow
       const result = await installer.install(config);
 
-      console.log(chalk.green('\n✨ Installation complete!'));
-      console.log(
-        chalk.cyan('BMAD Core and Selected Modules have been installed to:'),
-        chalk.bold(result.path || path.resolve(config.directory, 'bmad')),
-      );
-      console.log(chalk.yellow('\nThank you for helping test the early release version of the new BMad Core and BMad Method!'));
-      console.log(chalk.cyan('Check docs/alpha-release-notes.md in this repository for important information.'));
-      process.exit(0);
+      // Check if installation was cancelled
+      if (result && result.cancelled) {
+        process.exit(0);
+        return;
+      }
+
+      // Check if installation succeeded
+      if (result && result.success) {
+        console.log(chalk.green('\n✨ Installation complete!'));
+        console.log(
+          chalk.cyan('BMAD Core and Selected Modules have been installed to:'),
+          chalk.bold(result.path || path.resolve(config.directory, 'bmad')),
+        );
+        console.log(chalk.yellow('\nThank you for helping test the early release version of the new BMad Core and BMad Method!'));
+        console.log(chalk.cyan('Check docs/alpha-release-notes.md in this repository for important information.'));
+        process.exit(0);
+      }
     } catch (error) {
       // Check if error has a complete formatted message
       if (error.fullMessage) {
diff --git a/tools/cli/installers/lib/core/installer.js b/tools/cli/installers/lib/core/installer.js
index 12b4bc33..7a72ebe1 100644
--- a/tools/cli/installers/lib/core/installer.js
+++ b/tools/cli/installers/lib/core/installer.js
@@ -37,63 +37,80 @@ class Installer {
    * @param {Array} selectedModules - Selected modules from configuration
    * @returns {Object} Tool/IDE selection and configurations
    */
-  async collectToolConfigurations(projectDir, selectedModules) {
+  async collectToolConfigurations(projectDir, selectedModules, isFullReinstall = false) {
     // Prompt for tool selection
     const { UI } = require('../../../lib/ui');
     const ui = new UI();
     const toolConfig = await ui.promptToolSelection(projectDir, selectedModules);
 
+    // Check for already configured IDEs (but ignore them if doing a full reinstall)
+    const { Detector } = require('./detector');
+    const detector = new Detector();
+    const bmadDir = path.join(projectDir, 'bmad');
+    const existingInstall = await detector.detect(bmadDir);
+    const previouslyConfiguredIdes = isFullReinstall ? [] : existingInstall.ides || [];
+
     // Collect IDE-specific configurations if any were selected
     const ideConfigurations = {};
-    const bmadDir = path.join(projectDir, 'bmad');
 
     if (!toolConfig.skipIde && toolConfig.ides && toolConfig.ides.length > 0) {
-      console.log('\n'); // Add spacing before IDE questions
+      // Determine which IDEs are newly selected (not previously configured)
+      const newlySelectedIdes = toolConfig.ides.filter((ide) => !previouslyConfiguredIdes.includes(ide));
 
-      for (const ide of toolConfig.ides) {
-        // List of IDEs that have interactive prompts
-        const needsPrompts = ['claude-code', 'github-copilot', 'roo', 'cline', 'auggie', 'codex', 'qwen', 'gemini'].includes(ide);
+      if (newlySelectedIdes.length > 0) {
+        console.log('\n'); // Add spacing before IDE questions
 
-        if (needsPrompts) {
-          // Get IDE handler and collect configuration
-          try {
-            // Dynamically load the IDE setup module
-            const ideModule = require(`../ide/${ide}`);
+        for (const ide of newlySelectedIdes) {
+          // List of IDEs that have interactive prompts
+          const needsPrompts = ['claude-code', 'github-copilot', 'roo', 'cline', 'auggie', 'codex', 'qwen', 'gemini'].includes(ide);
 
-            // Get the setup class (handle different export formats)
-            let SetupClass;
-            const className =
-              ide
-                .split('-')
-                .map((part) => part.charAt(0).toUpperCase() + part.slice(1))
-                .join('') + 'Setup';
+          if (needsPrompts) {
+            // Get IDE handler and collect configuration
+            try {
+              // Dynamically load the IDE setup module
+              const ideModule = require(`../ide/${ide}`);
 
-            if (ideModule[className]) {
-              SetupClass = ideModule[className];
-            } else if (ideModule.default) {
-              SetupClass = ideModule.default;
-            } else {
-              // Skip if no setup class found
-              continue;
+              // Get the setup class (handle different export formats)
+              let SetupClass;
+              const className =
+                ide
+                  .split('-')
+                  .map((part) => part.charAt(0).toUpperCase() + part.slice(1))
+                  .join('') + 'Setup';
+
+              if (ideModule[className]) {
+                SetupClass = ideModule[className];
+              } else if (ideModule.default) {
+                SetupClass = ideModule.default;
+              } else {
+                // Skip if no setup class found
+                continue;
+              }
+
+              const ideSetup = new SetupClass();
+
+              // Check if this IDE has a collectConfiguration method
+              if (typeof ideSetup.collectConfiguration === 'function') {
+                console.log(chalk.cyan(`\nConfiguring ${ide}...`));
+                ideConfigurations[ide] = await ideSetup.collectConfiguration({
+                  selectedModules: selectedModules || [],
+                  projectDir,
+                  bmadDir,
+                });
+              }
+            } catch {
+              // IDE doesn't have a setup file or collectConfiguration method
+              console.warn(chalk.yellow(`Warning: Could not load configuration for ${ide}`));
             }
-
-            const ideSetup = new SetupClass();
-
-            // Check if this IDE has a collectConfiguration method
-            if (typeof ideSetup.collectConfiguration === 'function') {
-              console.log(chalk.cyan(`\nConfiguring ${ide}...`));
-              ideConfigurations[ide] = await ideSetup.collectConfiguration({
-                selectedModules: selectedModules || [],
-                projectDir,
-                bmadDir,
-              });
-            }
-          } catch {
-            // IDE doesn't have a setup file or collectConfiguration method
-            console.warn(chalk.yellow(`Warning: Could not load configuration for ${ide}`));
           }
         }
       }
+
+      // Log which IDEs are already configured and being kept
+      const keptIdes = toolConfig.ides.filter((ide) => previouslyConfiguredIdes.includes(ide));
+      if (keptIdes.length > 0) {
+        console.log(chalk.dim(`\nKeeping existing configuration for: ${keptIdes.join(', ')}`));
+      }
     }
 
     return {
@@ -139,12 +156,7 @@ class Installer {
     // Collect configurations for modules (core was already collected in UI.promptInstall if interactive)
     const moduleConfigs = await this.configCollector.collectAllConfigurations(config.modules || [], path.resolve(config.directory));
 
-    const toolSelection = await this.collectToolConfigurations(path.resolve(config.directory), config.modules);
-
-    // Merge tool selection into config
-    config.ides = toolSelection.ides;
-    config.skipIde = toolSelection.skipIde;
-    const ideConfigurations = toolSelection.configurations;
+    // Tool selection will be collected after we determine if it's a reinstall/update/new install
 
     const spinner = ora('Preparing installation...').start();
 
@@ -188,7 +200,7 @@ class Installer {
         const { action } = await this.promptUpdateAction();
         if (action === 'cancel') {
           console.log('Installation cancelled.');
-          return;
+          return { success: false, cancelled: true };
         }
 
         if (action === 'reinstall') {
@@ -208,12 +220,15 @@ class Installer {
 
           if (!confirmReinstall) {
             console.log('Installation cancelled.');
-            return;
+            return { success: false, cancelled: true };
           }
 
           // Remove existing installation
           await fs.remove(bmadDir);
           console.log(chalk.green('✓ Removed existing installation\n'));
+
+          // Mark this as a full reinstall so we re-collect IDE configurations
+          config._isFullReinstall = true;
         } else if (action === 'update') {
           // Store that we're updating for later processing
           config._isUpdate = true;
@@ -275,6 +290,21 @@ class Installer {
         }
       }
 
+      // Now collect tool configurations after we know if it's a reinstall
+      spinner.stop();
+      const toolSelection = await this.collectToolConfigurations(
+        path.resolve(config.directory),
+        config.modules,
+        config._isFullReinstall || false,
+      );
+
+      // Merge tool selection into config
+      config.ides = toolSelection.ides;
+      config.skipIde = toolSelection.skipIde;
+      const ideConfigurations = toolSelection.configurations;
+
+      spinner.start('Continuing installation...');
+
       // Create bmad directory structure
       spinner.text = 'Creating directory structure...';
       await this.createDirectoryStructure(bmadDir);
diff --git a/tools/cli/installers/lib/core/manifest.js b/tools/cli/installers/lib/core/manifest.js
index 610b428c..7410450f 100644
--- a/tools/cli/installers/lib/core/manifest.js
+++ b/tools/cli/installers/lib/core/manifest.js
@@ -10,25 +10,32 @@ class Manifest {
    * @param {Array} installedFiles - List of installed files (no longer used, files tracked in files-manifest.csv)
    */
   async create(bmadDir, data, installedFiles = []) {
-    const manifestPath = path.join(bmadDir, '_cfg', 'manifest.csv');
+    const manifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
+    const yaml = require('js-yaml');
 
     // Ensure _cfg directory exists
     await fs.ensureDir(path.dirname(manifestPath));
 
-    // Load module configs to get module metadata
-    // If core is installed, add it to modules list
-    const allModules = [...(data.modules || [])];
-    if (data.core) {
-      allModules.unshift('core'); // Add core at the beginning
-    }
-    const moduleConfigs = await this.loadModuleConfigs(allModules);
+    // Structure the manifest data
+    const manifestData = {
+      installation: {
+        version: data.version || require(path.join(process.cwd(), 'package.json')).version,
+        installDate: data.installDate || new Date().toISOString(),
+        lastUpdated: data.lastUpdated || new Date().toISOString(),
+      },
+      modules: data.modules || [],
+      ides: data.ides || [],
+    };
 
-    // Don't store installation path in manifest
+    // Write YAML manifest
+    const yamlContent = yaml.dump(manifestData, {
+      indent: 2,
+      lineWidth: -1,
+      noRefs: true,
+      sortKeys: false,
+    });
 
-    // Generate CSV content (no file metadata)
-    const csvContent = this.generateManifestCsv({ ...data, modules: allModules }, [], moduleConfigs);
-
-    await fs.writeFile(manifestPath, csvContent, 'utf8');
+    await fs.writeFile(manifestPath, yamlContent, 'utf8');
     return { success: true, path: manifestPath, filesTracked: 0 };
   }
 
@@ -38,14 +45,24 @@ class Manifest {
    * @returns {Object|null} Manifest data or null if not found
    */
   async read(bmadDir) {
-    const csvPath = path.join(bmadDir, '_cfg', 'manifest.csv');
+    const yamlPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
+    const yaml = require('js-yaml');
 
-    if (await fs.pathExists(csvPath)) {
+    if (await fs.pathExists(yamlPath)) {
       try {
-        const content = await fs.readFile(csvPath, 'utf8');
-        return this.parseManifestCsv(content);
+        const content = await fs.readFile(yamlPath, 'utf8');
+        const manifestData = yaml.load(content);
+
+        // Flatten the structure for compatibility with existing code
+        return {
+          version: manifestData.installation?.version,
+          installDate: manifestData.installation?.installDate,
+          lastUpdated: manifestData.installation?.lastUpdated,
+          modules: manifestData.modules || [],
+          ides: manifestData.ides || [],
+        };
       } catch (error) {
-        console.error('Failed to read CSV manifest:', error.message);
+        console.error('Failed to read YAML manifest:', error.message);
       }
     }
 
@@ -59,25 +76,37 @@ class Manifest {
    * @param {Array} installedFiles - Updated list of installed files
    */
   async update(bmadDir, updates, installedFiles = null) {
+    const yaml = require('js-yaml');
     const manifest = (await this.read(bmadDir)) || {};
 
     // Merge updates
     Object.assign(manifest, updates);
     manifest.lastUpdated = new Date().toISOString();
 
-    // If new file list provided, reparse metadata
-    let fileMetadata = manifest.files || [];
-    if (installedFiles) {
-      fileMetadata = await this.parseInstalledFiles(installedFiles);
-    }
+    // Convert back to structured format for YAML
+    const manifestData = {
+      installation: {
+        version: manifest.version,
+        installDate: manifest.installDate,
+        lastUpdated: manifest.lastUpdated,
+      },
+      modules: manifest.modules || [],
+      ides: manifest.ides || [],
+    };
 
-    const manifestPath = path.join(bmadDir, '_cfg', 'manifest.csv');
+    const manifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
     await fs.ensureDir(path.dirname(manifestPath));
 
-    const csvContent = this.generateManifestCsv({ ...manifest, ...updates }, fileMetadata);
-    await fs.writeFile(manifestPath, csvContent, 'utf8');
+    const yamlContent = yaml.dump(manifestData, {
+      indent: 2,
+      lineWidth: -1,
+      noRefs: true,
+      sortKeys: false,
+    });
 
-    return { ...manifest, ...updates, files: fileMetadata };
+    await fs.writeFile(manifestPath, yamlContent, 'utf8');
+
+    return manifest;
   }
 
   /**