Modify installation now will remove modules that get unselected, with an option to confirm the deletion

docs/A-Product-Brief/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

docs/B-Trigger-Map/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

docs/C-Platform-Requirements/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

docs/C-Scenarios/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

docs/D-Design-System/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

docs/E-PRD/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

docs/E-PRD/Design-Deliveries/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

docs/F-Testing/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

docs/G-Product-Development/.gitkeep

@@ -0,0 +1 @@
+# This file ensures the directory is tracked by git

tools/cli/installers/lib/core/installer.js

@@ -444,6 +444,60 @@ class Installer {
           config._isUpdate = true;
           config._existingInstall = existingInstall;
 
+          // Detect modules that were previously installed but are NOT in the new selection (to be removed)
+          const previouslyInstalledModules = new Set(existingInstall.modules.map((m) => m.id));
+          const newlySelectedModules = new Set(config.modules || []);
+
+          // Find modules to remove (installed but not in new selection)
+          // Exclude 'core' from being removable
+          const modulesToRemove = [...previouslyInstalledModules].filter((m) => !newlySelectedModules.has(m) && m !== 'core');
+
+          // If there are modules to remove, ask for confirmation
+          if (modulesToRemove.length > 0) {
+            const prompts = require('../../../lib/prompts');
+            spinner.stop();
+
+            console.log('');
+            console.log(chalk.yellow.bold('⚠️  Modules to be removed:'));
+            for (const moduleId of modulesToRemove) {
+              const moduleInfo = existingInstall.modules.find((m) => m.id === moduleId);
+              const displayName = moduleInfo?.name || moduleId;
+              const modulePath = path.join(bmadDir, moduleId);
+              console.log(chalk.red(`  - ${displayName} (${modulePath})`));
+            }
+            console.log('');
+
+            const confirmRemoval = await prompts.confirm({
+              message: `Remove ${modulesToRemove.length} module(s) from BMAD installation?`,
+              default: false,
+            });
+
+            if (confirmRemoval) {
+              // Remove module folders
+              for (const moduleId of modulesToRemove) {
+                const modulePath = path.join(bmadDir, moduleId);
+                try {
+                  if (await fs.pathExists(modulePath)) {
+                    await fs.remove(modulePath);
+                    console.log(chalk.dim(`  ✓ Removed: ${moduleId}`));
+                  }
+                } catch (error) {
+                  console.warn(chalk.yellow(`  Warning: Failed to remove ${moduleId}: ${error.message}`));
+                }
+              }
+              console.log(chalk.green(`  ✓ Removed ${modulesToRemove.length} module(s)`));
+            } else {
+              console.log(chalk.dim('  → Module removal cancelled'));
+              // Add the modules back to the selection since user cancelled removal
+              for (const moduleId of modulesToRemove) {
+                if (!config.modules) config.modules = [];
+                config.modules.push(moduleId);
+              }
+            }
+
+            spinner.start('Preparing update...');
+          }
+
           // Detect custom and modified files BEFORE updating (compare current files vs files-manifest.csv)
           const existingFilesManifest = await this.readFilesManifest(bmadDir);
           const { customFiles, modifiedFiles } = await this.detectCustomFiles(bmadDir, existingFilesManifest);

tools/cli/lib/ui.js

@@ -252,19 +252,52 @@ class UI {
         const { installedModuleIds } = await this.getExistingInstallation(confirmedDirectory);
 
         console.log(chalk.dim(`  Found existing modules: ${[...installedModuleIds].join(', ')}`));
-        const changeModuleSelection = await prompts.confirm({
-          message: 'Modify official module selection (BMad Method, BMad Builder)?',
+
+        // Ask about BMad Method Module (bmm)
+        const wantsBmm = await prompts.confirm({
+          message:
+            'Select the BMad Method Module for installation?\n ---> This is the Full BMad Method Agile AI Driven Development Framework Including BMad Quick Flow',
+          default: installedModuleIds.has('bmm'),
+        });
+
+        // Ask about BMad Builder Module (bmb)
+        const wantsBmb = await prompts.confirm({
+          message: 'Select the BMad Builder Module for installation?\n ---> Create Your Own Custom BMad Agents, Workflows and Modules',
+          default: installedModuleIds.has('bmb'),
+        });
+
+        let selectedOfficialModules = [];
+        if (wantsBmm) {
+          selectedOfficialModules.push('bmm');
+        }
+        if (wantsBmb) {
+          selectedOfficialModules.push('bmb');
+        }
+
+        // Ask about other external modules
+        // Check if any external modules are already installed (not bmm, bmb, or core)
+        const installedExternalModules = [...installedModuleIds].filter((id) => !['bmm', 'bmb', 'core'].includes(id));
+
+        let selectedExternalModules = [];
+        // If external modules are already installed, skip confirm and go straight to selection
+        // Otherwise ask if they want to choose external modules
+        if (installedExternalModules.length > 0) {
+          const externalModuleChoices = await this.getExternalModuleChoices();
+          selectedExternalModules = await this.selectExternalModules(externalModuleChoices, installedExternalModules);
+        } else {
+          const wantsExternalModules = await prompts.confirm({
+            message: 'Would you like to choose any other Recommended BMad Core Modules for installation?',
             default: false,
           });
 
-        let selectedModules = [];
-        if (changeModuleSelection) {
-          // Show module selection with existing modules pre-selected
-          const moduleChoices = await this.getModuleChoices(new Set(installedModuleIds), { hasCustomContent: false });
-          selectedModules = await this.selectModules(moduleChoices, [...installedModuleIds]);
-        } else {
-          selectedModules = [...installedModuleIds];
+          if (wantsExternalModules) {
+            const externalModuleChoices = await this.getExternalModuleChoices();
+            selectedExternalModules = await this.selectExternalModules(externalModuleChoices, []);
           }
+        }
+
+        // Combine official and external modules
+        let selectedModules = [...selectedOfficialModules, ...selectedExternalModules];
 
         // After module selection, ask about custom modules
         console.log('');
@@ -744,16 +777,23 @@ class UI {
   /**
    * Prompt for external module selection
    * @param {Array} externalModuleChoices - Available external module choices
+   * @param {Array} defaultSelections - Module codes to pre-select
    * @returns {Array} Selected external module codes
    */
-  async selectExternalModules(externalModuleChoices) {
+  async selectExternalModules(externalModuleChoices, defaultSelections = []) {
     // Build a message showing available modules
     const availableNames = externalModuleChoices.map((c) => c.name).join(', ');
     const message = `Select official BMad modules to install ${availableNames ? chalk.dim(`(${availableNames})`) : ''} ${chalk.dim('(↑/↓ navigates multiselect, SPACE toggles, A to toggles All, ENTER confirm)')}:`;
 
+    // Mark choices as checked based on defaultSelections
+    const choicesWithDefaults = externalModuleChoices.map((choice) => ({
+      ...choice,
+      checked: defaultSelections.includes(choice.value),
+    }));
+
     // Add a "None" option at the end for users who changed their mind
     const choicesWithSkipOption = [
-      ...externalModuleChoices,
+      ...choicesWithDefaults,
       {
         name: '⚠ None / I changed my mind - skip external module installation',
         value: '__NONE__',