refactor(installer): improve spinner handling during IDE setup

- Added logic to stop the spinner before calling setup() to prevent prompts from interfering with the spinner display.
- Restarted the spinner after setup() completes to maintain user feedback during IDE configuration updates.
- Enhanced configuration collection process in ClaudeCodeSetup to ensure user inputs are gathered before cleanup, improving user experience during setup.

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

@@ -1638,12 +1638,22 @@ class Installer {
         spinner.start('Updating IDE configurations...');
 
         for (const ide of toolConfig.ides) {
-          spinner.text = `Updating ${ide}...`;
+          // Stop spinner before setup() since it may prompt for configuration
+          // (setup() doesn't have preCollectedConfig in compile flow)
+          if (spinner.isSpinning) {
+            spinner.stop();
+          }
+
           await this.ideManager.setup(ide, projectDir, bmadDir, {
             selectedModules: installedModules,
             skipModuleInstall: true, // Skip module installation, just update IDE files
             verbose: config.verbose,
           });
+
+          // Restart spinner after setup() completes (prompts are done)
+          if (!spinner.isSpinning) {
+            spinner.start('Updating IDE configurations...');
+          }
         }
 
         spinner.succeed('IDE configurations updated');

tools/cli/installers/lib/ide/claude-code.js

@@ -108,7 +108,14 @@ class ClaudeCodeSetup extends BaseIdeSetup {
 
     console.log(chalk.cyan(`Setting up ${this.name}...`));
 
-    // Clean up old BMAD installation first
+    // Collect configuration BEFORE cleanup to avoid deleting files before user answers
+    let preCollectedConfig = options.preCollectedConfig;
+    if (!preCollectedConfig || !preCollectedConfig._alreadyConfigured) {
+      // Collect configuration interactively if not already provided
+      preCollectedConfig = await this.collectConfiguration(options);
+    }
+
+    // Clean up old BMAD installation AFTER collecting configuration
     await this.cleanup(projectDir);
 
     // Create .claude/commands directory structure
@@ -139,12 +146,12 @@ class ClaudeCodeSetup extends BaseIdeSetup {
 
     // Process Claude Code specific injections for installed modules
     // Use pre-collected configuration if available, or skip if already configured
-    if (options.preCollectedConfig && options.preCollectedConfig._alreadyConfigured) {
+    if (preCollectedConfig?._alreadyConfigured) {
       // IDE is already configured from previous installation, skip prompting
       // Just process with default/existing configuration
       await this.processModuleInjectionsWithConfig(projectDir, bmadDir, options, {});
-    } else if (options.preCollectedConfig) {
-      await this.processModuleInjectionsWithConfig(projectDir, bmadDir, options, options.preCollectedConfig);
+    } else if (preCollectedConfig) {
+      await this.processModuleInjectionsWithConfig(projectDir, bmadDir, options, preCollectedConfig);
     } else {
       await this.processModuleInjections(projectDir, bmadDir, options);
     }
@@ -291,21 +298,14 @@ class ClaudeCodeSetup extends BaseIdeSetup {
     let choices = subagentChoices;
     let location = installLocation;
 
+    // Collect configuration ONCE before processing modules if interactive and not already collected
+    if (interactive && !choices) {
+      // Check if any module has subagents before prompting
       for (const moduleName of modules) {
         const configData = await loadModuleInjectionConfig(handler, moduleName);
-
-      if (!configData) {
-        continue;
-      }
-
-      const { config, handlerBaseDir } = configData;
-
-      if (interactive) {
-        console.log(chalk.cyan(`\nConfiguring ${moduleName} ${handler.replace('-', ' ')} features...`));
-      }
-
-      if (interactive && config.subagents && !choices) {
-        choices = await this.promptSubagentInstallation(config.subagents);
+        if (configData?.config?.subagents) {
+          // Use the first module's config for prompting (they should all be similar)
+          choices = await this.promptSubagentInstallation(configData.config.subagents);
 
           if (choices.install !== 'none') {
             const inquirer = require('inquirer');
@@ -323,6 +323,23 @@ class ClaudeCodeSetup extends BaseIdeSetup {
             ]);
             location = locationAnswer.location;
           }
+          break; // Only prompt once
+        }
+      }
+    }
+
+    // Now process each module with the collected configuration
+    for (const moduleName of modules) {
+      const configData = await loadModuleInjectionConfig(handler, moduleName);
+
+      if (!configData) {
+        continue;
+      }
+
+      const { config, handlerBaseDir } = configData;
+
+      if (interactive) {
+        console.log(chalk.cyan(`\nConfiguring ${moduleName} ${handler.replace('-', ' ')} features...`));
       }
 
       if (config.injections && choices && choices.install !== 'none') {