diff --git a/tools/cli/commands/uninstall.js b/tools/cli/commands/uninstall.js
index 4b961978a..32cd576b2 100644
--- a/tools/cli/commands/uninstall.js
+++ b/tools/cli/commands/uninstall.js
@@ -43,12 +43,17 @@ module.exports = {
             },
           });
 
-          projectDir = path.resolve(customDir);
+          projectDir = path.resolve(customDir.trim());
         } else {
           projectDir = process.cwd();
         }
       }
 
+      if (!(await fs.pathExists(projectDir))) {
+        await prompts.log.error(`Directory does not exist: ${projectDir}`);
+        process.exit(1);
+      }
+
       const { bmadDir } = await installer.findBmadDir(projectDir);
 
       if (!(await fs.pathExists(bmadDir))) {
diff --git a/tools/cli/installers/lib/core/installer.js b/tools/cli/installers/lib/core/installer.js
index 18b822b2f..b7197d44d 100644
--- a/tools/cli/installers/lib/core/installer.js
+++ b/tools/cli/installers/lib/core/installer.js
@@ -1552,30 +1552,18 @@ class Installer {
 
     // 2. IDE CLEANUP (before _bmad/ deletion so configs are accessible)
     if (options.removeIdeConfigs !== false) {
-      await this.ideManager.ensureInitialized();
-      const cleanupOptions = { isUninstall: true };
-      const ideList = existingInstall.ides || [];
-      if (ideList.length > 0) {
-        await this.ideManager.cleanupByList(projectDir, ideList, cleanupOptions);
-      } else {
-        await this.ideManager.cleanup(projectDir, cleanupOptions);
-      }
+      await this.uninstallIdeConfigs(projectDir, existingInstall, { silent: options.silent });
       removed.ideConfigs = true;
     }
 
     // 3. OUTPUT FOLDER (only if explicitly requested)
     if (options.removeOutputFolder === true && outputFolder) {
-      const outputPath = path.join(projectDir, outputFolder);
-      if (await fs.pathExists(outputPath)) {
-        await fs.remove(outputPath);
-        removed.outputFolder = true;
-      }
+      removed.outputFolder = await this.uninstallOutputFolder(projectDir, outputFolder);
     }
 
     // 4. BMAD DIRECTORY (last, after everything that needs it)
     if (options.removeModules !== false) {
-      await fs.remove(bmadDir);
-      removed.modules = true;
+      removed.modules = await this.uninstallModules(projectDir);
     }
 
     return { success: true, removed, version: existingInstall.version };
@@ -1606,7 +1594,11 @@ class Installer {
    */
   async uninstallOutputFolder(projectDir, outputFolder) {
     if (!outputFolder) return false;
-    const outputPath = path.join(projectDir, outputFolder);
+    const resolvedProject = path.resolve(projectDir);
+    const outputPath = path.resolve(resolvedProject, outputFolder);
+    if (!outputPath.startsWith(resolvedProject + path.sep)) {
+      return false;
+    }
     if (await fs.pathExists(outputPath)) {
       await fs.remove(outputPath);
       return true;
diff --git a/tools/cli/installers/lib/ide/_config-driven.js b/tools/cli/installers/lib/ide/_config-driven.js
index cdae1c5b0..9541c75ed 100644
--- a/tools/cli/installers/lib/ide/_config-driven.js
+++ b/tools/cli/installers/lib/ide/_config-driven.js
@@ -548,7 +548,7 @@ LOAD and execute from: {project-root}/{{bmadFolderName}}/{{path}}
         if (!(await fs.pathExists(fullPath))) break;
         const remaining = await fs.readdir(fullPath);
         if (remaining.length > 0) break;
-        await fs.remove(fullPath);
+        await fs.rmdir(fullPath);
       } catch {
         break;
       }
diff --git a/tools/cli/installers/lib/ide/github-copilot.js b/tools/cli/installers/lib/ide/github-copilot.js
index 50f54778b..033e8d627 100644
--- a/tools/cli/installers/lib/ide/github-copilot.js
+++ b/tools/cli/installers/lib/ide/github-copilot.js
@@ -640,7 +640,7 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
     // handles marker-based replacement in a single read-modify-write pass,
     // which correctly preserves user content outside the markers.
     if (options.isUninstall) {
-      await this.cleanupCopilotInstructions(projectDir);
+      await this.cleanupCopilotInstructions(projectDir, options);
     }
   }
 
@@ -649,8 +649,9 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
    * If file becomes empty after stripping, delete it.
    * If a .bak backup exists and the main file was deleted, restore the backup.
    * @param {string} projectDir - Project directory
+   * @param {Object} [options] - Options (e.g. { silent: true })
    */
-  async cleanupCopilotInstructions(projectDir) {
+  async cleanupCopilotInstructions(projectDir, options = {}) {
     const instructionsPath = path.join(projectDir, this.githubDir, 'copilot-instructions.md');
     const backupPath = `${instructionsPath}.bak`;
 
@@ -680,7 +681,9 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
       // If backup exists, restore it
       if (await fs.pathExists(backupPath)) {
         await fs.rename(backupPath, instructionsPath);
-        await prompts.log.message('  Restored copilot-instructions.md from backup');
+        if (!options.silent) {
+          await prompts.log.message('  Restored copilot-instructions.md from backup');
+        }
       }
     } else {
       // Write cleaned content back (preserve original whitespace)