fix: prevent /model command from overwriting externally-added settings

packages/cli/src/config/settings.ts

@@ -375,7 +375,7 @@ export class LoadedSettings {
     setNestedPropertySafe(settingsFile.settings, key, value);
     setNestedPropertySafe(settingsFile.originalSettings, key, value);
     this._merged = this.computeMergedSettings();
-    saveSettings(settingsFile);
+    saveSettingsKey(settingsFile.path, key, value);
   }
 }
 
@@ -790,3 +790,30 @@ export function saveSettings(settingsFile: SettingsFile): void {
     throw error;
   }
 }
+
+/**
+ * Saves only a single key-value pair to the settings file on disk.
+ * Unlike saveSettings(), this builds a minimal update object so that
+ * only the specified key is written — all other content in the file
+ * (including entries added externally while the app was running) is preserved.
+ */
+export function saveSettingsKey(
+  filePath: string,
+  key: string,
+  value: unknown,
+): void {
+  try {
+    const dirPath = path.dirname(filePath);
+    if (!fs.existsSync(dirPath)) {
+      fs.mkdirSync(dirPath, { recursive: true });
+    }
+
+    const update: Record<string, unknown> = {};
+    setNestedPropertySafe(update, key, value);
+    updateSettingsFilePreservingFormat(filePath, update);
+  } catch (error) {
+    debugLogger.error('Error saving settings key.');
+    debugLogger.error(error instanceof Error ? error.message : String(error));
+    throw error;
+  }
+}

packages/cli/src/utils/commentJson.test.ts

@@ -167,6 +167,28 @@ describe('commentJson', () => {
       const unchangedContent = fs.readFileSync(testFilePath, 'utf-8');
       expect(unchangedContent).toBe(corruptedContent);
     });
+
+    it('should preserve keys not present in the update object', () => {
+      const originalContent = `{
+        "model": { "name": "old-model" },
+        "modelProviders": [
+          { "name": "provider1" },
+          { "name": "provider2" }
+        ]
+      }`;
+
+      fs.writeFileSync(testFilePath, originalContent, 'utf-8');
+
+      // Only update model.name — modelProviders should be untouched
+      updateSettingsFilePreservingFormat(testFilePath, {
+        model: { name: 'new-model' },
+      });
+
+      const updatedContent = fs.readFileSync(testFilePath, 'utf-8');
+      expect(updatedContent).toContain('"name": "new-model"');
+      expect(updatedContent).toContain('"provider1"');
+      expect(updatedContent).toContain('"provider2"');
+    });
   });
 });