Instead of generating the Podfile, just fill it with dependencies

cli/src/ios/update.ts

@@ -1,6 +1,6 @@
 import { checkCocoaPods, checkIOSProject, getIOSPlugins } from './common';
 import { CheckFunction, log, logInfo, logWarn, runCommand, runTask } from '../common';
-import { copySync, removeSync, writeFileAsync } from '../util/fs';
+import { copySync, readFileAsync, removeSync, writeFileAsync } from '../util/fs';
 import { Config } from '../config';
 import { join, resolve } from 'path';
 import { getPlatformElement, getPluginPlatform, getPlugins, getPluginType, Plugin, PluginType, printPlugins } from '../plugin';
@@ -94,11 +94,13 @@ export async function installCocoaPodsPlugins(config: Config, plugins: Plugin[],
 }
 
 export async function updatePodfile(config: Config, plugins: Plugin[], needsUpdate: boolean) {
-  const content = generatePodFile(config, plugins);
+  const dependenciesContent = generatePodFile(config, plugins);
   const projectName = config.ios.nativeProjectName;
   const podfilePath = resolve(config.app.rootDir, config.ios.name, projectName, 'Podfile');
-
-  await writeFileAsync(podfilePath, content, 'utf8');
+  let podfileContent = await readFileAsync(podfilePath, 'utf8');
+  podfileContent = podfileContent.replace(/(Automatic Capacitor Pod dependencies, do not delete)[\s\S]*(# Do not delete)/, '$1' + dependenciesContent + '\n  $2');
+  podfileContent = podfileContent.replace(/platform :ios, '[^']*'/ , `platform :ios, '${config.ios.minVersion}'`);
+  await writeFileAsync(podfilePath, podfileContent, 'utf8');
 
   if (needsUpdate) {
     await runCommand(`cd "${config.app.rootDir}" && cd "${config.ios.name}" && cd "${projectName}" && pod update && xcodebuild -project App.xcodeproj clean`);
@@ -112,30 +114,20 @@ export function generatePodFile(config: Config, plugins: Plugin[]) {
   const pods = capacitorPlugins
     .map((p) => `pod '${p.ios!.name}', :path => '../../node_modules/${p.id}/${p.ios!.path}'`);
   const cordovaPlugins = plugins.filter(p => p.ios!.type === PluginType.Cordova);
-  let dependencies = '';
+  let dependencies: Array<string> = [];
   cordovaPlugins.map((p: any) => {
     const frameworks = getPlatformElement(p, platform, 'framework');
     frameworks.map((framework: any) => {
       if (framework.$.type && framework.$.type === 'podspec') {
-        dependencies += `pod '${framework.$.src}', '${framework.$.spec}'\n      `;
+        dependencies.push(`pod '${framework.$.src}', '${framework.$.spec}'`);
       }
     });
   });
   return `
-# DO NOT MODIFY.
-# This Podfile was autogenerated by the Capacitor CLI.
-# It is used to resolve the native dependencies of Capacitor plugins.
-
-platform :ios, '${config.ios.minVersion}'
-use_frameworks!
-
-target 'App' do
   ${config.ios.capacitorRuntimePod}
   pod 'CordovaPlugins', :path => '../../node_modules/@capacitor/cli/assets/capacitor-cordova-ios-plugins'
   pod 'CordovaPluginsResources', :path => '../../node_modules/@capacitor/cli/assets/capacitor-cordova-ios-plugins'
-  ${pods.join('\n      ')}
-  ${dependencies}
-end`;
+  ${pods.join('\n      ')}${dependencies.join('\n      ')}`;
 }
 
 function getFrameworkName(framework: any) {

ios-template/App/Podfile

@@ -1,10 +1,10 @@
-# Uncomment the next line to define a global platform for your project
-# platform :ios, '9.0'
+platform :ios, '10.0'
+use_frameworks!
 
 target 'App' do
-  # Comment the next line if you're not using Swift and don't want to use dynamic frameworks
-  use_frameworks!
+  # Add your Pods here
 
-  # Pods for IonicRunner
+  # Automatic Capacitor Pod dependencies, do not delete
   pod 'Capacitor'
+  # Do not delete
 end