Issue 1:
Steps to Reproduce

flutter create --template=plugin -i swift health_stats

yields

Creating project health_stats...
health_stats/LICENSE (created)
health_stats/ios/health_stats.podspec (created)
health_stats/ios/.gitignore (created)
health_stats/ios/Assets/.gitkeep (created)
health_stats/health_stats.iml (created)
health_stats/.gitignore (created)
health_stats/android/settings.gradle (created)
health_stats/android/.gitignore (created)
health_stats/android/gradle.properties (created)
health_stats/android/src/main/AndroidManifest.xml (created)
health_stats/pubspec.yaml (created)
health_stats/README.md (created)
health_stats/ios/Classes/HealthStatsPlugin.m (created)
health_stats/ios/Classes/SwiftHealthStatsPlugin.swift (created)
health_stats/ios/Classes/HealthStatsPlugin.h (created)
health_stats/lib/health_stats.dart (created)
health_stats/android/build.gradle (created)
health_stats/android/src/main/java/com/example/healthstats/HealthStatsPlugin.java (created)
health_stats/health_stats_android.iml (created)
health_stats/.idea/runConfigurations/example_lib_main_dart.xml (created)
health_stats/.idea/libraries/Flutter_for_Android.xml (created)
health_stats/.idea/libraries/Dart_SDK.xml (created)
health_stats/.idea/modules.xml (created)
health_stats/.idea/workspace.xml (created)
health_stats/CHANGELOG.md (created)
Running "flutter packages get" in health_stats... 2,1s
health_stats/example/ios/Runner.xcworkspace/contents.xcworkspacedata (created)
health_stats/example/ios/Runner/Info.plist (created)
health_stats/example/ios/Runner/Assets.xcassets/LaunchImage.imageset/LaunchImage@2x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/LaunchImage.imageset/LaunchImage@3x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/LaunchImage.imageset/README.md (created)
health_stats/example/ios/Runner/Assets.xcassets/LaunchImage.imageset/Contents.json (created)
health_stats/example/ios/Runner/Assets.xcassets/LaunchImage.imageset/LaunchImage.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-76x76@2x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-29x29@1x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-40x40@1x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-20x20@1x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-1024x1024@1x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-83.5x83.5@2x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-20x20@3x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Contents.json (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-20x20@2x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-29x29@3x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-40x40@2x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-60x60@3x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-60x60@2x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-76x76@1x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-40x40@3x.png (created)
health_stats/example/ios/Runner/Assets.xcassets/AppIcon.appiconset/Icon-App-29x29@2x.png (created)
health_stats/example/ios/Runner/Base.lproj/LaunchScreen.storyboard (created)
health_stats/example/ios/Runner/Base.lproj/Main.storyboard (created)
health_stats/example/ios/Runner.xcodeproj/project.xcworkspace/contents.xcworkspacedata (created)
health_stats/example/ios/Runner.xcodeproj/xcshareddata/xcschemes/Runner.xcscheme (created)
health_stats/example/ios/Flutter/Debug.xcconfig (created)
health_stats/example/ios/Flutter/Release.xcconfig (created)
health_stats/example/ios/Flutter/AppFrameworkInfo.plist (created)
health_stats/example/ios/.gitignore (created)
health_stats/example/test/widget_test.dart (created)
health_stats/example/health_stats_example.iml (created)
health_stats/example/.gitignore (created)
health_stats/example/.metadata (created)
health_stats/example/android/app/src/main/res/mipmap-mdpi/ic_launcher.png (created)
health_stats/example/android/app/src/main/res/mipmap-hdpi/ic_launcher.png (created)
health_stats/example/android/app/src/main/res/drawable/launch_background.xml (created)
health_stats/example/android/app/src/main/res/mipmap-xxxhdpi/ic_launcher.png (created)
health_stats/example/android/app/src/main/res/mipmap-xxhdpi/ic_launcher.png (created)
health_stats/example/android/app/src/main/res/values/styles.xml (created)
health_stats/example/android/app/src/main/res/mipmap-xhdpi/ic_launcher.png (created)
health_stats/example/android/app/src/main/AndroidManifest.xml (created)
health_stats/example/android/gradle/wrapper/gradle-wrapper.properties (created)
health_stats/example/android/.gitignore (created)
health_stats/example/android/gradle.properties (created)
health_stats/example/android/settings.gradle (created)
health_stats/example/pubspec.yaml (created)
health_stats/example/README.md (created)
health_stats/example/ios/Runner/Runner-Bridging-Header.h (created)
health_stats/example/ios/Runner/AppDelegate.swift (created)
health_stats/example/ios/Runner.xcodeproj/project.pbxproj (created)
health_stats/example/lib/main.dart (created)
health_stats/example/android/app/build.gradle (created)
health_stats/example/android/app/src/main/java/com/example/healthstatsexample/MainActivity.java (created)
health_stats/example/android/build.gradle (created)
health_stats/example/health_stats_example_android.iml (created)
health_stats/example/android.iml (created)
health_stats/example/.idea/runConfigurations/main_dart.xml (created)
health_stats/example/.idea/libraries/Flutter_for_Android.xml (created)
health_stats/example/.idea/libraries/Dart_SDK.xml (created)
health_stats/example/.idea/modules.xml (created)
health_stats/example/.idea/workspace.xml (created)
Wrote 90 files.

Running "flutter packages get" in example... 8,3s

[✓] Flutter is fully installed. (Channel beta, v0.1.5, on Mac OS X 10.13.3 17D102, locale nl-NL)
[✓] Android toolchain - develop for Android devices is fully installed. (Android SDK 26.0.3)
[✓] iOS toolchain - develop for iOS devices is fully installed. (Xcode 9.3)
[✓] Android Studio is fully installed. (version 3.0)
[✓] VS Code is fully installed. (version 1.21.1)
[✓] Connected devices is fully installed. (1 available)

All done! In order to run your application, type:

$ cd health_stats/example
$ flutter run

Your main program file is lib/main.dart in the health_stats/example directory.

Your plugin code is in lib/health_stats.dart in the health_stats directory.

Host platform code is in the android/ and ios/ directories under health_stats.
To edit platform code in an IDE see https://flutter.io/platform-plugins/#edit-code.

then

cd health_stats/example

Logs

flutter run

yields

Launching lib/main.dart on iPhone van Jeroen Meijer in debug mode...
Automatically signing iOS for device deployment using specified development team in Xcode project: [REMOVED]
Running pod install... 0,9s
Running Xcode clean... 1,0s
Starting Xcode build...
Xcode build done 1,2s
Failed to build iOS app
Error output from Xcode build:
↳
** BUILD FAILED **

Xcode's output:
↳
=== BUILD TARGET health_stats OF PROJECT Pods WITH CONFIGURATION Debug ===
<module-includes>:1:9: note: in file included from <module-includes>:1:
#import "Headers/health_stats-umbrella.h"
^
/Users/jeroen/Projects/health_stats/example/ios/Pods/Target Support Files/health_stats/health_stats-umbrella.h:13:9: error: include of non-modular header inside framework module 'health_stats': '/Users/jeroen/Projects/health_stats/ios/Classes/HealthStatsPlugin.h'
#import "HealthStatsPlugin.h"
^
<unknown>:0: error: could not build Objective-C module 'health_stats'
Could not build the precompiled application for the device.

Error launching application on iPhone van Jeroen Meijer.

flutter analyze

yields

Analyzing /Users/jeroen/Projects/health_stats/example...
No issues found!
Ran in 5.1s

Flutter Doctor

flutter doctor -v

yields

[✓] Flutter (Channel beta, v0.1.5, on Mac OS X 10.13.3 17D102, locale nl-NL)
• Flutter version 0.1.5 at /Developer/flutter
• Framework revision 3ea4d06340 (4 weeks ago), 2018-02-22 11:12:39 -0800
• Engine revision ead227f118
• Dart version 2.0.0-dev.28.0.flutter-0b4f01f759

[✓] Android toolchain - develop for Android devices (Android SDK 26.0.3)
• Android SDK at /Users/jeroen/Library/Developer/Xamarin/android-sdk-macosx
• Android NDK location not configured (optional; useful for native profiling support)
• Platform android-27, build-tools 26.0.3
• ANDROID_HOME = /Users/jeroen/Library/Developer/Xamarin/android-sdk-macosx
• Java binary at: /Applications/Android Studio.app/Contents/jre/jdk/Contents/Home/bin/java
• Java version OpenJDK Runtime Environment (build 1.8.0_152-release-915-b08)

[✓] iOS toolchain - develop for iOS devices (Xcode 9.3)
• Xcode at /Applications/Xcode-beta.app/Contents/Developer
• Xcode 9.3, Build version 9Q127n
• ios-deploy 1.9.2
• CocoaPods version 1.4.0

[✓] Android Studio (version 3.0)
• Android Studio at /Applications/Android Studio.app/Contents
• Java version OpenJDK Runtime Environment (build 1.8.0_152-release-915-b08)

[✓] VS Code (version 1.21.1)
• VS Code at /Applications/Visual Studio Code.app/Contents
• Dart Code extension version 2.10.0

[✓] Connected devices (1 available)
• iPhone van Jeroen Meijer • [REMOVED] • ios • iOS 11.3

EDIT

The same now also happens when creating a plugin omitting the -i swift. Generating any project with --template=plugin yields the same result.

Issue 2:
Steps to Reproduce

set -x

mkdir -p Made_Podfiles_use_symlinks_to_local_pods_NOT_WORKING/
pushd Made_Podfiles_use_symlinks_to_local_pods_NOT_WORKING/

flutter create -t plugin -i swift --org com.failed failed > /dev/null
pushd failed/example
flutter build ios --debug
popd

flutter create -t plugin -i swift --org com.success success > /dev/null
pushd success/example
wget -q https://raw.githubusercontent.com/mravn-google/flutter/3723ec0383f79420486bb4ee5acf06ebd190b5cf/packages/flutter_tools/templates/cocoapods/Podfile-swift
cp Podfile-swift ios/Podfile
flutter build ios --debug
popd

popd

Flutter Doctor

➜ ~ flutter doctor -v
[✓] Flutter (Channel master, v0.1.8-pre.43, on Mac OS X 10.13.3 17D102, locale en-KR)
• Flutter version 0.1.8-pre.43 at /Users/?????/flutter
• Framework revision fe334e1652 (3 hours ago), 2018-03-02 17:54:51 -0800
• Engine revision 97b22348c8
• Dart version 2.0.0-dev.32.0.flutter-ee15c8eb68

[✓] Android toolchain - develop for Android devices (Android SDK 27.0.3)
• Android SDK at /Users/?????/Library/Android/sdk
• Android NDK location not configured (optional; useful for native profiling support)
• Platform android-27, build-tools 27.0.3
• ANDROID_HOME = /Users/?????/Library/Android/sdk
• Java binary at: /Applications/Android Studio.app/Contents/jre/jdk/Contents/Home/bin/java
• Java version OpenJDK Runtime Environment (build 1.8.0_152-release-915-b08)
• All Android licenses accepted.

[✓] iOS toolchain - develop for iOS devices (Xcode 9.2)
• Xcode at /Applications/Xcode.app/Contents/Developer
• Xcode 9.2, Build version 9C40b
• ios-deploy 1.9.2
• CocoaPods version 1.3.1

[✓] Android Studio (version 3.0)
• Android Studio at /Applications/Android Studio.app/Contents
• Java version OpenJDK Runtime Environment (build 1.8.0_152-release-915-b08)

[✓] IntelliJ IDEA Community Edition (version 2017.3.4)
• IntelliJ at /Applications/IntelliJ IDEA CE.app
• Flutter plugin version 22.1.2
• Dart plugin version 173.4548.30

[✓] VS Code
• VS Code at /Applications/Visual Studio Code.app/Contents
• Dart Code extension version 2.8.0

[✓] Connected devices (1 available)
• ????????????????????????????????????? • ios • iOS 11.2.6

• No issues found!