Is this a bug report?

Yes

Have you read the Contributing Guidelines?

Yes

Environment

Environment:
OS: macOS Sierra 10.12.6
Node: 8.6.0
Yarn: 1.1.0
npm: 5.3.0
Watchman: 4.1.0
Xcode: Xcode 9.0.1 Build version 9A1004
Android Studio: 1.4 AI-141.2288178

Packages: (wanted => installed)
react: 16.0.0 => 16.0.0
react-native: 0.50.1 => 0.50.1

Steps to Reproduce

(Write your steps here:)

1. react-native-git-upgrade
2. rm -rf node_modules/
3. yarn

Expected Behavior

XCode to successfully load the project

Actual Behavior

XCode fails to load the project. Says the the project.pbxproj is missing (which is true)