Is this a bug report?

Yes

Have you read the Contributing Guidelines?

Yes

Environment

Environment:
  OS:  Linux 4.10
  Node:  6.10.3
  Yarn:  1.1.0
  npm:  3.10.10
  Watchman:  4.7.0
Error: unable to print environment info
{ Error: not found: xcodebuild
    (snip stacktrace)

Steps to Reproduce

1. Run react-native init MyProject --version 0.48.3
2. Rename your com.myproject package / applicationId to com.my.new.project according to this SO answer: https://stackoverflow.com/a/37390022/543864
3. Run react-native-git-upgrade to upgrade to 0.49.1 (or higher) which failes silently like described in react-native-git-upgrade changes nothing #12112

There is a similar issue #11163 from when MainApplication.java was introduced in 0.29.

Expected Behavior

Running react-native-git-upgrade in step 3 uses the current Android package name by either parsing AndroidManifest.xml or accepting the package name as a param (ie. react-native-git-upgrade --package com.my.new.project and patches MainApplication.java in the correct path (ie. com/my/new/project).

It looks like react-native init took a package param in version 0.38 which was later removed. That code could be used as a basis for either a --package option to react-native-git-upgrade or parsing AndroidManifest.xml. What is the best approach?

Actual Behavior

Running react-native-git-upgrade in step 3 fails silently like described in #12112 because it tried to patch a file that is not in the git index. It tried to patch com/myproject/MainApplication.java instead of com/my/new/project/MainApplication.java.

Reproducible Demo

Follow the steps under Steps to Reproduce.