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react-native-git-upgrade deletes my non-versioned files and fails

See original GitHub issue

Description

I installed react-native-git-upgrade@0.2.5 and ran it on my project.

Reproduction

$ react-native-git-upgrade
git-upgrade info Check for updates
git-upgrade info Read package.json files
git-upgrade info Check declared version
git-upgrade info Check matching versions
git-upgrade info Check React peer dependency
git-upgrade info Check that Git is installed
git-upgrade info Get information from NPM registry
git-upgrade info Upgrading to React Native 0.41.2, React ~15.4.0
git-upgrade info Setup temporary working directory
git-upgrade info Configure Git environment
git-upgrade info Init Git repository
git-upgrade info Add all files to commit
git-upgrade info Commit current project sources
git-upgrade info Create a tag before updating sources
git-upgrade info Generate old version template
git-upgrade info Add updated files to commit
git-upgrade info Commit old version template
git-upgrade info Install the new version
npm WARN deprecated node-uuid@1.4.7: use uuid module instead
git-upgrade info Generate new version template
git-upgrade info Add updated files to commit
git-upgrade info Commit new version template
git-upgrade info Generate the patch between the 2 versions
git-upgrade info Save the patch in temp directory
git-upgrade info Reset the 2 temporary commits
git-upgrade info Apply the patch
fatal: unrecognized input
git-upgrade WARN The upgrade process succeeded but there might be conflicts to be resolved. See above for the list of files that have merge conflicts.
git-upgrade info Upgrade done
$

And in the end, no file is modified, and some files are missing, for example android/app/google-services.json (present in my .gitignore)