A bit of background:
My team upgraded to cocoapods 1.0 on our main develop branch. After it was committed and push I tried to merge it into my branch. There was a merge conflict in the project.pbxproj. I tried to fix the conflict with FileMerge. After FileMerge opened it would not load up the program. Right clicking on the icon revealed the Application Not Responding message.
Through the research that I've done, the problem is with FileMerge. It can't handle the case when there is a difference on a line that contains an emoji. I've submitted a bug report to Apple, and I've also created an issue on the cocoapods github page (https://github.com/CocoaPods/CocoaPods/issues/5374).
I hope that this will save you time figuring out why FileMerge is randomly broken.
For the record, Cocoapods has updated the repository, and fixed the issue.