Committing and pushing through the terminal worked. After though, there was one more file that showed up in source control (in Xcode) with "!" next to it. I was done after I committed that one. Maybe that was what was stopping Xcode. If that was the problem, Xcode should make it more clear.
I thought it had something to do with me having so many files. But I was able to commit a batch of like ~1k files in Xcode.
Topic:
Developer Tools & Services
SubTopic:
Xcode
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