GenAI tool to iterate across a large number of files

I’ve got a use-case for refactoring a large project, with a lot of bigger files. I’m wondering if there’s a GenAI CLI tool that will go file by file (to avoid overloading the context window of the model used) and apply the changes specified in a prompt to each file individually. I’m open to IDEs or other tools, beyond CLI tools as well.

We’ve all seen the headlines about AWS refactoring thousands of files to a newer version of Java. How does this type of thing actually get done?

If I try to do it with Github Copilot, Cursor, etc., I can guarantee it would overload the context window and start to hallucinate its output.