Can I merge files in git?

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I have three files Shell-ijk-ArrayList.java, Shell-ijk-Vektor.java and Shell-ikj-ArrayList.java in this git-repository. I have "merged" them manually to MatrixMultiplication.java. Now I would like to get rid of the other three, but I want to keep the history of them. What is the best way to do this?

I have found git merge-file, but when I try

git merge-file MatrixMultiplication.java Shell-ijk-ArrayList.java Shell-ijk-Vektor.java 

I get

error: Could not stat MatrixMultiplication.java

I could simply remove the old files with git rm, but then I'll lose the history, won't I?

I could also move it with git mv, but what would be a good folder for outdated files?

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