You can record to the index the deletion of that file (git add -- MyDeletedFile.hpp), and all you need to do is a git commit.
Once the commit is done, Git will no longer show that file in the status.
The OP Rahul Iyer mentions in the comments having to do two commits, the second one handling the deleted file. That could happen when the deleted file has not the same case (mydeletedfile.hpp vs. MyDeletedFile.hpp)
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