how to delete from history some files, and commits with them?

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Hello.

I'm using git for several small
projects, and now one of those pgojects
have to be divided into two independent
parts. So I want to divide git history
respectively. I can create two clones
and run filter-branch in both to delete
files. But I can't find how I may
delete empty commits after that.
Naturally, I'd prefer to do all process
automatically: removing unnecessary
files and deleting empty commits
without searching to its' hashes.

Can you suggest any solution?

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