Boy have I got the thing for you. git absorb - https://github.com/tummychow/git-absorb

The way to work with it is:

    git add file1
    git commit -m "Fix some bug in file1"
    git add file2
    git commit -m "Add a feature flag for file1"
    # Oh no, first commit was borked, need to fix it
    git add file1
    git absorb
    # this will now automatically create one or more fixup commits
    git rebase -i --autosquash $(git merge-base master)
    # voila, tidy history and each commit works