I am not sure if the easiest way is to change the .git
folder into where it should be.
cd /var/dir/working/
mv .git ../.git # move the .git folder to the parent directory
cd .. # go to parent directory
git status # then you can see a lot of delete and untracked
git add . # output nothing
git status # after add all, you can see those delete and untracked are converted
# to renaming, and some untracked from "parent directory"
git commit -m "Include parent directory" # you may see a lot of renaming,
# and new file from parent dir, that's it