I have a git repo in /foo/bar/baz with a large commit history and multiple branches.
I now want /foo/qux to be in the same repo as /f
Rather than create a new repository, move what's in your current repository into the right place: create a new directory bar in your current directory and move the current content in (so your code is in /foo/bar/bar). Then create a baz directory next to your new bar directory (/foo/bar/baz). mv /foo /foo2; mv /foo2/bar /foo; rmdir /foo2 and you're done :).
Git's rename tracking means that your history will still work and Git's hashing of content means that even though you've moved things around, you're still referencing the same objects in the repository.