git - how do I clone into a non-empty directory?

Question

I have directory A with files matching directory B. Directory A may have other needed files. Directory B is a git repo.

I want to clone directory B to directory A but git-clone won't allow me to since the directory is non-empty.

I was hoping it would just clone .git and since all the files match I could go from there?

I can't clone into an empty directory because I have files in directory A that are not in directory B and I want to keep them.

Copying .git is not an option since I want refs to push/pull with and I don't want to set them up manually.

Is there any way to do this?

Update: I think this works, can anyone see any problems? -->

cd a
git clone --no-hardlinks --no-checkout ../b a.tmp 
mv a.tmp/.git .
rm -rf a.tmp
git unstage # apparently git thinks all the files are deleted if you don't do this

Answer 1

Maybe I misunderstood your question, but wouldn't it be simpler if you copy/move the files from A to the git repo B and add the needed ones with git add?

UPDATE: From the git doc:

Cloning into an existing directory is only allowed if the directory is empty.

SOURCE: http://www.kernel.org/pub/software/scm/git/docs/git-clone.html

Answer 2

Given a directory, a, of files files matching a git repository, b, of tracked files:

git clone --no-checkout b a/a.tmp # might want --no-hardlinks for cloning local repo
mv a/a.tmp/.git a/
rm -rf a/a.tmp
cd a
git unstage # git thinks all files are deleted, this reverses that behaviour