Clone/commit of private repo corrupts every time

[bigUNO]

When trying to clone a private repo in bitbucket.org, the git directory gets corrupted. I can clone HelloWorld and make commits so the logic in that portion of the code works.

git commit -m "example go-git commit"
panic: runtime error: invalid memory address or nil pointer dereference
[signal 0xc0000005 code=0x0 addr=0x8 pc=0x728dc8]

goroutine 1 [running]:
gopkg.in/src-d/go-git%2ev4.(*buildTreeHelper).copyTreeToStorageRecursive(0xc0423eddb8, 0xc042414540, 0x21, 0x0, 0x0, 0x0, 0xc000000000, 0x44260e, 0x0)
        C:/Users/johnsol/go/src/gopkg.in/src-d/go-git.v4/worktree_commit.go:167 +0x78
gopkg.in/src-d/go-git%2ev4.(*buildTreeHelper).copyTreeToStorageRecursive(0xc0423eddb8, 0xc04210cee0, 0x17, 0xc042191540, 0x0, 0x0, 0xc000000000, 0x44260e, 0x0)
        C:/Users/johnsol/go/src/gopkg.in/src-d/go-git.v4/worktree_commit.go:175 +0x218
gopkg.in/src-d/go-git%2ev4.(*buildTreeHelper).copyTreeToStorageRecursive(0xc0423eddb8, 0xc04210ce20, 0x15, 0xc0421914a0, 0x0, 0x0, 0xc000000000, 0x0, 0x0)
        C:/Users/johnsol/go/src/gopkg.in/src-d/go-git.v4/worktree_commit.go:175 +0x218
gopkg.in/src-d/go-git%2ev4.(*buildTreeHelper).copyTreeToStorageRecursive(0xc0423eddb8, 0xc0421e2080, 0xd, 0xc0421913b0, 0x0, 0x0, 0x0, 0x0, 0x0)
        C:/Users/johnsol/go/src/gopkg.in/src-d/go-git.v4/worktree_commit.go:175 +0x218
gopkg.in/src-d/go-git%2ev4.(*buildTreeHelper).copyTreeToStorageRecursive(0xc0423eddb8, 0xc042182040, 0x4, 0xc042191360, 0x0, 0x0, 0x0, 0x0, 0x0)
        C:/Users/johnsol/go/src/gopkg.in/src-d/go-git.v4/worktree_commit.go:175 +0x218
gopkg.in/src-d/go-git%2ev4.(*buildTreeHelper).copyTreeToStorageRecursive(0xc0423eddb8, 0x0, 0x0, 0xc042191090, 0x0, 0x0, 0xc000000000, 0xc042204bd0, 0x9a5da0)
        C:/Users/johnsol/go/src/gopkg.in/src-d/go-git.v4/worktree_commit.go:175 +0x218
gopkg.in/src-d/go-git%2ev4.(*buildTreeHelper).BuildTree(0xc0423f1db8, 0xc042204bd0, 0x0, 0x0, 0x0, 0x7ffe0014, 0x1d346842c37a532)
        C:/Users/johnsol/go/src/gopkg.in/src-d/go-git.v4/worktree_commit.go:127 +0x254
gopkg.in/src-d/go-git%2ev4.(*Worktree).Commit(0xc0423dd3c0, 0x801da2, 0xe, 0xc0423edf38, 0x0, 0x0, 0x0, 0x0, 0x40f05c)
        C:/Users/johnsol/go/src/gopkg.in/src-d/go-git.v4/worktree_commit.go:39 +0x149
main.copyMachine()
        C:/Users/johnsol/go/src/duplicator/duplicator.go:89 +0x4e6
main.main()
        C:/Users/johnsol/go/src/duplicator/duplicator.go:102 +0x27
exit status 2

When inspecting the repo after the program runs I get the following message.

λ git status
fatal: internal error: ce_mode is 40000

I'm wondering if this has more to do with SSH/Pageant on Windows. (I'm not a native Windows user). Can someone get me pointed in the right direction?

[bigUNO]

Snippet of code

const (
	url = "reverseflapjack@bitbucket.org:foo/bar.git"
	//url       = "https://github.com/octocat/Hello-World.git"
	directory = "hw"
	testfile  = "test.txt"
)

func defaultSignature() *object.Signature {
	return &object.Signature{
		Name:  "reverseflapjack",
		Email: "flapmyjacks@example.com",
		When:  time.Now(),
	}
}
....

	// clone the given repository to the given directory
	Info("git clone %s %s --recursive", url, directory) // logging
	r, err := git.PlainClone(directory, false, &git.CloneOptions{
		URL: url,
	})
	CheckIfError(err)

	w, err := r.Worktree()
	CheckIfError(err)
	// ... we need a file to commit so let's create a new file inside of the
	// worktree of the project using the go standard library.
	Info("echo \"hellow world!\" > example-git-file")
	filename := filepath.Join(directory, "example-git-file")
	err = ioutil.WriteFile(filename, []byte("hello world!"), 0644)
	CheckIfError(err)

	// Adds the new file to the staging area.
	Info("git add example-git-file")
	_, err = w.Add("example-git-file")
	CheckIfError(err)

	// We can verify the current status of the worktree using the method Status.
	Info("git status --porcelain")
	status, err := w.Status()
	CheckIfError(err)

	fmt.Println(status)

	// Commits the current staging are to the repository, with the new file
	// just created. We should provide the object.Signature of Author of the
	// commit.
	Info("git commit -m \"example go-git commit\"")
	commit, err := w.Commit("Adds test file", &git.CommitOptions{Author: defaultSignature()})
	CheckIfError(err)

	// Prints the current HEAD to verify that all worked well.
	Info("git show -s")
	// makes the commit
	obj, err := r.CommitObject(commit)
	CheckIfError(err)

	fmt.Println(obj)

[mcuadros]

Are you using windows? Looks like the generated .git/index is corrupted do to invalid mode. But I can replicate this on Linux.