[BUG] `git submodule update --init --recursive` stores gitdir in full path into `.git` of nested submodules

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Hi,

`git submodule update --init --recursive` stores `gitdir` in full path into `.git` of nested submodules.
So, working directory is not portable to another directory.

On following example, `Carthage/Checkouts/Quick/Externals/Nimble/` is nested submodule and `Carthage/Checkouts/Quick/Externals/Nimble/.git` contains full path.
https://gist.github.com/norio-nomura/17ce4bdf0151185e77d9b1fcfb5a469d

Thanks,
--
Norio Nomura @norio_nomura

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