Built-in checkout: wrong behaviour in subdirectories

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Hi,

The following test shows a problem since commit 782c2d6 (Build in checkout):

mkdir testrep
cd testrep
git init

: >file1
git add file1
git commit -m 'initial'

git branch dev

mkdir dir1
cd dir1
# this creates dir1/file1
git checkout dev

Regards,
Clemens
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