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If you need to clone a GIT repository into an existing directory with files, use the following commands in command prompt in order.
git init
git init add origin PATH/TO/REPO
git fetch
git reset origin/master
git checkout -t origin/master
git init add origin PATH/TO/REPO
git fetch
git reset origin/master
git checkout -t origin/master
After this, you can easily use your favorite GUI tool like TortoiseGIT or command line to sync files.