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First get to the existing directory
$ cd my/folder/
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Now start a new git repository
$ git init
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Identify if the current elements on the directory are needed or not and add them to the .gitignore file. When ready...
$ vim .gitignore
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When ready create the first commit on the server
$ git add .;git commit -m'my first commit'
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Now add the remote from where you want to clone
$ git remote add origin https|ssh:path/to/the/repository.git
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Now just pull and merge with local git
$ git pull origin master
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If you have some merge conflicts resolve them and commit your changes.
You are ready to go!