I have a git repository which has many branches my requirement is to create a new empty branch so that its independent of the earlier branches.
That's not a good practice, but if you want really start with a new branch without relation to master you must use --orphan argument of checkout :
git checkout --orphan version2
# and remove your project files
You'll get more detail about --orphan arguments in the doc : http://git-scm.com/docs/git-checkout
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