[Rails] advice upgrading to rails 3.1 from 2.3

Hey all,
I have a fairly large application in Rails 2.3 I would like to
upgrade the site to Rails 3.1
Now, the advice i need here is..
What is most likely a cleaner solution? Do i cd into my rails app, do
a backup and rails new . over the top and go through and fix what is
broken then?
Or, would it be cleaner to start fresh, and move my older code into
place on a file by file basis?

One more question. My existing app uses prototype, i will likely want
to start in JQuery soon, but need both to work for a while, is this
going to be a problem?

thanks

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