In 3.2.x and 3.3.3 if you enter a short query there is a bar below with the following options:
[ Edit ] [ Explain SQL ] [ Create PHP Code ] [ Refresh ]
If you enter a long query, scrollbars are used to allow the query to scroll (though after a certain point it still gets truncated with ...). The bar mentioned above no longer appears.
It's then necessary to open the query window using the icon at the top left and copy and paste your query if history is not enabled. As mentioned above, at a certain point the query gets truncated making cut and paste impossible too.
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I'm not sure if there is, perhaps, just a CSS issue hiding those links. I've tested on Firefox3.6.3 and Chrome 5.0.375.55 both have the same issue.
This bug was fixed in repository and will be part of a future release; thanks for reporting.