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Step to reproduce:
$ echo 'file("/some/file")' | python `which 2to3` -
(replace python with whichever python executable version you wish to
use, e.g. ~/python-trunk/python or /usr/local/bin/python3.2 )
Expected result:
Anything referring to the fact that the "file" type no longer exists in
python 3.x, whether it be a warning or a refactoring.
Actual result:
RefactoringTool: No files need to be modified.
Just a report for now, I don't have the time to write a patch.

Patch attached. Unit test and documentation included.
COMMITMSG:
Adds a new fixer to lib2to3 which replaces the deprecated builtin "file" with "open".

Woops. Removed the extra comments. Updated patch attached.

Unfortunately this patch would also replace legitimate uses of a "file" function.

I thought the whole point was that file[1] was removed in 3.0[2]? Or, are you saying that if somebody overloaded file with def file(...)? If that is the case would it be reasonable to check like this?
>>> file in list(__builtins__.__dict__.values())
True
>>> def file():
... pass
... 
>>> file in list(__builtins__.__dict__.values())
False
>>> 
[1] - http://docs.python.org/library/functions.html?highlight=file#file
[2] - http://docs.python.org/3.1/whatsnew/3.0.html#builtins 

Yes, the idea was that it doesn't seem outlandish for someone to do:
def file(something):
 do_stuff()
You can use lib2to3.fixer_util.is_probably_builtin for this... modified the patch and attached.