I know nothing about Pyflakes - does it take a file on standard input (Eg at your prompt do you do `pyflakes somefile.py`)? If so you should be able to use a unix script to just pass the currently open file (via the env vars mentioned in the manual) to pyflakes and send output to STDERR if you've got a problem. bonus points if you use AppleScript to save the document first or attach it as a save event (checking document type or extension first).
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