Cannot refactor

when i try refactor > change signature on a function definition I get a pop saying "Cannot Refactor. Source is not under root". The file i'm working on does live within the current project. It works on other projects.
Is there something I'm doing wrong?
the actual message is "Cannot perform Refactoring. Function is not under the source root"
I blew away the .PyCharm20 folder and that seems to have fixed it
I have the same problem on PyCharm 3.0.2 (upgraded from 2.7). Can you be more verbose which folder is need to be deleted? On Mac OS there are at least 4 PyCharm30 folders:

./../Library/Application Support/PyCharm30
I had the same problem on 3.0.2 on Windows.  I removed the .PyCharm30/system folder which didn't fix it.

It turns out that I was using a different project interpreter with extra paths added.  Once I switched the Project Interpreter back to the default Python2.7 interpreter that fixed the refactoring.

You might check your Project Interpreter settings.

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