Other p2p programs such as LimeWire sometimes see users using their program folder as the download location, then after they update the program find their downloads have all been erased by the updated program.

Download files inside the Phex folder might be something which could work. Though I'm not a very friend of it. Since the Phex version update and uninstall problem would exist.

The preferences would never go there, specially because since system can be multi-user and out of privacy preferences should be only user related and accessible.

BTW: It sounds strange, but its defiantly not that easy to determine the Phex installation folder... Additionally Phex is not really required to be installed. You could put Phex files onto a network share and use it from Windows, Unix and OS X system in parallel.

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