Regular iOS App Store apps can exchange files with computers via iTunes by turning on UIFileSharingEnabled
in their Info.plist. The files exchanged are placed in and/or retrieved from the Documents
directory for the app. Jailbreak/Cydia apps, being System apps, don't have such a directory--so I'm assuming they can't use this feature to exchange files with a computer? (Obviously jailbreak devices have more options to exchange files like ssh.)
EDIT: Just to be clear, I'm talking about system apps, not regular apps that happen to be headed for Cydia for whatever reason.