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I have a couple of mp3 (caf) and jpg files that I would like to use in a script.
I used to transfer these via iFunBox, but in the later versions of iOS wthis doesn't work anymore. Also my prefered Syncios is not able to access Pythonista anymore.
What is the easiest way to transfer this type of files?

You can upload them to Dropbox and use one of the various Dropbox interaction scripts on this forum to download them into Pythonista. Alternatively upload them to some kind of web server (local ones started by an app like "USB Disk Pro" work as well, that's what I usually so) and download them using the wget command in stash.