Why would you not be able to access the filesystem of a device you own and are in possession of? Is this some kind of walled-garden thing I'm too Apple-free to understand?
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In most non Apple Desktops, the most you'd get from connecting your iPad/iPhone is access to the photos and videos. You'd need to use iTunes to access the music or device documents.
On Macs it "Just works" and gives you full access to music and files.
While I can't access my iPads videos and music in Mint. It's nice to at least get me access to the documents, along side the camera videos and pictures. Not as good as I'd like it to be, but a lot better than what you can do with Windows... without installing iTunes.
Different protocols? Like android's mtp? Never had an apple device, what do they use?
SMB works on Apple stuff. I thought you had Nemo on an ipad...
Oh how I wish I had nemo on the iPad rather than apple's own files app. The issue with SMB is getting files off of the iPad, this is a little easier for me since I can do so from my PC. And I'm not dealing with Apple's files app silently crashing on me.
Checkout syncthing. They have an iOS port but of course its paid as apple is always paid.