Calibre will not help (on Mac) if you want to copy .notebook or .sdr folders.
Of course there is open-source OpenMTP GUI for that.
For command line on Mac (maybe linux too) you can install
mtplib which includes 'demonstration' command line tools that can list devices, copy files, etc.
Code:
mtp-albumart mtp-files mtp-newfolder mtp-thumb
mtp-albums mtp-filetree mtp-newplaylist mtp-tracks
mtp-connect mtp-folders mtp-playlists mtp-trexist
mtp-delfile mtp-format mtp-reset
mtp-detect mtp-getfile mtp-sendfile
mtp-emptyfolders mtp-getplaylist mtp-sendtr
What I'm looking for is Python library to do MTP. There's one for 2.x but it does not work with Python 3. Of course calibre has one; if I get some time I might try to see if I can make a freestanding version of that.
That said, kudos for this tool!