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There are several orphanend open-source projects aiming to support NetMD Walkman devices under Linux, namely:
libnetmd: A library to connect to NetMD Walkman - http://libnetmd.sourceforge.net/ and http://www.unmaintained-free-software.org/wiki/Libnetmd
Patch for libnetmd to add support for MZ-RH1 and -RH10, also minor casting fixes: http://users.physik.fu-berlin.de/~glaubitz/linux-minidisc/0001-cast-fixes-MZ-NH600-MZ-RH1-MZ-RH10-support-adde.patch
gnetmd: A GUI for libnetmd - http://www.pdr.cx/projects/gnetmd/main/
Xmd: NetMD software for Mac OS X - http://www.sorted.org/Xmd/
WinNMD: non-free Windows software - http://winnmd.net/
FreeMD: how the NetMD protocol works, and a shell to set track titles etc.
The NetMD protocol is based on the AV/C Digital Interface Command Set, an 1394 TA specification:
Loading files on the MiniDisc Player, in particular the role of the EKB, is described in the US Patent 7228568 (retrieved via http://www.pat2pdf.org/), which contains some hilariously bad cryptography (and is in any other way utterly trivial). This answers many, but not all, questions about the file transfer logs.
TODO: Check other Sony patents.
There is a funding project, supporting a resume of the development of the libnetmd software, see http://www.cofundos.org/project.php?id=122.