The user directories aren't important.

unicode.6.font is:

11	9
0x0000	0x00FF	lsr.10
0x0100	0x01f0	../lucida/EuroLatin.5.0
0x2000	0x20aa	../lucida/GenPunct.5.0
0x2200	0x22f1	../lucida/MathOps1.5.0

The /lib/ndb files should be your own, just edit the proto.

/sys/lib/music on our side was just some music files in a
format we're not allowed to release code for.

You shouldn't be using disk/mkfs, you should be using
disk/mksacfs.

The idea is to make a read only file system with what you want in
it to serve as a root file system.  We'll be releasing an update
with a journaling flash file system for the rest of the flash
soon.  I want to test it out a bit first.

That means that the eventual flash memory layout will be:

bootldr
kernel
parameters
compressed read only file system (sac)
journal based real file system (flashfs)

The bootldr is the linux one that you can load following the
instructions on the handhelds.org page.