make run-cosmos handed the emulator a boot image AND a disk, so it took the
direct path every time: memory placed from outside, nothing on the disk
consulted about it. The whole boot chain was built and tested and then not
used by the one command that runs the system.
The disk is formatted with a boot area now, stage two goes into slot zero
as raw bytes, and the system is an ordinary file at /System/Boot/cosmos.bin
- which is what boot.cfg would choose between if there were one. There is
not: stage two falls back to that name when the file is missing, and a
clean install with nothing to configure is the right default.
run-cosmos names no image, so the machine starts itself. The old behaviour
is run-cosmos-direct, which is worth keeping and worth naming honestly: it
is what a debugger does, and it is what to use when the thing being
debugged is the boot chain, since it skips the boot chain.
/Source gains stage1.asm and stage2.asm, so the machine can rebuild what
starts it. Everything stage two includes is already in /Lib, so Asm
stage2.asm on the machine produces the bytes a boot slot takes. Stage one
is the exception and always will be: it is the ROM, and the one part of
this that a disk cannot replace.
Second slot left empty, which is what makes replacing the first survivable.