Re-organize the source tree as a monorepo mirroring the FHS

The source layout now mirrors the runtime filesystem hierarchy
(docs/danos-file-system-hierarchy-FSH.md): what lives under system/ in the
source is what a running danos represents under /system. Each service and
driver is a sub-project directory that is its own Zig module — cross-project
references go by module name, never by a path into another project's files.

Moves (all git mv, history preserved):
- src/            -> system/            (danos internals; the self-representation)
    root.zig      -> danos.zig          (the kernel<->user contract module)
    kernel/arch/  -> kernel/architecture/   (arch -> architecture)
    device/       -> devices/           (what /system/devices reflects)
    boot/         -> /boot              (the loaders, top level)
- sbin/           -> split by role:
    init, vfs     -> system/services/<name>/<name>.zig
    hpetd, busd   -> system/drivers/<name>/<name>.zig
    vfs-test      -> system/services/vfs/vfs-test.zig  (inside the vfs project)
- lib/            -> library/runtime/   (room for other libraries beside runtime)

The VFS wire protocol becomes its own module, system/services/vfs/protocol.zig
("vfs-protocol"): the vfs sub-project exposes its interface, and the runtime's
file layer imports it by name. First instance of the "protocol module" pattern
(docs/driver-model.md); usb/block will expose theirs the same way.

Also: fix a naming-standard violation in the protocol — Op -> Operation (and
req -> request, _pad -> _padding). Docs updated: /system/services added to the
FHS doc, a repository-layout section added to the docs index, and stale source
paths swept across comments and docs.

Runtime boot paths are unchanged (the bootloader still loads /sbin/init);
aligning the runtime filesystem to the FHS is a separate follow-up. Suite 35/35
plus host tests green.

docs/syscall.md

@@ -6,7 +6,7 @@ System calls (syscalls) are the bridge between your programs and the operating s
 > `isr.s` does the `swapgs` + kernel-stack switch and reuses the interrupt
 > dispatcher). The `int 0x80` gate is kept alongside as a minimal test path. The
 > current call set is still a placeholder — `0 = exit(code)`, `1 = ping`,
-> `2 = write(ptr, len)`, `3 = sleep(ms)` (see `src/kernel/process.zig`); the
+> `2 = write(ptr, len)`, `3 = sleep(ms)` (see `system/kernel/process.zig`); the
 > handler dispatches on whether the caller is a scheduled process (its own address
 > space) or a borrowed test thread. The microkernel set below (IPC_Call /
 > IPC_ReplyWait / Yield) replaces it once a second user server exists.