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.

system/devices/device-tree.zig

@@ -0,0 +1,16 @@
+//! Device-tree (Flattened Device Tree / FDT) discovery backend — stub.
+//!
+//! This is the second backend the platform facade dispatches to, for machines
+//! that describe hardware with a device-tree blob instead of ACPI (typically
+//! ARM). It is intentionally unimplemented: the bootloader has no DTB handoff
+//! field yet, so this path is currently unreachable. It exists so the facade
+//! already routes to a backend rather than hard-coding ACPI — wiring the FDT
+//! parser in later is a local change here, not an architectural one.
+
+const device_model = @import("device-model.zig");
+
+/// Populate `device_tree` from a device-tree blob. Not implemented yet.
+pub fn discover(device_tree: *device_model.DeviceTree) !void {
+    _ = device_tree;
+    return error.Unsupported;
+}