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.

library/runtime/device.zig

@@ -0,0 +1,67 @@
+//! User-space device access: enumerate the kernel's device table, claim a device,
+//! map its MMIO, and bind its interrupt. A driver uses these to find and take
+//! ownership of its hardware; the claim is the capability the kernel checks before
+//! mapping registers or routing an IRQ.
+
+const danos = @import("danos");
+const sc = @import("system-call.zig");
+
+pub const DeviceDescriptor = danos.DeviceDescriptor;
+pub const ResourceDescriptor = danos.ResourceDescriptor;
+pub const DeviceClass = danos.DeviceClass;
+pub const ResourceKind = danos.ResourceKind;
+
+inline fn failed(r: usize) bool {
+    return r > ~@as(usize, 0) - 4095;
+}
+
+/// Copy up to `buffer.len` device descriptors into `buffer`; returns the total count.
+pub fn enumerate(buffer: []DeviceDescriptor) usize {
+    return sc.systemCall2(.device_enumerate, @intFromPtr(buffer.ptr), buffer.len);
+}
+
+/// Take exclusive ownership of device `id`. Returns false if taken or invalid.
+pub fn claim(id: u64) bool {
+    return !failed(sc.systemCall1(.device_claim, id));
+}
+
+/// Map resource `resource_index` (which must be an MMIO window) of claimed device
+/// `device_id` into this address space; returns the register base virtual address.
+pub fn mmioMap(device_id: u64, resource_index: u64) ?usize {
+    const r = sc.systemCall2(.mmio_map, device_id, resource_index);
+    return if (failed(r)) null else r;
+}
+
+/// `DeviceDescriptor.parent` for a device with no parent.
+pub const no_parent = danos.no_parent;
+
+/// Publish `descriptor` as a child of `parent_id`, which this process must have claimed.
+/// Returns the new device id. The child is left unclaimed, so whichever driver owns
+/// that class of device can `claim` it — that is how a bus hands off a device.
+///
+/// Every resource in `descriptor` must be **contained** in a parent resource of the same
+/// kind: a sub-window of the parent's MMIO, or one of its IRQs. The kernel refuses
+/// anything else, because a device descriptor is a licence to map physical memory and
+/// a bus driver may only subdivide what it already owns. `descriptor.id` and `descriptor.parent`
+/// are ignored. A device with no resources at all is fine — a USB device is reached
+/// through its controller, not by MMIO.
+pub fn register(parent_id: u64, descriptor: *const DeviceDescriptor) ?u64 {
+    const r = sc.systemCall2(.device_register, parent_id, @intFromPtr(descriptor));
+    return if (failed(r)) null else r;
+}
+
+/// Bind resource `resource_index` (which must be an IRQ) of claimed device `device_id` to
+/// `endpoint`. From then on the interrupt arrives as an asynchronous notification:
+/// `ipc.replyWait` on that endpoint returns with the high bit set in `badge` and the
+/// low bits carrying the GSI. The kernel masks the line before waking you.
+pub fn irqBind(device_id: u64, resource_index: u64, endpoint: usize) bool {
+    return !failed(sc.systemCall3(.irq_bind, device_id, resource_index, endpoint));
+}
+
+/// Re-arm a bound IRQ. Call this **after** quieting the device (clearing whatever
+/// status register holds its line asserted) — the kernel left the line masked
+/// precisely because it could not do that for you. Skip it and the interrupt never
+/// fires again; call it before the device is quiet and a level-triggered line storms.
+pub fn irqAck(device_id: u64, resource_index: u64) bool {
+    return !failed(sc.systemCall2(.irq_ack, device_id, resource_index));
+}