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/services/init/init.zig

@@ -0,0 +1,39 @@
+//! /sbin/init — the first user-space program, PID 1. Built as its own
+//! freestanding binary (see build.zig), shipped on the boot volume at sbin/init,
+//! loaded by the bootloader, and started in ring 3 as a scheduled process by the
+//! kernel (system/kernel/process.zig). It links against the shared user runtime
+//! library `runtime` and talks to the kernel only through `runtime`'s system_call wrappers.
+//!
+//! Today it proves the C-convention heap works, then settles into a heartbeat:
+//! it prints a line and sleeps, forever — enough to show the system reaches user
+//! space and stays alive with a real process scheduled alongside the kernel's
+//! idle loop. It grows into the real init (service supervision) once there are
+//! other user programs to supervise.
+
+const runtime = @import("runtime");
+
+pub fn main() void {
+    // Prove the heap end to end: allocate through the runtime allocator (which
+    // mmaps pages from the kernel and carves them with the free list), write into
+    // that heap buffer (exercising the widened debug_write bounds check), and
+    // free it. A fault here would kill init before it heartbeats — so the init
+    // test doubles as the heap regression test. (C code links the same heap via
+    // the extern malloc/free symbols; Zig code uses this allocator.)
+    const gpa = runtime.allocator();
+    if (gpa.alloc(u8, 64)) |buffer| {
+        const message = "init: heap ok\n";
+        @memcpy(buffer[0..message.len], message);
+        _ = runtime.system.write(buffer[0..message.len]);
+        gpa.free(buffer);
+    } else |_| {}
+
+    while (true) {
+        _ = runtime.system.write("init: heartbeat\n");
+        runtime.system.sleep(1000);
+    }
+}
+
+pub const panic = runtime.panic;
+comptime {
+    _ = &runtime.start._start; // pull the runtime entry shim into the image
+}