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/system-call.zig

@@ -0,0 +1,52 @@
+//! Raw `system_call` instruction wrappers for user space — one per arity.
+//!
+//! ABI: number in rax, arguments in rdi, rsi, rdx, r10, r8, r9, result in rax.
+//! The `system_call` instruction itself clobbers rcx (it holds the return rip) and
+//! r11 (the saved rflags); the kernel entry stub preserves everything else.
+//! Note argument #3 goes in **r10, not rcx** — rcx is unavailable across the
+//! instruction, so the kernel reads the 4th argument from r10.
+
+const danos = @import("danos");
+const SystemCall = danos.SystemCall;
+
+pub inline fn systemCall0(n: SystemCall) usize {
+    return asm volatile ("syscall"
+        : [ret] "={rax}" (-> usize),
+        : [n] "{rax}" (@intFromEnum(n)),
+        : .{ .rcx = true, .r11 = true, .memory = true });
+}
+
+pub inline fn systemCall1(n: SystemCall, a0: usize) usize {
+    return asm volatile ("syscall"
+        : [ret] "={rax}" (-> usize),
+        : [n] "{rax}" (@intFromEnum(n)), [a0] "{rdi}" (a0),
+        : .{ .rcx = true, .r11 = true, .memory = true });
+}
+
+pub inline fn systemCall2(n: SystemCall, a0: usize, a1: usize) usize {
+    return asm volatile ("syscall"
+        : [ret] "={rax}" (-> usize),
+        : [n] "{rax}" (@intFromEnum(n)), [a0] "{rdi}" (a0), [a1] "{rsi}" (a1),
+        : .{ .rcx = true, .r11 = true, .memory = true });
+}
+
+pub inline fn systemCall3(n: SystemCall, a0: usize, a1: usize, a2: usize) usize {
+    return asm volatile ("syscall"
+        : [ret] "={rax}" (-> usize),
+        : [n] "{rax}" (@intFromEnum(n)), [a0] "{rdi}" (a0), [a1] "{rsi}" (a1), [a2] "{rdx}" (a2),
+        : .{ .rcx = true, .r11 = true, .memory = true });
+}
+
+pub inline fn systemCall4(n: SystemCall, a0: usize, a1: usize, a2: usize, a3: usize) usize {
+    return asm volatile ("syscall"
+        : [ret] "={rax}" (-> usize),
+        : [n] "{rax}" (@intFromEnum(n)), [a0] "{rdi}" (a0), [a1] "{rsi}" (a1), [a2] "{rdx}" (a2), [a3] "{r10}" (a3),
+        : .{ .rcx = true, .r11 = true, .memory = true });
+}
+
+pub inline fn systemCall5(n: SystemCall, a0: usize, a1: usize, a2: usize, a3: usize, a4: usize) usize {
+    return asm volatile ("syscall"
+        : [ret] "={rax}" (-> usize),
+        : [n] "{rax}" (@intFromEnum(n)), [a0] "{rdi}" (a0), [a1] "{rsi}" (a1), [a2] "{rdx}" (a2), [a3] "{r10}" (a3), [a4] "{r8}" (a4),
+        : .{ .rcx = true, .r11 = true, .memory = true });
+}