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/paging.md

@@ -7,7 +7,7 @@ which live in memory we'd like to reclaim and don't control), switches CR3 onto
 them, and — crucially — maps with **real permissions**.
 
 It's x86_64-specific (the 4-level table format is an Intel/AMD thing), so it lives
-behind the [arch](arch.md) boundary in `src/kernel/arch/x86_64/paging.zig`.
+behind the [arch](arch.md) boundary in `system/kernel/architecture/x86_64/paging.zig`.
 
 ## The format
 
@@ -27,7 +27,7 @@ address to the low load address in its bootstrap tables and jumps in). The entir
 alongside a **physmap** — a straight window onto all of physical memory at
 `physmap_base + phys`. Wherever the kernel needs to touch a physical address (a
 page-table frame, an ACPI table, a device register), it adds that constant:
-`danos.physToVirt(phys)`. The layout constants live in `src/root.zig`:
+`danos.physToVirt(phys)`. The layout constants live in `system/danos.zig`:
 
 | region | virtual base | PML4 slot |
 |--------|--------------|-----------|