docs: Document the boxes

Add a top-level `README.md` mapping the boxes and per-machine docs under
`docs/boxes/` (grouped `colony/`, `home/`, `misc/`), one file per host, VM and
container documenting role, services and networking with source pointers.

Also point `AGENTS.md` at the new docs.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

docs/boxes/colony/colony.md

@@ -0,0 +1,39 @@
+# colony (host)
+
+The physical dedicated server in Amsterdam and the VM host for everything in
+this group.
+
+- **Source:** [`nixos/boxes/colony/default.nix`](../../../nixos/boxes/colony/default.nix)
+  (VM instances in [`nixos/boxes/colony/vms/default.nix`](../../../nixos/boxes/colony/vms/default.nix))
+- **nixpkgs:** `mine-stable`
+
+## Role
+
+Bare-metal AMD host. It does little application work itself — its job is to run
+the VMs and provide them with storage, networking and backups.
+
+- **Virtualisation:** QEMU/KVM (`kvm-amd`, IOMMU on) via the `my.vms` module. VM
+  disks are LVM logical volumes (`vm-<name>-<disk>`) in the `main` volume group;
+  `estuary` additionally gets a WAN NIC by PCI passthrough.
+- **Storage:** LVM-thin (`services.lvm.boot.thin`), `/persist` for state,
+  `/mnt/backup` for the local borg repo. `smartd` + `rasdaemon` for health.
+- **Backups:** `my.borgthin` snapshots the persist/data LVs of the host and its
+  VMs into `/mnt/backup/main`, which is then `rsync`'d (along with LVM metadata)
+  to rsync.net (`zh2855.rsync.net`).
+- **Monitoring:** netdata (with freeipmi), smartd.
+
+## Networking
+
+- Two bridges: `base` (the colony "base" network, shared with `estuary`) and
+  `vms` (the VM network). Dummy interfaces keep the bridges up so dependent VMs
+  can start.
+- Default gateway / edge is `estuary`; `colony` itself holds the `routing` and
+  `internal` (a.k.a. `vm`) assignments and routes container/OCI/Tailscale
+  prefixes to `shill` and `whale2`.
+- `my.firewall` trusts the `vms` interface and forwards customer prefixes
+  (`vm-mail`, `vm-darts`) through.
+
+## VMs hosted here
+
+`estuary`, `shill`, `whale2`, `git` (all NixOS, documented in this directory),
+plus the non-NixOS `mail` and `darts` (see [README](README.md#non-nixos-vms)).