Reorganize the source checkout layout

Separate tracked source from generated artifacts so the repo root stops accumulating helper scripts, manifests, and local runtime outputs.

Move manual shell entrypoints under scripts/, manifests under config/, and the Firecracker API reference under docs/reference/. Make build and runtimebundle now target build/bin, build/runtime, and build/dist as the canonical source-checkout paths.

Update runtime discovery, helper scripts, tests, and docs to follow the new layout while keeping legacy source-checkout runtime fallbacks for existing local bundles during migration.

Validated with bash -n on the moved scripts, make build, and GOCACHE=/tmp/banger-gocache go test ./....

runtime-bundle.toml

@@ -1,33 +0,0 @@
-# Template manifest for local or published runtime bundle archives.
-# Keep this checked-in file empty by default; use a local manifest copy with
-# concrete `url` and `sha256` values when bootstrapping `./runtime/`.
-version = "v0"
-url = ""
-sha256 = ""
-bundle_root = "runtime"
-required_paths = [
-  "firecracker",
-  "customize.sh",
-  "packages.sh",
-  "namegen",
-  "banger-vsock-agent",
-  "packages.apt",
-  "id_ed25519",
-  "rootfs-docker.ext4",
-  "wtf/root/boot/vmlinux-6.8.0-94-generic",
-  "wtf/root/boot/initrd.img-6.8.0-94-generic",
-  "wtf/root/lib/modules/6.8.0-94-generic",
-]
-
-[bundle_metadata]
-firecracker_bin = "firecracker"
-ssh_key_path = "id_ed25519"
-namegen_path = "namegen"
-customize_script = "customize.sh"
-vsock_agent_path = "banger-vsock-agent"
-default_packages_file = "packages.apt"
-default_rootfs = "rootfs-docker.ext4"
-default_work_seed = "rootfs-docker.work-seed.ext4"
-default_kernel = "wtf/root/boot/vmlinux-6.8.0-94-generic"
-default_initrd = "wtf/root/boot/initrd.img-6.8.0-94-generic"
-default_modules_dir = "wtf/root/lib/modules/6.8.0-94-generic"