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 ./....
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