Final cleanup after checkpoint 3 and remove the completed implementation plan

docs/policy/architecture.md

@@ -211,6 +211,13 @@ envelope with `json.RawMessage` payloads; extract modules should own typed Go
 structs at their boundaries and encode into that generic envelope before
 returning to framework code.
 
+Output-stage warnings are intentionally out-of-band. An `OutputEncoder` may
+return warnings about serialization, formatting, truncation, or destination
+concerns, but those warnings are appended to the runner result after encoding
+and are not expected to appear inside the encoded artifact bytes. CLI,
+diagnostic, or reporting layers should surface output-stage warnings from the
+runner result.
+
 Schemas should be versioned per extractor, with a separate envelope/manifest
 format version.