Cleanup and complete the pipeline refactor

docs/internal/pipeline.md

@@ -60,10 +60,11 @@ extractor, merger, or normalizer request. LLM-backed modules pass that material
 onward as named Scriptorium prompt inputs.
 
 The CLI carries raw input bytes into `pipeline.RunInput`. Input adapters parse
-those bytes into the source document, while LLM-backed modules that need the
-original transcript material can pass the same bytes as a prompt input with
-origin metadata. The raw input payload is not written to manifests or default
-diagnostics.
+those bytes into the source document. Chunk, merge, and normalize requests
+receive the original source material as `SourceInput`; extraction requests
+receive chunk-scoped source material built from the current `SourceChunk`
+content, media type, and origin metadata. The raw input payload is not written
+to manifests or default diagnostics.
 
 The CLI also carries an optional run `session_id`. The runner makes it available
 to chunk, extract, merge, and normalize requests; LLM-backed modules forward it
@@ -186,6 +187,11 @@ Runner-side raw validation chains receive the raw module output plus
 stage, lane, module, source, and chunk provenance. Empty raw validation chains
 approve output by default.
 
+Pipeline-configured validator lists are not part of the current runner
+contract. Non-empty configured validator lists are rejected during configuration
+validation or resolved-run validation so they cannot appear in manifests without
+executing.
+
 Validator rejection is a non-fatal run outcome: the rejected output is recorded
 in `RunOutput.Rejected` and does not pass to the next stage. Validator execution
 errors are framework-level errors and retry according to the relevant binding.