Canonicalize chunk units before extraction

docs/internal/modules.md

@@ -49,6 +49,10 @@ The `generic` chunker splits source units into ordered chunks. It validates the
 source document, clones source units, assigns chunk IDs such as `chunk-000001`,
 and records chunk metadata for start unit, end unit, and unit count.
 
+The pipeline runner canonicalizes chunk units from the source document by ID
+before extractors and mergers run. Chunker-owned context should stay in
+`SourceChunk.Metadata`.
+
 Options:
 
 - `max_units`: positive integer, default `50`;

docs/internal/pipeline.md

@@ -97,6 +97,11 @@ invariants before running extractors:
 - every chunk source unit must exist in the source document;
 - source units inside each chunk must appear in source-document order.
 
+After validation, the runner rebuilds each chunk from source-document units by
+ID, preserving the chunk boundary order and cloning chunk metadata. Extractors
+and downstream stages therefore see canonical source units, while
+`SourceChunk.Metadata` remains the supported place for chunker-owned context.
+
 The framework does not require complete source-unit coverage and does not reject
 overlap between different chunks. Stricter policies, such as full coverage or
 non-overlap, belong to individual chunk modules when they are part of that