Document extraction reference support

docs/operations.md

@@ -35,7 +35,8 @@ The `json` output module writes these files:
 - `index.json`: file index with paths to the manifest, artifact files,
   rejected artifacts, and warnings.
 - `manifest.json`: run manifest with resolved pipeline provenance, top-level
-  module metadata, module keys, validation status, and timing.
+  module metadata, module keys, reference provenance, validation status, and
+  timing.
 - `artifacts/<artifact-type>.json`: approved artifacts grouped by artifact
   type. For the current D&D spell extractor, this includes
   `artifacts/dnd.spell_cast.json` when spell-cast artifacts are approved.
@@ -110,6 +111,10 @@ stderr, and writes warnings to durable output and diagnostics when retained.
 The run manifest `validation_status` indicates whether final artifacts were
 approved or rejected after validation.
 
+Reference-related warnings include empty bound reference files and D&D spell
+relatedness warnings such as `spell_not_near_source`. Empty references are still
+passed to extractors so optional slots can be intentionally blank.
+
 ## Cleanup
 
 It is safe to remove specific old run directories after their output and