Introduce target-aware resolved reference storage

docs/integrations/json-output.md

@@ -100,8 +100,9 @@ Fields with empty values may be omitted by JSON encoding.
 
 `source_digests` contains source document digests only. Bound references are
 recorded separately under `references`, which contains provenance only:
-lane ID, slot name, origin type and URI, digest, media type, byte size, and
-binding source. Reference content is not written to durable output.
+target stage, lane ID when present, slot name, origin type and URI, digest,
+media type, byte size, and binding source. Reference content is not written to
+durable output.
 
 When references are bound, the manifest section has this shape:
 
@@ -109,6 +110,7 @@ When references are bound, the manifest section has this shape:
 {
   "references": [
     {
+      "stage": "extract",
       "lane_id": "spells",
       "slot_name": "roster",
       "origin_type": "file",

docs/internal/pipeline.md

@@ -37,8 +37,9 @@ bindings override or add lane bindings, runtime `--reference` requests override
 config bindings, and runtime unbinds remove optional bindings. Flat runtime slot
 names are resolved only when exactly one selected lane declares the slot;
 otherwise the CLI requires `lane.slot`. Resolution validates bindings against
-extractor specs and records lane-scoped binding metadata. It does not read
-reference files or include reference bytes in source digests.
+extractor specs and stores the bindings in target-aware resolved reference
+holders. It does not read reference files or include reference bytes in source
+digests.
 
 During run preparation, resolved file references are materialized before any
 LLM-backed pipeline work. Config bindings resolve relative to the config file,
@@ -51,8 +52,8 @@ bound files. Media-type acceptance is checked only when a slot declares
 `AcceptedMediaTypes`; unknown extensions are recorded as
 `application/octet-stream`. Reference content is omitted from diagnostics and
 manifests. The CLI writes provenance-only resolved reference diagnostics, and
-the run manifest records lane-scoped reference provenance separately from source
-digests.
+the run manifest records target-stage reference provenance separately from
+source digests.
 
 Prompt bundles can declare reference slots and use `reference` and
 `hasreference` template functions. Bundle loading validates string-literal slot

docs/operations.md

@@ -63,9 +63,9 @@ Implemented diagnostics artifacts:
   path, selected lanes, run ID, and pipeline digest when available.
 - `effective-config.json`: resolved config with API keys redacted.
 - `resolved-pipeline.json`: resolved module bindings and pipeline digest.
-- `resolved-references.json`: lane-scoped resolved reference provenance,
-  including origin, digest, media type, byte size, and binding source, without
-  reference content.
+- `resolved-references.json`: resolved reference provenance, including target
+  stage, lane ID when present, origin, digest, media type, byte size, and
+  binding source, without reference content.
 - `run-manifest.json`: the same run manifest written to durable output when it
   is available, including top-level module metadata when present.
 - `warnings.json`: warning list.