Document extraction reference support

docs/cli.md

@@ -20,7 +20,7 @@ a bearer token.
 
 ```text
 notarius help
-notarius run <pipeline-id> --input path/to/source.json [--config path/to/config.yml] [--only lane-a,lane-b]
+notarius run <pipeline-id> --input path/to/source.json [--config path/to/config.yml] [--only lane-a,lane-b] [--reference slot=path] [--without-reference slot]
 notarius config validate --config path/to/config.yml [--pipeline pipeline-id] [--only lane-a,lane-b]
 notarius pipelines list --config path/to/config.yml [--json]
 ```
@@ -46,11 +46,59 @@ Flags:
   invocation.
 - `--llm-profile id`: override every effective module binding to use one LLM
   profile.
+- `--reference slot=path`: bind a reference path to an extractor reference
+  slot. Repeatable. Use `lane.slot=path` when multiple selected lanes declare
+  the same slot.
+- `--without-reference slot`: remove a configured optional reference binding.
+  Repeatable. Use `lane.slot` when multiple selected lanes declare the same
+  slot.
 
 On success, the command prints the completed pipeline ID, approved and rejected
 artifact counts, and the output directory. If the run completes with warnings,
 the warning count is printed to stderr.
 
+Reference flags are resolved against selected artifact lanes before the run
+starts. Flat slot names are accepted only when exactly one selected lane
+declares that slot. Bound reference files are read before extraction, validated
+as UTF-8 text, and passed only to the lane extractor that declares the slot.
+Reference content is not written to diagnostics, logs, errors, or manifests.
+
+Reference binding precedence is:
+
+1. pipeline-level config `references`;
+2. lane-level config `references`;
+3. `--reference` run flags;
+4. `--without-reference` run flags.
+
+`--reference` binds or replaces one slot for one selected lane. Use
+`slot=path` when the selected lanes declare the slot unambiguously:
+
+```sh
+go run ./cmd/notarius run dnd-session \
+  --config examples/dnd-spells.config.yml \
+  --input examples/seriatim-minimal-transcript.json \
+  --reference roster=./campaign-roster.txt
+```
+
+Use `lane.slot=path` when multiple selected lanes declare the same slot or when
+you want to target a specific lane:
+
+```sh
+go run ./cmd/notarius run dnd-session \
+  --config examples/dnd-spells.config.yml \
+  --input examples/seriatim-minimal-transcript.json \
+  --reference spells.glossary=./campaign-glossary.txt
+```
+
+Use `--without-reference` to remove a configured optional binding for a run:
+
+```sh
+go run ./cmd/notarius run dnd-session \
+  --config examples/dnd-spells.config.yml \
+  --input examples/seriatim-minimal-transcript.json \
+  --without-reference glossary
+```
+
 For durable output, diagnostics, retention, and failure inspection, see
 [Operations](operations.md).
 

docs/config.md

@@ -27,6 +27,9 @@ llm_profiles:
 pipelines:
   dnd-session:
     input: seriatim
+    references:
+      roster: ./dnd-spells-roster.txt
+      glossary: ./dnd-spells-glossary.txt
     chunk:
       module: generic
       options:
@@ -121,6 +124,9 @@ Pipeline fields:
 - `artifacts`: required for pipeline resolution. It maps artifact lane IDs to
   lane definitions.
 - `output`: optional module binding. Default module is `json`.
+- `references`: optional map of extractor reference slot names to reference
+  paths. These bindings are defaults for artifact lanes whose extractor declares
+  the matching slot.
 
 Artifact lane fields:
 
@@ -129,11 +135,52 @@ Artifact lane fields:
 - `normalize`: optional module binding. Default module is `noop`.
 - `validators`: optional list of module bindings. The production CLI currently
   does not register validator modules.
+- `references`: optional map of extractor reference slot names to reference
+  paths. Lane bindings override pipeline-level bindings for the same slot.
 
 `notarius run` and `notarius config validate --pipeline` resolve the pipeline
 against the production module catalog and fail fast for unknown or incompatible
 module keys.
 
+Reference bindings are validated against extractor-declared slots during
+pipeline resolution. Required slots must be bound after config defaults,
+lane-level bindings, and run-time `--reference` or `--without-reference`
+overrides are applied. Config-relative paths are resolved relative to the
+config file; CLI reference paths are resolved relative to the current working
+directory. Bound files must be UTF-8 text and are passed only to lane
+extractors that declare the slot. Reference content is not written to
+diagnostics, logs, errors, or manifests.
+
+Pipeline-level `references` are defaults. They apply only to selected lanes
+whose extractor declares the slot:
+
+```yaml
+pipelines:
+  dnd-session:
+    input: seriatim
+    references:
+      roster: ./campaign/party-roster.txt
+      glossary: ./campaign/glossary.txt
+    artifacts:
+      spells:
+        extract: dnd/spells
+```
+
+Lane-level `references` override or add bindings for one lane:
+
+```yaml
+pipelines:
+  dnd-session:
+    input: seriatim
+    references:
+      glossary: ./campaign/glossary.txt
+    artifacts:
+      spells:
+        extract: dnd/spells
+        references:
+          roster: ./campaign/session-roster.txt
+```
+
 ## Module Bindings
 
 Every module binding may use shorthand:
@@ -182,6 +229,14 @@ The `generic` chunker accepts:
 The `dnd/scenes` chunker requires transcript source capabilities, calls the
 configured structured LLM provider, and does not accept module options.
 
+The `dnd/spells` extractor declares optional text reference slots:
+
+- `roster`
+- `glossary`
+
+The extractor uses these references only as supporting disambiguation material;
+spell casts still must be present in the source transcript.
+
 ## Diagnostics
 
 `diagnostics` fields:
@@ -215,3 +270,5 @@ Pipeline resolution additionally checks:
 - required module keys are present;
 - module keys are registered for the expected slot;
 - module capability requirements are satisfied.
+- bound reference slots are declared by selected lane extractors;
+- required reference slots are bound for selected lanes.

docs/integrations/dnd-spell-artifacts.md

@@ -17,6 +17,14 @@ The extractor requires source chunks and transcript source capability. It
 returns generic artifact candidates that are serialized by the JSON output
 module.
 
+The extractor accepts optional UTF-8 text references:
+
+- `roster`: campaign roster or player-character notes.
+- `glossary`: campaign glossary or spell/name notes.
+
+References are supporting disambiguation material only. They are not source
+evidence and are not addressable through `source_refs`.
+
 ## Artifact Envelope
 
 Approved artifacts use the generic artifact envelope documented in
@@ -120,6 +128,11 @@ Rejection reason codes:
 - `invalid_source_ref`: at least one source reference fails generic source
   reference validation.
 
+Warning reason codes:
+
+- `spell_not_near_source`: the extracted spell name was not found in the cited
+  source text.
+
 Rejected candidates are written to `rejected.json` by the JSON output module.
 
 ## Manifest Metadata

docs/integrations/json-output.md

@@ -98,6 +98,30 @@ approved.
 
 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.
+
+When references are bound, the manifest section has this shape:
+
+```json
+{
+  "references": [
+    {
+      "lane_id": "spells",
+      "slot_name": "roster",
+      "origin_type": "file",
+      "origin_uri": "file:///absolute/path/roster.txt",
+      "digest": "sha256:...",
+      "media_type": "text/plain; charset=utf-8",
+      "size_bytes": 123,
+      "binding_source": "config"
+    }
+  ]
+}
+```
+
 `module_metadata` is omitted when no singleton module provides metadata.
 
 `validation_status` is `approved` when no candidates were rejected and

docs/internal/diagnostics.md

@@ -33,6 +33,7 @@ Implemented artifact names:
 - `invocation.json`
 - `effective-config.json`
 - `resolved-pipeline.json`
+- `resolved-references.json`
 - `source-document.json`
 - `run-manifest.json`
 - `run-report.json`

docs/internal/modules.md

@@ -20,6 +20,22 @@ A production module package should provide:
 Module specs should describe capabilities accurately. Resolution uses specs to
 reject incompatible pipelines before execution.
 
+Extractor modules that accept auxiliary reference material must declare slots
+through both `ReferenceSlots()` and `ModuleSpec().ReferenceSlots`. The runtime
+slot list and registry metadata should match so config validation can inspect
+slots without constructing extractor instances. A slot declaration names the
+slot, whether it is required, accepted media types, whether multiple items are
+allowed, and any byte limit.
+
+Reference content is delivered only to the lane extractor through
+`contracts.ExtractionRequest.References`. It is not source evidence and must not
+be converted into `SourceRef` values. If a module prompt uses references, load
+the prompt bundle with the same declared slots and render with
+`RenderUserSystemWithReferences`. Prompt templates may use the `reference`
+function for content and the `hasreference` function for conditional sections.
+Prompt metadata hashes remain based on template source, not rendered reference
+bytes.
+
 Chunk modules receive the structured LLM client through `contracts.ChunkRequest`
 when they need model-backed chunking. The pipeline runner validates generic
 chunk result invariants before extraction; module-owned policies may be stricter
@@ -124,12 +140,18 @@ metadata under `artifact_lanes[].metadata.extractor`. Durable artifact payload
 details belong in the
 [D&D spell artifact contract](../integrations/dnd-spell-artifacts.md).
 
+The extractor declares optional `roster` and `glossary` reference slots accepting
+UTF-8 text. Its prompt frames references as supporting disambiguation material
+only; spell-cast artifacts must still be grounded in the source transcript.
+
 ## D&D Spell Validators
 
 The spell extractor returns two built-in validators:
 
 - `dnd/spells/shape`: rejects malformed payloads and missing required fields.
 - `dnd/spells/source_refs`: rejects candidates without valid source references.
+  It also emits a warning when the extracted spell name is not found in the
+  cited source text.
 
 Reason codes include:
 
@@ -137,6 +159,7 @@ Reason codes include:
 - `missing_required_field`
 - `missing_source_ref`
 - `invalid_source_ref`
+- `spell_not_near_source`
 
 These validators are supplied by the extractor when no validators are configured
 for the lane.

docs/internal/pipeline.md

@@ -30,6 +30,33 @@ before execution:
 
 The CLI writes the resolved pipeline and digest to diagnostics.
 
+Pipeline profiles and artifact lanes may include reference binding maps keyed by
+extractor reference slot name. During resolution, pipeline-level bindings act as
+defaults for selected lanes whose extractor declares the slot, lane-level
+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.
+
+During run preparation, resolved file references are materialized before any
+LLM-backed pipeline work. Config bindings resolve relative to the config file,
+CLI bindings resolve relative to the current working directory, and materialized
+reference content is passed only to the matching lane extractor through
+`ExtractionRequest`. Materialization accepts UTF-8 text files, computes
+`sha256:` content digests, records file origins, enforces declared byte limits,
+and warns for empty bound files. 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.
+
+Prompt bundles can declare reference slots and use `reference` and
+`hasreference` template functions. Bundle loading validates string-literal slot
+names against the declaration. Rendering receives a lane reference set from the
+caller; unbound optional slots render as empty strings, and `hasreference`
+returns true only when at least one bound item has content.
+
 ## Registries And Module Specs
 
 `pipeline.Registries` holds concrete constructors for execution. A
@@ -44,6 +71,10 @@ Every production module registers a `ModuleSpec` with:
 - `Provides`: capabilities added after that module runs;
 - `Requires`: capabilities that must already be available.
 
+Extractor specs may also declare reference slots. Slot declarations are
+available from registry metadata without constructing extractor instances.
+Non-extractor module specs must not declare reference slots.
+
 Capability checks prevent incompatible pipeline composition before a run starts.
 
 ## Runner Input And Output
@@ -152,7 +183,7 @@ On successful execution, the manifest validation status is:
 
 The manifest records run ID, pipeline ID, pipeline digest, module keys, top-level
 module metadata, artifact lanes, LLM profile metadata, source digest,
-validation status, and timing.
+reference provenance, validation status, and timing.
 
 Singleton pipeline modules may add non-secret metadata by implementing
 `contracts.ManifestMetadataProvider`. The runner records that metadata under

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.
@@ -62,6 +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.
 - `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.
@@ -107,6 +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

docs/troubleshooting.md

@@ -102,6 +102,34 @@ go run ./cmd/notarius run dnd-session \
 - For `config validate`, include `--pipeline` when using `--only`.
 - Confirm the lane ID exists under `pipelines.<id>.artifacts`.
 
+## Reference Binding Failure
+
+Symptoms include:
+
+- `reference slot "..." is not declared`
+- `reference slot "..." is declared by multiple selected lanes`
+- `required reference slot "..." is not bound`
+- `--reference must use slot=path or lane.slot=path`
+- `--without-reference must use slot or lane.slot`
+- `read "...": no such file`
+- `must be UTF-8 text`
+- `is ... bytes, limit ...`
+
+Fix:
+
+- Confirm the selected extractor declares the slot. The implemented
+  `dnd/spells` extractor declares optional `roster` and `glossary` slots.
+- Use `lane.slot=path` when more than one selected lane declares the same slot.
+- Use `--without-reference slot` to remove optional config bindings; do not pass
+  an empty `--reference slot=`.
+- Check whether a path came from config or CLI. Config paths are relative to
+  the config file. CLI reference paths are relative to the current working
+  directory.
+- Ensure the file is readable UTF-8 text and within any byte limit declared by
+  the extractor.
+- If diagnostics are retained, inspect `resolved-pipeline.json`,
+  `resolved-references.json`, and `error.log`.
+
 ## Seriatim Input Validation Failure
 
 Symptoms include `seriatim input`, `parse JSON`, `segments must not be empty`,

examples/dnd-spells-glossary.txt

@@ -0,0 +1,2 @@
+Cure Wounds: healing spell cast by touch.
+Shield: defensive reaction spell.

examples/dnd-spells-roster.txt

@@ -0,0 +1,3 @@
+Aria: party cleric and recurring healer.
+Borin: fighter ally.
+Bandit mage: hostile spellcaster.

examples/dnd-spells.config.yml

@@ -7,6 +7,9 @@ llm_profiles:
 pipelines:
   dnd-session:
     input: seriatim
+    references:
+      roster: ./dnd-spells-roster.txt
+      glossary: ./dnd-spells-glossary.txt
     chunk:
       module: generic
       options:

internal/cli/run.go

@@ -25,7 +25,7 @@ const defaultOutputRoot = "./notarius-output"
 
 const usage = `Usage:
   notarius help
-  notarius run <pipeline-id> --input path/to/source.json [--config path/to/config.yml] [--only lane-a,lane-b]
+  notarius run <pipeline-id> --input path/to/source.json [--config path/to/config.yml] [--only lane-a,lane-b] [--reference slot=path] [--without-reference slot]
   notarius config validate --config path/to/config.yml [--pipeline pipeline-id] [--only lane-a,lane-b]
   notarius pipelines list --config path/to/config.yml [--json]
 `
@@ -95,6 +95,10 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 	outputDir := fs.String("output-dir", "", "output directory")
 	diagnosticsDir := fs.String("diagnostics-dir", "", "diagnostics directory")
 	llmProfile := fs.String("llm-profile", "", "LLM profile override")
+	referenceFlags := stringListFlag{}
+	withoutReferenceFlags := stringListFlag{}
+	fs.Var(&referenceFlags, "reference", "reference binding, as slot=path or lane.slot=path")
+	fs.Var(&withoutReferenceFlags, "without-reference", "unbind a reference, as slot or lane.slot")
 	if err := fs.Parse(reorderRunArgs(args)); err != nil {
 		fmt.Fprintf(stderr, "notarius: %v\n", err)
 		return 2
@@ -121,6 +125,16 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 		fmt.Fprintf(stderr, "notarius: %v\n", err)
 		return 2
 	}
+	referenceRequests, err := parseReferenceFlags(referenceFlags)
+	if err != nil {
+		fmt.Fprintf(stderr, "notarius: %v\n", err)
+		return 2
+	}
+	referenceUnbindRequests, err := parseReferenceUnbindFlags(withoutReferenceFlags)
+	if err != nil {
+		fmt.Fprintf(stderr, "notarius: %v\n", err)
+		return 2
+	}
 
 	cfg, loadedConfigPath, err := loadConfig(*configPath, opts)
 	if err != nil {
@@ -155,15 +169,33 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 	if err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
 	}
+	referenceOverrides, referenceUnbinds, err := resolveCLIReferenceRequests(cfg, pipelineID, only, catalog, referenceRequests, referenceUnbindRequests)
+	if err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
+	}
 	effective, err := cfg.Resolve(config.ResolveInput{
 		PipelineID:         pipelineID,
 		Only:               only,
 		Catalog:            catalog,
 		LLMProfileOverride: *llmProfile,
+		ReferenceOverrides: referenceOverrides,
+		ReferenceUnbinds:   referenceUnbinds,
 	})
 	if err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
 	}
+	workingDir, err := os.Getwd()
+	if err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("resolve working directory: %w", err))
+	}
+	materialized, referenceWarnings, err := pipeline.MaterializeReferences(effective.ResolvedPipeline, catalog, pipeline.ReferenceMaterializationOptions{
+		ConfigPath: loadedConfigPath,
+		WorkingDir: workingDir,
+	})
+	if err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
+	}
+	effective.ResolvedPipeline = materialized
 	invocation.PipelineDigest = effective.ResolvedPipeline.Digest
 	if err := runDir.WriteInvocationMetadata(invocation); err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics invocation metadata: %w", err))
@@ -174,6 +206,9 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 	if err := runDir.WriteResolvedPipeline(effective.ResolvedPipeline); err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics resolved pipeline: %w", err))
 	}
+	if err := runDir.WriteResolvedReferences(pipeline.ReferenceProvenance(effective.ResolvedPipeline)); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics resolved references: %w", err))
+	}
 
 	profileIDs := effectiveLLMProfileIDs(effective.ResolvedPipeline)
 	if len(profileIDs) != 1 {
@@ -205,6 +240,7 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 		StartedAt:   startedAt,
 		LLMProfiles: llmProfiles,
 		Metadata:    runMetadata(*outputDir, *diagnosticsDir),
+		Warnings:    referenceWarnings,
 	})
 	if err != nil {
 		if output.Manifest.PipelineID != "" {
@@ -412,7 +448,7 @@ func reorderRunArgs(args []string) []string {
 
 func runFlagTakesValue(arg string) bool {
 	switch arg {
-	case "--config", "--input", "--only", "--output-dir", "--diagnostics-dir", "--llm-profile":
+	case "--config", "--input", "--only", "--output-dir", "--diagnostics-dir", "--llm-profile", "--reference", "--without-reference":
 		return true
 	default:
 		return false
@@ -661,6 +697,255 @@ func parseOnly(raw string) ([]string, error) {
 	return result, nil
 }
 
+type stringListFlag []string
+
+func (flag *stringListFlag) String() string {
+	if flag == nil {
+		return ""
+	}
+	return strings.Join(*flag, ",")
+}
+
+func (flag *stringListFlag) Set(value string) error {
+	*flag = append(*flag, value)
+	return nil
+}
+
+type cliReferenceRequest struct {
+	LaneID   string
+	SlotName string
+	Source   string
+}
+
+type cliReferenceUnbindRequest struct {
+	LaneID   string
+	SlotName string
+}
+
+func parseReferenceFlags(values []string) ([]cliReferenceRequest, error) {
+	if len(values) == 0 {
+		return nil, nil
+	}
+	requests := make([]cliReferenceRequest, 0, len(values))
+	for _, raw := range values {
+		name, source, ok := strings.Cut(raw, "=")
+		if !ok {
+			return nil, fmt.Errorf("--reference must use slot=path or lane.slot=path")
+		}
+		if strings.TrimSpace(source) == "" {
+			return nil, fmt.Errorf("--reference path must not be empty; use --without-reference to unbind")
+		}
+		laneID, slotName, err := parseReferenceSelector(name, "--reference")
+		if err != nil {
+			return nil, err
+		}
+		requests = append(requests, cliReferenceRequest{
+			LaneID:   laneID,
+			SlotName: slotName,
+			Source:   strings.TrimSpace(source),
+		})
+	}
+	return requests, nil
+}
+
+func parseReferenceUnbindFlags(values []string) ([]cliReferenceUnbindRequest, error) {
+	if len(values) == 0 {
+		return nil, nil
+	}
+	requests := make([]cliReferenceUnbindRequest, 0, len(values))
+	for _, raw := range values {
+		if strings.Contains(raw, "=") {
+			return nil, fmt.Errorf("--without-reference must use slot or lane.slot")
+		}
+		laneID, slotName, err := parseReferenceSelector(raw, "--without-reference")
+		if err != nil {
+			return nil, err
+		}
+		requests = append(requests, cliReferenceUnbindRequest{
+			LaneID:   laneID,
+			SlotName: slotName,
+		})
+	}
+	return requests, nil
+}
+
+func parseReferenceSelector(raw string, flagName string) (string, string, error) {
+	selector := strings.TrimSpace(raw)
+	if selector == "" {
+		return "", "", fmt.Errorf("%s reference slot must not be empty", flagName)
+	}
+	if strings.Count(selector, ".") > 1 {
+		return "", "", fmt.Errorf("%s must use slot or lane.slot", flagName)
+	}
+	laneID := ""
+	slotName := selector
+	if strings.Contains(selector, ".") {
+		before, after, _ := strings.Cut(selector, ".")
+		laneID = strings.TrimSpace(before)
+		slotName = strings.TrimSpace(after)
+		if laneID == "" || slotName == "" {
+			return "", "", fmt.Errorf("%s must use non-empty lane.slot values", flagName)
+		}
+	}
+	return laneID, slotName, nil
+}
+
+func resolveCLIReferenceRequests(
+	cfg config.Config,
+	pipelineID string,
+	only []string,
+	catalog pipeline.ModuleCatalog,
+	referenceRequests []cliReferenceRequest,
+	unbindRequests []cliReferenceUnbindRequest,
+) ([]pipeline.ReferenceBinding, []pipeline.ReferenceUnbind, error) {
+	if len(referenceRequests) == 0 && len(unbindRequests) == 0 {
+		return nil, nil, nil
+	}
+
+	selected, err := selectedReferenceLanes(cfg, pipelineID, only, catalog)
+	if err != nil {
+		return nil, nil, err
+	}
+
+	overrides := make([]pipeline.ReferenceBinding, 0, len(referenceRequests))
+	for _, request := range referenceRequests {
+		laneID, err := resolveCLIReferenceLane(selected, request.LaneID, request.SlotName)
+		if err != nil {
+			return nil, nil, err
+		}
+		overrides = append(overrides, pipeline.ReferenceBinding{
+			LaneID:        laneID,
+			SlotName:      request.SlotName,
+			Source:        request.Source,
+			BindingSource: contracts.ReferenceBindingSourceCLI,
+		})
+	}
+
+	unbinds := make([]pipeline.ReferenceUnbind, 0, len(unbindRequests))
+	for _, request := range unbindRequests {
+		laneID, err := resolveCLIReferenceLane(selected, request.LaneID, request.SlotName)
+		if err != nil {
+			return nil, nil, err
+		}
+		unbinds = append(unbinds, pipeline.ReferenceUnbind{
+			LaneID:   laneID,
+			SlotName: request.SlotName,
+		})
+	}
+
+	return overrides, unbinds, nil
+}
+
+type selectedReferenceLane struct {
+	id    string
+	slots map[string]struct{}
+}
+
+func selectedReferenceLanes(cfg config.Config, pipelineID string, only []string, catalog pipeline.ModuleCatalog) ([]selectedReferenceLane, error) {
+	profile, ok := lookupCLIReferencePipeline(cfg.Pipelines, pipelineID)
+	if !ok {
+		return nil, fmt.Errorf("pipeline %q is not configured", strings.TrimSpace(pipelineID))
+	}
+
+	lanesByID := make(map[string]pipeline.ArtifactLaneProfile, len(profile.Artifacts))
+	for rawLaneID, lane := range profile.Artifacts {
+		laneID := strings.TrimSpace(rawLaneID)
+		if laneID == "" {
+			return nil, fmt.Errorf("pipeline %q artifact lane id must not be empty", strings.TrimSpace(pipelineID))
+		}
+		if _, ok := lanesByID[laneID]; ok {
+			return nil, fmt.Errorf("pipeline %q artifact lane %q is duplicated after trimming", strings.TrimSpace(pipelineID), laneID)
+		}
+		lanesByID[laneID] = lane
+	}
+
+	selectedIDs := make([]string, 0, len(lanesByID))
+	if len(only) == 0 {
+		for laneID := range lanesByID {
+			selectedIDs = append(selectedIDs, laneID)
+		}
+	} else {
+		seen := make(map[string]struct{}, len(only))
+		for _, rawLaneID := range only {
+			laneID := strings.TrimSpace(rawLaneID)
+			if laneID == "" {
+				return nil, fmt.Errorf("pipeline %q selected artifact lane id must not be empty", strings.TrimSpace(pipelineID))
+			}
+			if _, ok := lanesByID[laneID]; !ok {
+				return nil, fmt.Errorf("pipeline %q selected artifact lane %q is not declared", strings.TrimSpace(pipelineID), laneID)
+			}
+			if _, ok := seen[laneID]; !ok {
+				selectedIDs = append(selectedIDs, laneID)
+				seen[laneID] = struct{}{}
+			}
+		}
+	}
+	sort.Strings(selectedIDs)
+
+	selected := make([]selectedReferenceLane, 0, len(selectedIDs))
+	for _, laneID := range selectedIDs {
+		lane := lanesByID[laneID]
+		extractModule := strings.TrimSpace(lane.Extract.Module)
+		if extractModule == "" {
+			return nil, fmt.Errorf("pipeline %q lane %q extract module must not be empty", strings.TrimSpace(pipelineID), laneID)
+		}
+		if catalog.Extractors == nil {
+			return nil, fmt.Errorf("pipeline %q lane %q extract module %q: module %q is not registered", strings.TrimSpace(pipelineID), laneID, extractModule, extractModule)
+		}
+		spec, ok := catalog.Extractors.Spec(extractModule)
+		if !ok {
+			return nil, fmt.Errorf("pipeline %q lane %q extract module %q: module %q is not registered", strings.TrimSpace(pipelineID), laneID, extractModule, extractModule)
+		}
+		slotSet := make(map[string]struct{}, len(spec.ReferenceSlots))
+		for _, slot := range spec.ReferenceSlots {
+			slotSet[slot.Name] = struct{}{}
+		}
+		selected = append(selected, selectedReferenceLane{id: laneID, slots: slotSet})
+	}
+	return selected, nil
+}
+
+func lookupCLIReferencePipeline(profiles map[string]pipeline.PipelineProfile, pipelineID string) (pipeline.PipelineProfile, bool) {
+	pipelineID = strings.TrimSpace(pipelineID)
+	for rawID, profile := range profiles {
+		if strings.TrimSpace(rawID) == pipelineID {
+			return profile, true
+		}
+	}
+	return pipeline.PipelineProfile{}, false
+}
+
+func resolveCLIReferenceLane(selected []selectedReferenceLane, requestedLaneID string, slotName string) (string, error) {
+	slotName = strings.TrimSpace(slotName)
+	requestedLaneID = strings.TrimSpace(requestedLaneID)
+	if requestedLaneID != "" {
+		for _, lane := range selected {
+			if lane.id == requestedLaneID {
+				if _, ok := lane.slots[slotName]; !ok {
+					return "", fmt.Errorf("reference slot %q is not declared by selected lane %q", slotName, requestedLaneID)
+				}
+				return requestedLaneID, nil
+			}
+		}
+		return "", fmt.Errorf("reference lane %q is not selected", requestedLaneID)
+	}
+
+	matches := make([]string, 0, 1)
+	for _, lane := range selected {
+		if _, ok := lane.slots[slotName]; ok {
+			matches = append(matches, lane.id)
+		}
+	}
+	switch len(matches) {
+	case 0:
+		return "", fmt.Errorf("reference slot %q is not declared by any selected lane", slotName)
+	case 1:
+		return matches[0], nil
+	default:
+		return "", fmt.Errorf("reference slot %q is declared by multiple selected lanes (%s); use lane.slot", slotName, strings.Join(matches, ", "))
+	}
+}
+
 func sortedPipelineIDs(cfg config.Config) []string {
 	ids := make([]string, 0, len(cfg.Pipelines))
 	for id := range cfg.Pipelines {

internal/cli/run_test.go

@@ -8,12 +8,14 @@ import (
 	"os"
 	"path/filepath"
 	"reflect"
+	"sort"
 	"strings"
 	"testing"
 
 	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
 	"gitea.maximumdirect.net/eric/notarius/internal/core/config"
 	"gitea.maximumdirect.net/eric/notarius/internal/core/diagnostics"
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
 	"gitea.maximumdirect.net/eric/notarius/internal/modules/chunk/dnd/scenes"
@@ -737,6 +739,219 @@ func TestRunPipelineLLMProfileOverrideSelectsFactoryProfile(t *testing.T) {
 	}
 }
 
+func TestRunPipelineReferenceFlagBindsUnambiguousSlot(t *testing.T) {
+	configPath := writeTestConfig(t, testConfigYAML("example", "events"))
+	inputPath := filepath.Join(t.TempDir(), "missing.json")
+	referencePath := writeFile(t, "roster.yml", "Aria\n")
+	diagnosticsDir := t.TempDir()
+	var stdout bytes.Buffer
+	var stderr bytes.Buffer
+
+	code := RunWithOptions([]string{
+		"run", "example",
+		"--config", configPath,
+		"--input", inputPath,
+		"--diagnostics-dir", diagnosticsDir,
+		"--reference", "roster=" + referencePath,
+	}, &stdout, &stderr, Options{
+		Catalog: fakeCatalog(t, pipeline.ModuleSpec{
+			Key:      "fake/extract",
+			Stage:    pipeline.StageExtract,
+			Requires: []string{"chunks"},
+			Provides: []string{"artifact"},
+			ReferenceSlots: []contracts.ReferenceSlot{
+				{Name: "roster"},
+			},
+		}),
+	})
+
+	if code != 1 || !strings.Contains(stderr.String(), "read input") {
+		t.Fatalf("RunWithOptions() code = %d stderr=%q, want read input failure after resolution", code, stderr.String())
+	}
+	resolved := readResolvedPipeline(t, diagnosticsDir)
+	refs := resolved.ArtifactLanes[0].References
+	want := []pipeline.ReferenceBinding{
+		{LaneID: "events", SlotName: "roster", Source: referencePath, BindingSource: contracts.ReferenceBindingSourceCLI},
+	}
+	if !reflect.DeepEqual(refs, want) {
+		t.Fatalf("resolved references = %#v, want %#v", refs, want)
+	}
+}
+
+func TestRunPipelineReferenceFlagBindsLaneQualifiedSlot(t *testing.T) {
+	configPath := writeTestConfig(t, testConfigYAML("example", "events", "notes"))
+	inputPath := filepath.Join(t.TempDir(), "missing.json")
+	referencePath := writeFile(t, "notes.yml", "Notes\n")
+	diagnosticsDir := t.TempDir()
+	var stdout bytes.Buffer
+	var stderr bytes.Buffer
+
+	code := RunWithOptions([]string{
+		"run", "example",
+		"--config", configPath,
+		"--input", inputPath,
+		"--only", "events,notes",
+		"--diagnostics-dir", diagnosticsDir,
+		"--reference", "notes.roster=" + referencePath,
+	}, &stdout, &stderr, Options{
+		Catalog: fakeCatalog(t, pipeline.ModuleSpec{
+			Key:      "fake/extract",
+			Stage:    pipeline.StageExtract,
+			Requires: []string{"chunks"},
+			Provides: []string{"artifact"},
+			ReferenceSlots: []contracts.ReferenceSlot{
+				{Name: "roster"},
+			},
+		}),
+	})
+
+	if code != 1 || !strings.Contains(stderr.String(), "read input") {
+		t.Fatalf("RunWithOptions() code = %d stderr=%q, want read input failure after resolution", code, stderr.String())
+	}
+	resolved := readResolvedPipeline(t, diagnosticsDir)
+	events := resolvedArtifactLane(t, resolved, "events")
+	if len(events.References) != 0 {
+		t.Fatalf("events references = %#v, want none", events.References)
+	}
+	notes := resolvedArtifactLane(t, resolved, "notes")
+	if len(notes.References) != 1 || notes.References[0].Source != referencePath {
+		t.Fatalf("notes references = %#v, want lane-qualified binding", notes.References)
+	}
+}
+
+func TestRunPipelineReferenceFlagRejectsAmbiguousFlatSlot(t *testing.T) {
+	configPath := writeTestConfig(t, testConfigYAML("example", "events", "notes"))
+	inputPath := writeSeriatimInput(t)
+	diagnosticsDir := t.TempDir()
+	var stdout bytes.Buffer
+	var stderr bytes.Buffer
+
+	code := RunWithOptions([]string{
+		"run", "example",
+		"--config", configPath,
+		"--input", inputPath,
+		"--diagnostics-dir", diagnosticsDir,
+		"--reference", "roster=./roster.yml",
+	}, &stdout, &stderr, Options{
+		Catalog: fakeCatalog(t, pipeline.ModuleSpec{
+			Key:      "fake/extract",
+			Stage:    pipeline.StageExtract,
+			Requires: []string{"chunks"},
+			Provides: []string{"artifact"},
+			ReferenceSlots: []contracts.ReferenceSlot{
+				{Name: "roster"},
+			},
+		}),
+	})
+
+	if code != 1 {
+		t.Fatalf("RunWithOptions() code = %d, want 1", code)
+	}
+	if !strings.Contains(stderr.String(), "multiple selected lanes") || !strings.Contains(stderr.String(), "lane.slot") {
+		t.Fatalf("stderr = %q, want ambiguous reference error", stderr.String())
+	}
+}
+
+func TestRunPipelineReferenceFlagsRejectMalformedValues(t *testing.T) {
+	tests := []struct {
+		name string
+		args []string
+		want string
+	}{
+		{name: "missing equals", args: []string{"--reference", "roster"}, want: "slot=path"},
+		{name: "empty path", args: []string{"--reference", "roster="}, want: "path must not be empty"},
+		{name: "empty slot", args: []string{"--reference", "=./roster.yml"}, want: "slot must not be empty"},
+		{name: "too many selector parts", args: []string{"--reference", "a.b.c=./roster.yml"}, want: "lane.slot"},
+		{name: "unbind with equals", args: []string{"--without-reference", "roster=./roster.yml"}, want: "slot or lane.slot"},
+	}
+
+	for _, test := range tests {
+		t.Run(test.name, func(t *testing.T) {
+			configPath := writeTestConfig(t, testConfigYAML("example", "events"))
+			inputPath := writeSeriatimInput(t)
+			var stdout bytes.Buffer
+			var stderr bytes.Buffer
+			args := []string{"run", "example", "--config", configPath, "--input", inputPath}
+			args = append(args, test.args...)
+
+			code := RunWithOptions(args, &stdout, &stderr, Options{Catalog: fakeCatalog(t)})
+			if code != 2 {
+				t.Fatalf("RunWithOptions() code = %d, want 2", code)
+			}
+			if !strings.Contains(stderr.String(), test.want) {
+				t.Fatalf("stderr = %q, want substring %q", stderr.String(), test.want)
+			}
+		})
+	}
+}
+
+func TestRunPipelineWithoutReferenceRemovesOptionalConfigBinding(t *testing.T) {
+	configPath := writeTestConfig(t, testConfigYAMLWithReferences("example", "events", map[string]string{"roster": "./config-roster.yml"}))
+	inputPath := filepath.Join(t.TempDir(), "missing.json")
+	diagnosticsDir := t.TempDir()
+	var stdout bytes.Buffer
+	var stderr bytes.Buffer
+
+	code := RunWithOptions([]string{
+		"run", "example",
+		"--config", configPath,
+		"--input", inputPath,
+		"--diagnostics-dir", diagnosticsDir,
+		"--without-reference", "roster",
+	}, &stdout, &stderr, Options{
+		Catalog: fakeCatalog(t, pipeline.ModuleSpec{
+			Key:      "fake/extract",
+			Stage:    pipeline.StageExtract,
+			Requires: []string{"chunks"},
+			Provides: []string{"artifact"},
+			ReferenceSlots: []contracts.ReferenceSlot{
+				{Name: "roster"},
+			},
+		}),
+	})
+
+	if code != 1 || !strings.Contains(stderr.String(), "read input") {
+		t.Fatalf("RunWithOptions() code = %d stderr=%q, want read input failure after resolution", code, stderr.String())
+	}
+	resolved := readResolvedPipeline(t, diagnosticsDir)
+	if refs := resolved.ArtifactLanes[0].References; len(refs) != 0 {
+		t.Fatalf("references = %#v, want unbound optional slot", refs)
+	}
+}
+
+func TestRunPipelineWithoutReferenceFailsWhenRequiredSlotWouldBeMissing(t *testing.T) {
+	configPath := writeTestConfig(t, testConfigYAMLWithReferences("example", "events", map[string]string{"roster": "./config-roster.yml"}))
+	inputPath := writeSeriatimInput(t)
+	diagnosticsDir := t.TempDir()
+	var stdout bytes.Buffer
+	var stderr bytes.Buffer
+
+	code := RunWithOptions([]string{
+		"run", "example",
+		"--config", configPath,
+		"--input", inputPath,
+		"--diagnostics-dir", diagnosticsDir,
+		"--without-reference", "roster",
+	}, &stdout, &stderr, Options{
+		Catalog: fakeCatalog(t, pipeline.ModuleSpec{
+			Key:      "fake/extract",
+			Stage:    pipeline.StageExtract,
+			Requires: []string{"chunks"},
+			Provides: []string{"artifact"},
+			ReferenceSlots: []contracts.ReferenceSlot{
+				{Name: "roster", Required: true},
+			},
+		}),
+	})
+
+	if code != 1 {
+		t.Fatalf("RunWithOptions() code = %d, want 1", code)
+	}
+	if !strings.Contains(stderr.String(), "required reference slot") || !strings.Contains(stderr.String(), "roster") {
+		t.Fatalf("stderr = %q, want required reference error", stderr.String())
+	}
+}
+
 func TestRunPipelineWritesDurableOutputFiles(t *testing.T) {
 	diagnosticsDir := t.TempDir()
 	outputDir := t.TempDir()
@@ -770,6 +985,74 @@ func TestRunPipelineWritesDurableOutputFiles(t *testing.T) {
 	assertNoTemporaryFiles(t, runOutputDir)
 }
 
+func TestRunPipelineReferenceBytesProduceDistinctManifests(t *testing.T) {
+	run := func(t *testing.T, referenceText string) artifacts.RunManifest {
+		t.Helper()
+
+		diagnosticsDir := t.TempDir()
+		outputDir := t.TempDir()
+		configDir := t.TempDir()
+		referencePath := filepath.Join(configDir, "roster.txt")
+		if err := os.WriteFile(referencePath, []byte(referenceText), 0o644); err != nil {
+			t.Fatalf("write reference: %v", err)
+		}
+		configPath := filepath.Join(configDir, "config.yml")
+		if err := os.WriteFile(configPath, []byte(testConfigYAMLWithReferencesAndDiagnostics("example", "events", diagnosticsDir, map[string]string{"roster": "roster.txt"})), 0o644); err != nil {
+			t.Fatalf("write config: %v", err)
+		}
+		inputPath := writeFile(t, "source.txt", "source text")
+		var stdout bytes.Buffer
+		var stderr bytes.Buffer
+
+		code := RunWithOptions([]string{"run", "example", "--config", configPath, "--input", inputPath, "--output-dir", outputDir}, &stdout, &stderr, Options{
+			Catalog: fakeCatalog(t, pipeline.ModuleSpec{
+				Key:      "fake/extract",
+				Stage:    pipeline.StageExtract,
+				Requires: []string{"chunks"},
+				Provides: []string{"artifact"},
+				ReferenceSlots: []contracts.ReferenceSlot{
+					{Name: "roster"},
+				},
+			}),
+			Registries:       fakeExecutionRegistries(t),
+			LLMClientFactory: fakeLLMFactory(newFakeRunLLMClient(false), nil),
+		})
+		if code != 0 {
+			t.Fatalf("RunWithOptions() code = %d, stderr=%q", code, stderr.String())
+		}
+
+		var manifest artifacts.RunManifest
+		readJSONFile(t, filepath.Join(onlyChildDir(t, outputDir), "manifest.json"), &manifest)
+		if len(manifest.References) != 1 {
+			t.Fatalf("manifest references = %#v, want one entry", manifest.References)
+		}
+		if !reflect.DeepEqual(manifest.SourceDigests, []string{"sha256:source"}) {
+			t.Fatalf("source digests = %#v, want source-only digest", manifest.SourceDigests)
+		}
+
+		var resolvedReferences []artifacts.ReferenceProvenance
+		readJSONFile(t, filepath.Join(onlyChildDir(t, diagnosticsDir), diagnostics.ArtifactResolvedReferences), &resolvedReferences)
+		if !reflect.DeepEqual(resolvedReferences, manifest.References) {
+			t.Fatalf("resolved references = %#v, want manifest references %#v", resolvedReferences, manifest.References)
+		}
+		resolvedReferenceJSON := string(readFile(t, filepath.Join(onlyChildDir(t, diagnosticsDir), diagnostics.ArtifactResolvedReferences)))
+		if strings.Contains(resolvedReferenceJSON, referenceText) || strings.Contains(resolvedReferenceJSON, "content") {
+			t.Fatalf("resolved references diagnostics contains content: %s", resolvedReferenceJSON)
+		}
+		return manifest
+	}
+
+	first := run(t, "first roster")
+	second := run(t, "second roster")
+
+	if first.References[0].Digest == second.References[0].Digest {
+		t.Fatalf("reference digests match for different bytes: %q", first.References[0].Digest)
+	}
+	if first.PipelineDigest != second.PipelineDigest {
+		t.Fatalf("pipeline digests differ = %q vs %q, want reference bytes outside pipeline identity", first.PipelineDigest, second.PipelineDigest)
+	}
+}
+
 func TestRunPipelineRejectsUnsafeOutputFileName(t *testing.T) {
 	diagnosticsDir := t.TempDir()
 	outputDir := t.TempDir()
@@ -1305,6 +1588,51 @@ func testConfigYAMLForPipelines(pipelines map[string][]string) string {
 	return b.String()
 }
 
+func testConfigYAMLWithReferences(pipelineID string, laneID string, references map[string]string) string {
+	var b strings.Builder
+	b.WriteString("version: 1\n")
+	b.WriteString("pipelines:\n")
+	b.WriteString("  " + pipelineID + ":\n")
+	b.WriteString("    input: fake/input\n")
+	b.WriteString("    artifacts:\n")
+	b.WriteString("      " + laneID + ":\n")
+	b.WriteString("        extract: fake/extract\n")
+	b.WriteString("        references:\n")
+	keys := make([]string, 0, len(references))
+	for key := range references {
+		keys = append(keys, key)
+	}
+	sort.Strings(keys)
+	for _, key := range keys {
+		b.WriteString("          " + key + ": " + references[key] + "\n")
+	}
+	return b.String()
+}
+
+func testConfigYAMLWithReferencesAndDiagnostics(pipelineID string, laneID string, diagnosticsDir string, references map[string]string) string {
+	var b strings.Builder
+	b.WriteString("version: 1\n")
+	b.WriteString("diagnostics:\n")
+	b.WriteString("  work_dir: " + diagnosticsDir + "\n")
+	b.WriteString("  retention: always\n")
+	b.WriteString("pipelines:\n")
+	b.WriteString("  " + pipelineID + ":\n")
+	b.WriteString("    input: fake/input\n")
+	b.WriteString("    artifacts:\n")
+	b.WriteString("      " + laneID + ":\n")
+	b.WriteString("        extract: fake/extract\n")
+	b.WriteString("        references:\n")
+	keys := make([]string, 0, len(references))
+	for key := range references {
+		keys = append(keys, key)
+	}
+	sort.Strings(keys)
+	for _, key := range keys {
+		b.WriteString("          " + key + ": " + references[key] + "\n")
+	}
+	return b.String()
+}
+
 func mvpConfigYAML(pipelineID string, extractor string) string {
 	return `version: 1
 pipelines:
@@ -1553,6 +1881,153 @@ func registriesWithOutput(t *testing.T, encoder contracts.OutputEncoder) pipelin
 	return registries
 }
 
+func fakeExecutionRegistries(t *testing.T) pipeline.Registries {
+	t.Helper()
+	inputs := pipeline.NewInputAdapterRegistry()
+	chunkers := pipeline.NewChunkerRegistry()
+	extractors := pipeline.NewExtractorRegistry()
+	mergers := pipeline.NewMergerRegistry()
+	normalizers := pipeline.NewNormalizerRegistry()
+	outputs := pipeline.NewOutputEncoderRegistry()
+
+	if err := inputs.RegisterWithSpec(pipeline.ModuleSpec{Key: "fake/input", Stage: pipeline.StageInput, Provides: []string{"source"}}, func() (contracts.InputAdapter, error) {
+		return fakeRunInputAdapter{}, nil
+	}); err != nil {
+		t.Fatalf("register fake input: %v", err)
+	}
+	if err := chunkers.RegisterWithSpec(pipeline.ModuleSpec{Key: "generic", Stage: pipeline.StageChunk, Requires: []string{"source"}, Provides: []string{"chunks"}}, func() (contracts.Chunker, error) {
+		return fakeRunChunker{}, nil
+	}); err != nil {
+		t.Fatalf("register fake chunker: %v", err)
+	}
+	if err := extractors.RegisterWithSpec(pipeline.ModuleSpec{
+		Key:      "fake/extract",
+		Stage:    pipeline.StageExtract,
+		Requires: []string{"chunks"},
+		Provides: []string{"artifact"},
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{Name: "roster"},
+		},
+	}, func() (contracts.Extractor, error) {
+		return fakeRunExtractor{}, nil
+	}); err != nil {
+		t.Fatalf("register fake extractor: %v", err)
+	}
+	if err := mergers.RegisterWithSpec(pipeline.ModuleSpec{Key: "appendorder", Stage: pipeline.StageMerge, Requires: []string{"artifact"}, Provides: []string{"merged"}}, func() (contracts.Merger, error) {
+		return fakeRunMerger{}, nil
+	}); err != nil {
+		t.Fatalf("register fake merger: %v", err)
+	}
+	if err := normalizers.RegisterWithSpec(pipeline.ModuleSpec{Key: "noop", Stage: pipeline.StageNormalize, Requires: []string{"merged"}, Provides: []string{"normalized"}}, func() (contracts.Normalizer, error) {
+		return fakeRunNormalizer{}, nil
+	}); err != nil {
+		t.Fatalf("register fake normalizer: %v", err)
+	}
+	if err := jsonoutput.Register(outputs); err != nil {
+		t.Fatalf("register json output: %v", err)
+	}
+
+	return pipeline.Registries{
+		Inputs:      inputs,
+		Chunkers:    chunkers,
+		Extractors:  extractors,
+		Mergers:     mergers,
+		Normalizers: normalizers,
+		Outputs:     outputs,
+	}
+}
+
+type fakeRunInputAdapter struct{}
+
+func (fakeRunInputAdapter) Key() string {
+	return "fake/input"
+}
+
+func (fakeRunInputAdapter) Parse(ctx context.Context, req contracts.ParseRequest) (*source.SourceDocument, error) {
+	return &source.SourceDocument{
+		ID:     "source",
+		Kind:   "text",
+		Format: "test",
+		Digest: "sha256:source",
+		Units: []source.SourceUnit{
+			{ID: "unit-1", Kind: "text", Text: string(req.Raw)},
+		},
+	}, nil
+}
+
+type fakeRunChunker struct{}
+
+func (fakeRunChunker) Key() string {
+	return "generic"
+}
+
+func (fakeRunChunker) Chunk(ctx context.Context, req contracts.ChunkRequest) (contracts.ChunkResult, error) {
+	return contracts.ChunkResult{
+		Chunks: []contracts.SourceChunk{
+			{ID: "chunk-1", SourceID: req.Source.ID, Index: 0, Units: req.Source.Units},
+		},
+	}, nil
+}
+
+type fakeRunExtractor struct{}
+
+func (fakeRunExtractor) Key() string {
+	return "fake/extract"
+}
+
+func (fakeRunExtractor) ArtifactType() string {
+	return "fake.artifact"
+}
+
+func (fakeRunExtractor) SchemaVersion() string {
+	return "v1"
+}
+
+func (fakeRunExtractor) ReferenceSlots() []contracts.ReferenceSlot {
+	return []contracts.ReferenceSlot{{Name: "roster"}}
+}
+
+func (fakeRunExtractor) Validators() []contracts.Validator {
+	return nil
+}
+
+func (fakeRunExtractor) Extract(ctx context.Context, req contracts.ExtractionRequest) (contracts.ExtractionResult, error) {
+	return contracts.ExtractionResult{
+		Candidates: []artifacts.ArtifactCandidate{
+			{
+				Payload: []byte(`{"value":true}`),
+				SourceRefs: []source.SourceRef{
+					{SourceID: "source", StartUnitID: "unit-1", EndUnitID: "unit-1"},
+				},
+			},
+		},
+	}, nil
+}
+
+type fakeRunMerger struct{}
+
+func (fakeRunMerger) Key() string {
+	return "appendorder"
+}
+
+func (fakeRunMerger) Merge(ctx context.Context, req contracts.MergeRequest) (contracts.MergeResult, error) {
+	var candidates []artifacts.ArtifactCandidate
+	for _, chunkArtifacts := range req.ChunkArtifacts {
+		candidates = append(candidates, chunkArtifacts.Candidates...)
+	}
+	return contracts.MergeResult{Candidates: candidates}, nil
+}
+
+type fakeRunNormalizer struct{}
+
+func (fakeRunNormalizer) Key() string {
+	return "noop"
+}
+
+func (fakeRunNormalizer) Normalize(ctx context.Context, req contracts.NormalizeRequest) (contracts.NormalizeResult, error) {
+	return contracts.NormalizeResult{Candidates: append([]artifacts.ArtifactCandidate(nil), req.Candidates...)}, nil
+}
+
 func onlyChildDir(t *testing.T, root string) string {
 	t.Helper()
 	children := childDirs(t, root)
@@ -1596,6 +2071,25 @@ func readJSONFile(t *testing.T, path string, out any) {
 	}
 }
 
+func readResolvedPipeline(t *testing.T, diagnosticsDir string) pipeline.ResolvedPipeline {
+	t.Helper()
+	runDir := onlyChildDir(t, diagnosticsDir)
+	var resolved pipeline.ResolvedPipeline
+	readJSONFile(t, filepath.Join(runDir, diagnostics.ArtifactResolvedPipeline), &resolved)
+	return resolved
+}
+
+func resolvedArtifactLane(t *testing.T, resolved pipeline.ResolvedPipeline, laneID string) pipeline.ResolvedArtifactLane {
+	t.Helper()
+	for _, lane := range resolved.ArtifactLanes {
+		if lane.ID == laneID {
+			return lane
+		}
+	}
+	t.Fatalf("lane %q not found in resolved pipeline", laneID)
+	return pipeline.ResolvedArtifactLane{}
+}
+
 func assertNoTemporaryFiles(t *testing.T, root string) {
 	t.Helper()
 	if err := filepath.WalkDir(root, func(path string, entry os.DirEntry, err error) error {
@@ -1611,7 +2105,7 @@ func assertNoTemporaryFiles(t *testing.T, root string) {
 	}
 }
 
-func fakeCatalog(t *testing.T) pipeline.ModuleCatalog {
+func fakeCatalog(t *testing.T, overrides ...pipeline.ModuleSpec) pipeline.ModuleCatalog {
 	t.Helper()
 	inputs := pipeline.NewInputAdapterRegistry()
 	chunkers := pipeline.NewChunkerRegistry()
@@ -1621,12 +2115,24 @@ func fakeCatalog(t *testing.T) pipeline.ModuleCatalog {
 	validators := pipeline.NewValidatorRegistry()
 	outputs := pipeline.NewOutputEncoderRegistry()
 
-	mustRegisterInput(t, inputs, pipeline.ModuleSpec{Key: "fake/input", Stage: pipeline.StageInput, Provides: []string{"source"}})
+	specs := map[string]pipeline.ModuleSpec{
-	mustRegisterChunker(t, chunkers, pipeline.ModuleSpec{Key: "generic", Stage: pipeline.StageChunk, Requires: []string{"source"}, Provides: []string{"chunks"}})
+		"fake/input":   {Key: "fake/input", Stage: pipeline.StageInput, Provides: []string{"source"}},
-	mustRegisterExtractor(t, extractors, pipeline.ModuleSpec{Key: "fake/extract", Stage: pipeline.StageExtract, Requires: []string{"chunks"}, Provides: []string{"artifact"}})
+		"generic":      {Key: "generic", Stage: pipeline.StageChunk, Requires: []string{"source"}, Provides: []string{"chunks"}},
-	mustRegisterMerger(t, mergers, pipeline.ModuleSpec{Key: "appendorder", Stage: pipeline.StageMerge, Requires: []string{"artifact"}, Provides: []string{"merged"}})
+		"fake/extract": {Key: "fake/extract", Stage: pipeline.StageExtract, Requires: []string{"chunks"}, Provides: []string{"artifact"}},
-	mustRegisterNormalizer(t, normalizers, pipeline.ModuleSpec{Key: "noop", Stage: pipeline.StageNormalize, Requires: []string{"merged"}, Provides: []string{"normalized"}})
+		"appendorder":  {Key: "appendorder", Stage: pipeline.StageMerge, Requires: []string{"artifact"}, Provides: []string{"merged"}},
-	mustRegisterOutput(t, outputs, pipeline.ModuleSpec{Key: "json", Stage: pipeline.StageOutput, Requires: []string{"normalized"}})
+		"noop":         {Key: "noop", Stage: pipeline.StageNormalize, Requires: []string{"merged"}, Provides: []string{"normalized"}},
+		"json":         {Key: "json", Stage: pipeline.StageOutput, Requires: []string{"normalized"}},
+	}
+	for _, override := range overrides {
+		specs[override.Key] = override
+	}
+
+	mustRegisterInput(t, inputs, specs["fake/input"])
+	mustRegisterChunker(t, chunkers, specs["generic"])
+	mustRegisterExtractor(t, extractors, specs["fake/extract"])
+	mustRegisterMerger(t, mergers, specs["appendorder"])
+	mustRegisterNormalizer(t, normalizers, specs["noop"])
+	mustRegisterOutput(t, outputs, specs["json"])
 
 	return pipeline.ModuleCatalog{
 		Inputs:      inputs,

internal/core/artifacts/artifacts.go

@@ -48,6 +48,17 @@ type LLMProfileManifest struct {
 	Model    string `json:"model,omitempty"`
 }
 
+type ReferenceProvenance struct {
+	LaneID        string `json:"lane_id"`
+	SlotName      string `json:"slot_name"`
+	OriginType    string `json:"origin_type"`
+	OriginURI     string `json:"origin_uri,omitempty"`
+	Digest        string `json:"digest,omitempty"`
+	MediaType     string `json:"media_type,omitempty"`
+	SizeBytes     int64  `json:"size_bytes,omitempty"`
+	BindingSource string `json:"binding_source,omitempty"`
+}
+
 type RunManifest struct {
 	RunID            string                    `json:"run_id,omitempty"`
 	PipelineID       string                    `json:"pipeline_id,omitempty"`
@@ -61,6 +72,7 @@ type RunManifest struct {
 	OutputEncoder    string                    `json:"output_encoder,omitempty"`
 	ModuleMetadata   map[string]map[string]any `json:"module_metadata,omitempty"`
 	ArtifactLanes    []ArtifactLaneManifest    `json:"artifact_lanes,omitempty"`
+	References       []ReferenceProvenance     `json:"references,omitempty"`
 	LLMProfiles      []LLMProfileManifest      `json:"llm_profiles,omitempty"`
 	SchemaVersion    string                    `json:"schema_version,omitempty"`
 	ValidationStatus string                    `json:"validation_status,omitempty"`

internal/core/artifacts/artifacts_test.go

@@ -183,6 +183,43 @@ func TestRunManifestIncludesPipelineAndArtifactLaneFields(t *testing.T) {
 	assertHasKeys(t, lane, "id", "extractor", "merger", "normalizer", "validators", "metadata")
 }
 
+func TestRunManifestIncludesReferenceProvenance(t *testing.T) {
+	manifest := RunManifest{
+		References: []ReferenceProvenance{
+			{
+				LaneID:        "events",
+				SlotName:      "roster",
+				OriginType:    "file",
+				OriginURI:     "file:///tmp/roster.txt",
+				Digest:        "sha256:reference",
+				MediaType:     "text/plain; charset=utf-8",
+				SizeBytes:     12,
+				BindingSource: "config",
+			},
+		},
+	}
+
+	gotJSON, err := json.Marshal(manifest)
+	if err != nil {
+		t.Fatalf("json.Marshal() error = %v", err)
+	}
+
+	var got RunManifest
+	if err := json.Unmarshal(gotJSON, &got); err != nil {
+		t.Fatalf("json.Unmarshal() error = %v", err)
+	}
+	if len(got.References) != 1 {
+		t.Fatalf("len(References) = %d, want 1", len(got.References))
+	}
+	reference := got.References[0]
+	if reference.LaneID != "events" || reference.SlotName != "roster" || reference.OriginType != "file" || reference.OriginURI != "file:///tmp/roster.txt" {
+		t.Fatalf("reference provenance = %#v, want lane-scoped origin details", reference)
+	}
+	if reference.Digest != "sha256:reference" || reference.MediaType != "text/plain; charset=utf-8" || reference.SizeBytes != 12 || reference.BindingSource != "config" {
+		t.Fatalf("reference provenance = %#v, want digest/media/size/source details", reference)
+	}
+}
+
 func TestRunManifestIncludesTopLevelModuleMetadata(t *testing.T) {
 	manifest := RunManifest{
 		ModuleMetadata: map[string]map[string]any{

internal/core/config/config.go

@@ -73,6 +73,7 @@ func clonePipelineProfile(in pipeline.PipelineProfile) pipeline.PipelineProfile
 	out.Input = cloneModuleBinding(in.Input)
 	out.Chunk = cloneModuleBinding(in.Chunk)
 	out.Output = cloneModuleBinding(in.Output)
+	out.References = cloneStringMap(in.References)
 	if len(in.Artifacts) > 0 {
 		out.Artifacts = make(map[string]pipeline.ArtifactLaneProfile, len(in.Artifacts))
 		for key, lane := range in.Artifacts {
@@ -87,6 +88,7 @@ func cloneArtifactLaneProfile(in pipeline.ArtifactLaneProfile) pipeline.Artifact
 	out.Extract = cloneModuleBinding(in.Extract)
 	out.Merge = cloneModuleBinding(in.Merge)
 	out.Normalize = cloneModuleBinding(in.Normalize)
+	out.References = cloneStringMap(in.References)
 	if len(in.Validators) > 0 {
 		out.Validators = make([]pipeline.ModuleBinding, len(in.Validators))
 		for i, binding := range in.Validators {
@@ -96,6 +98,17 @@ func cloneArtifactLaneProfile(in pipeline.ArtifactLaneProfile) pipeline.Artifact
 	return out
 }
 
+func cloneStringMap(in map[string]string) map[string]string {
+	if len(in) == 0 {
+		return nil
+	}
+	out := make(map[string]string, len(in))
+	for key, value := range in {
+		out[key] = value
+	}
+	return out
+}
+
 func cloneModuleBinding(in pipeline.ModuleBinding) pipeline.ModuleBinding {
 	out := in
 	if len(in.Options) > 0 {

internal/core/config/effective_config.go

@@ -14,12 +14,16 @@ type ResolveInput struct {
 	Only               []string
 	Catalog            pipeline.ModuleCatalog
 	LLMProfileOverride string
+	ReferenceOverrides []pipeline.ReferenceBinding
+	ReferenceUnbinds   []pipeline.ReferenceUnbind
 }
 
 type EffectiveConfig struct {
 	Config             Config
 	PipelineID         string
 	Only               []string
+	ReferenceOverrides []pipeline.ReferenceBinding
+	ReferenceUnbinds   []pipeline.ReferenceUnbind
 	ResolvedPipeline   pipeline.ResolvedPipeline
 }
 
@@ -46,7 +50,11 @@ func (c Config) Resolve(input ResolveInput) (EffectiveConfig, error) {
 		applyLLMProfileOverride(&profile, override)
 	}
 
-	resolved, err := pipeline.ResolvePipeline(profile, pipeline.ResolveOptions{Only: input.Only}, input.Catalog)
+	resolved, err := pipeline.ResolvePipeline(profile, pipeline.ResolveOptions{
+		Only:               input.Only,
+		ReferenceOverrides: append([]pipeline.ReferenceBinding(nil), input.ReferenceOverrides...),
+		ReferenceUnbinds:   append([]pipeline.ReferenceUnbind(nil), input.ReferenceUnbinds...),
+	}, input.Catalog)
 	if err != nil {
 		return EffectiveConfig{}, fmt.Errorf("resolve pipeline %q: %w", pipelineID, err)
 	}
@@ -55,6 +63,8 @@ func (c Config) Resolve(input ResolveInput) (EffectiveConfig, error) {
 		Config:             cloneConfig(c),
 		PipelineID:         pipelineID,
 		Only:               append([]string(nil), input.Only...),
+		ReferenceOverrides: append([]pipeline.ReferenceBinding(nil), input.ReferenceOverrides...),
+		ReferenceUnbinds:   append([]pipeline.ReferenceUnbind(nil), input.ReferenceUnbinds...),
 		ResolvedPipeline:   resolved,
 	}, nil
 }

internal/core/config/file_config.go

@@ -39,6 +39,7 @@ type FilePipelineProfile struct {
 	Chunk      *fileModuleBinding                 `yaml:"chunk,omitempty"`
 	Artifacts  map[string]FileArtifactLaneProfile `yaml:"artifacts,omitempty"`
 	Output     *fileModuleBinding                 `yaml:"output,omitempty"`
+	References map[string]string                  `yaml:"references,omitempty"`
 }
 
 type FileArtifactLaneProfile struct {
@@ -46,6 +47,7 @@ type FileArtifactLaneProfile struct {
 	Merge      *fileModuleBinding  `yaml:"merge,omitempty"`
 	Normalize  *fileModuleBinding  `yaml:"normalize,omitempty"`
 	Validators []fileModuleBinding `yaml:"validators,omitempty"`
+	References map[string]string   `yaml:"references,omitempty"`
 }
 
 type FileConcurrencyConfig struct {
@@ -212,6 +214,18 @@ func (c *Config) applyFileConfigWithLookup(fileCfg FileConfig, lookup func(strin
 		if _, _, err := normalizedMapKeys(filePipeline.Artifacts, fmt.Sprintf("pipeline %q artifact lane id", pipelineID)); err != nil {
 			return err
 		}
+		if _, _, err := normalizedMapKeys(filePipeline.References, fmt.Sprintf("pipeline %q reference slot", pipelineID)); err != nil {
+			return err
+		}
+		for rawLaneID, fileLane := range filePipeline.Artifacts {
+			laneID := strings.TrimSpace(rawLaneID)
+			if laneID == "" {
+				continue
+			}
+			if _, _, err := normalizedMapKeys(fileLane.References, fmt.Sprintf("pipeline %q lane %q reference slot", pipelineID, laneID)); err != nil {
+				return err
+			}
+		}
 	}
 
 	for _, profileID := range profileIDs {
@@ -256,6 +270,7 @@ func (c *Config) applyFileConfigWithLookup(fileCfg FileConfig, lookup func(strin
 			ID:         pipelineID,
 			Input:      filePipeline.Input.toPipelineBinding(),
 			Artifacts:  make(map[string]pipeline.ArtifactLaneProfile, len(filePipeline.Artifacts)),
+			References: normalizedStringMap(filePipeline.References),
 		}
 		if filePipeline.Chunk != nil {
 			profile.Chunk = filePipeline.Chunk.toPipelineBinding()
@@ -267,6 +282,7 @@ func (c *Config) applyFileConfigWithLookup(fileCfg FileConfig, lookup func(strin
 			fileLane := filePipeline.Artifacts[rawLaneIDs[laneID]]
 			lane := pipeline.ArtifactLaneProfile{
 				Extract:    fileLane.Extract.toPipelineBinding(),
+				References: normalizedStringMap(fileLane.References),
 			}
 			if fileLane.Merge != nil {
 				lane.Merge = fileLane.Merge.toPipelineBinding()
@@ -318,6 +334,25 @@ func normalizedMapKeys[T any](values map[string]T, keyName string) ([]string, ma
 	return keys, rawByNormalized, nil
 }
 
+func normalizedStringMap(values map[string]string) map[string]string {
+	if len(values) == 0 {
+		return nil
+	}
+	out := make(map[string]string, len(values))
+	keys := make([]string, 0, len(values))
+	rawByNormalized := make(map[string]string, len(values))
+	for rawKey := range values {
+		key := strings.TrimSpace(rawKey)
+		rawByNormalized[key] = rawKey
+		keys = append(keys, key)
+	}
+	sort.Strings(keys)
+	for _, key := range keys {
+		out[key] = strings.TrimSpace(values[rawByNormalized[key]])
+	}
+	return out
+}
+
 func resolveAPIKeyEnv(envName string, lookup func(string) (string, bool)) (string, error) {
 	name := strings.TrimSpace(envName)
 	if name == "" {

internal/core/config/file_config_test.go

@@ -144,6 +144,31 @@ pipelines:
 	}
 }
 
+func TestParseFileConfigReferenceMaps(t *testing.T) {
+	cfg := parseAndApplyConfig(t, `
+version: 1
+pipelines:
+  example:
+    input: fake/input
+    references:
+      " roster ": " ./shared-roster.yml "
+    artifacts:
+      events:
+        extract: fake/extract
+        references:
+          " lore ": " ./lore.md "
+`)
+
+	profile := cfg.Pipelines["example"]
+	if !reflect.DeepEqual(profile.References, map[string]string{"roster": "./shared-roster.yml"}) {
+		t.Fatalf("pipeline references = %#v, want trimmed map", profile.References)
+	}
+	gotLaneRefs := profile.Artifacts["events"].References
+	if !reflect.DeepEqual(gotLaneRefs, map[string]string{"lore": "./lore.md"}) {
+		t.Fatalf("lane references = %#v, want trimmed map", gotLaneRefs)
+	}
+}
+
 func TestParseFileConfigValidatorMixedBindingForms(t *testing.T) {
 	cfg := parseAndApplyConfig(t, `
 version: 1
@@ -297,6 +322,58 @@ pipelines:
 	}
 }
 
+func TestApplyFileConfigRejectsDuplicateTrimmedReferenceSlots(t *testing.T) {
+	tests := []struct {
+		name string
+		raw  string
+		want string
+	}{
+		{
+			name: "pipeline",
+			raw: `
+version: 1
+pipelines:
+  example:
+    input: fake/input
+    references:
+      roster: ./first.yml
+      " roster ": ./second.yml
+`,
+			want: `pipeline "example" reference slot`,
+		},
+		{
+			name: "lane",
+			raw: `
+version: 1
+pipelines:
+  example:
+    input: fake/input
+    artifacts:
+      events:
+        extract: fake/extract
+        references:
+          roster: ./first.yml
+          " roster ": ./second.yml
+`,
+			want: `pipeline "example" lane "events" reference slot`,
+		},
+	}
+
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			fileCfg, err := ParseFileConfigYAML([]byte(tc.raw))
+			if err != nil {
+				t.Fatalf("ParseFileConfigYAML: %v", err)
+			}
+			cfg := Default()
+			err = cfg.applyFileConfigWithLookup(fileCfg, emptyLookup)
+			if err == nil || !strings.Contains(err.Error(), tc.want) || !strings.Contains(err.Error(), "duplicated") {
+				t.Fatalf("expected duplicate reference slot error, got %v", err)
+			}
+		})
+	}
+}
+
 func TestApplyFileConfigAllowsRetryOnlyLLMProfile(t *testing.T) {
 	cfg := parseAndApplyConfig(t, `
 version: 1

internal/core/config/redaction.go

@@ -24,6 +24,8 @@ func (e EffectiveConfig) RedactedDiagnosticsPayload() any {
 		Config:             e.Config.Redacted(),
 		PipelineID:         e.PipelineID,
 		Only:               append([]string(nil), e.Only...),
+		ReferenceOverrides: append([]pipeline.ReferenceBinding(nil), e.ReferenceOverrides...),
+		ReferenceUnbinds:   append([]pipeline.ReferenceUnbind(nil), e.ReferenceUnbinds...),
 		ResolvedPipeline:   cloneResolvedPipeline(e.ResolvedPipeline),
 	}
 }
@@ -47,6 +49,8 @@ func cloneResolvedArtifactLane(in pipeline.ResolvedArtifactLane) pipeline.Resolv
 	out.Extract = cloneModuleBinding(in.Extract)
 	out.Merge = cloneModuleBinding(in.Merge)
 	out.Normalize = cloneModuleBinding(in.Normalize)
+	out.References = append([]pipeline.ReferenceBinding(nil), in.References...)
+	out.ReferenceSet = pipeline.CloneReferenceSet(in.ReferenceSet)
 	if len(in.Validators) > 0 {
 		out.Validators = make([]pipeline.ModuleBinding, len(in.Validators))
 		for i, binding := range in.Validators {

internal/core/config/redaction_test.go

@@ -3,6 +3,7 @@ package config
 import (
 	"testing"
 
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
 )
 
@@ -65,12 +66,21 @@ func TestEffectiveConfigRedactedDiagnosticsPayloadRedactsAndCopies(t *testing.T)
 	cfg.LLMProfiles[pipeline.DefaultLLMProfile] = profile
 	lane := cfg.Pipelines["example"].Artifacts["events"]
 	lane.Extract.Options = map[string]any{"temperature": 0.2}
+	lane.References = map[string]string{"roster": "./roster.yml"}
 	cfg.Pipelines["example"].Artifacts["events"] = lane
 
 	effective, err := cfg.Resolve(ResolveInput{
 		PipelineID: "example",
 		Only:       []string{"events"},
-		Catalog:    fakeCatalog(t),
+		Catalog: fakeCatalog(t, pipeline.ModuleSpec{
+			Key:      "fake/extract",
+			Stage:    pipeline.StageExtract,
+			Requires: []string{"chunks"},
+			Provides: []string{"artifact"},
+			ReferenceSlots: []contracts.ReferenceSlot{
+				{Name: "roster"},
+			},
+		}),
 	})
 	if err != nil {
 		t.Fatalf("Resolve: %v", err)
@@ -98,4 +108,8 @@ func TestEffectiveConfigRedactedDiagnosticsPayloadRedactsAndCopies(t *testing.T)
 	if effective.ResolvedPipeline.ArtifactLanes[0].Extract.Options["temperature"] != 0.2 {
 		t.Fatalf("expected resolved pipeline options to be copied")
 	}
+	payload.ResolvedPipeline.ArtifactLanes[0].References[0].Source = "./changed.yml"
+	if effective.ResolvedPipeline.ArtifactLanes[0].References[0].Source != "./roster.yml" {
+		t.Fatalf("expected resolved pipeline references to be copied")
+	}
 }

internal/core/config/validation.go

@@ -98,11 +98,17 @@ func validatePipelineProfiles(profiles map[string]pipeline.PipelineProfile, llmP
 		if err := validateBindingLLMProfile(id, "", "output", profile.Output, llmProfiles); err != nil {
 			return err
 		}
+		if err := validateReferenceMap(id, "", profile.References); err != nil {
+			return err
+		}
 		for rawLaneID, lane := range profile.Artifacts {
 			laneID := strings.TrimSpace(rawLaneID)
 			if laneID == "" {
 				return fmt.Errorf("pipeline %q artifact lane id must not be empty", id)
 			}
+			if err := validateReferenceMap(id, laneID, lane.References); err != nil {
+				return err
+			}
 			if err := validateBindingLLMProfile(id, laneID, "extract", lane.Extract, llmProfiles); err != nil {
 				return err
 			}
@@ -122,6 +128,33 @@ func validatePipelineProfiles(profiles map[string]pipeline.PipelineProfile, llmP
 	return nil
 }
 
+func validateReferenceMap(pipelineID string, laneID string, references map[string]string) error {
+	seen := make(map[string]struct{}, len(references))
+	for rawSlotName, rawSource := range references {
+		slotName := strings.TrimSpace(rawSlotName)
+		if slotName == "" {
+			if laneID != "" {
+				return fmt.Errorf("pipeline %q lane %q reference slot name must not be empty", pipelineID, laneID)
+			}
+			return fmt.Errorf("pipeline %q reference slot name must not be empty", pipelineID)
+		}
+		if _, ok := seen[slotName]; ok {
+			if laneID != "" {
+				return fmt.Errorf("pipeline %q lane %q reference slot %q is duplicated after trimming", pipelineID, laneID, slotName)
+			}
+			return fmt.Errorf("pipeline %q reference slot %q is duplicated after trimming", pipelineID, slotName)
+		}
+		seen[slotName] = struct{}{}
+		if strings.TrimSpace(rawSource) == "" {
+			if laneID != "" {
+				return fmt.Errorf("pipeline %q lane %q reference slot %q source must not be empty", pipelineID, laneID, slotName)
+			}
+			return fmt.Errorf("pipeline %q reference slot %q source must not be empty", pipelineID, slotName)
+		}
+	}
+	return nil
+}
+
 func validateBindingLLMProfile(
 	pipelineID string,
 	laneID string,

internal/core/config/validation_test.go

@@ -116,6 +116,73 @@ func TestValidateRejectsInvalidDiagnosticsRetention(t *testing.T) {
 	}
 }
 
+func TestValidateRejectsInvalidReferenceMaps(t *testing.T) {
+	tests := []struct {
+		name   string
+		mutate func(Config) Config
+		want   []string
+	}{
+		{
+			name: "empty pipeline slot",
+			mutate: func(cfg Config) Config {
+				profile := cfg.Pipelines["example"]
+				profile.References = map[string]string{" ": "./roster.yml"}
+				cfg.Pipelines["example"] = profile
+				return cfg
+			},
+			want: []string{"example", "reference slot", "empty"},
+		},
+		{
+			name: "empty pipeline source",
+			mutate: func(cfg Config) Config {
+				profile := cfg.Pipelines["example"]
+				profile.References = map[string]string{"roster": " "}
+				cfg.Pipelines["example"] = profile
+				return cfg
+			},
+			want: []string{"example", "roster", "source", "empty"},
+		},
+		{
+			name: "empty lane slot",
+			mutate: func(cfg Config) Config {
+				profile := cfg.Pipelines["example"]
+				lane := profile.Artifacts["events"]
+				lane.References = map[string]string{" ": "./roster.yml"}
+				profile.Artifacts["events"] = lane
+				cfg.Pipelines["example"] = profile
+				return cfg
+			},
+			want: []string{"example", "events", "reference slot", "empty"},
+		},
+		{
+			name: "empty lane source",
+			mutate: func(cfg Config) Config {
+				profile := cfg.Pipelines["example"]
+				lane := profile.Artifacts["events"]
+				lane.References = map[string]string{"roster": " "}
+				profile.Artifacts["events"] = lane
+				cfg.Pipelines["example"] = profile
+				return cfg
+			},
+			want: []string{"example", "events", "roster", "source", "empty"},
+		},
+	}
+
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			err := tc.mutate(validConfig()).Validate()
+			if err == nil {
+				t.Fatal("Validate() error = nil, want error")
+			}
+			for _, want := range tc.want {
+				if !strings.Contains(err.Error(), want) {
+					t.Fatalf("Validate() error = %q, want substring %q", err.Error(), want)
+				}
+			}
+		})
+	}
+}
+
 func TestValidateRejectsEmptyIDs(t *testing.T) {
 	tests := []struct {
 		name   string

internal/core/diagnostics/artifacts.go

@@ -4,6 +4,7 @@ const (
 	ArtifactInvocationMetadata = "invocation.json"
 	ArtifactEffectiveConfig    = "effective-config.json"
 	ArtifactResolvedPipeline   = "resolved-pipeline.json"
+	ArtifactResolvedReferences = "resolved-references.json"
 	ArtifactSourceDocument     = "source-document.json"
 	ArtifactRunManifest        = "run-manifest.json"
 	ArtifactRunReport          = "run-report.json"

internal/core/diagnostics/artifacts_test.go

@@ -7,6 +7,7 @@ func TestArtifactNamesUseExtractionOrientedNames(t *testing.T) {
 		ArtifactInvocationMetadata,
 		ArtifactEffectiveConfig,
 		ArtifactResolvedPipeline,
+		ArtifactResolvedReferences,
 		ArtifactSourceDocument,
 		ArtifactRunManifest,
 		ArtifactRunReport,

internal/core/diagnostics/run_dir.go

@@ -149,6 +149,10 @@ func (r *RunDirectory) WriteResolvedPipeline(payload any) error {
 	return r.WriteJSONArtifact(ArtifactResolvedPipeline, payload)
 }
 
+func (r *RunDirectory) WriteResolvedReferences(payload any) error {
+	return r.WriteJSONArtifact(ArtifactResolvedReferences, payload)
+}
+
 func (r *RunDirectory) WriteSourceDocument(payload any) error {
 	return r.WriteJSONArtifact(ArtifactSourceDocument, payload)
 }

internal/core/diagnostics/run_dir_test.go

@@ -191,6 +191,9 @@ func TestWriteTypedArtifacts(t *testing.T) {
 	if err := runDir.WriteResolvedPipeline(map[string]any{"pipeline": "test"}); err != nil {
 		t.Fatalf("WriteResolvedPipeline: %v", err)
 	}
+	if err := runDir.WriteResolvedReferences([]artifacts.ReferenceProvenance{{LaneID: "events", SlotName: "roster"}}); err != nil {
+		t.Fatalf("WriteResolvedReferences: %v", err)
+	}
 	if err := runDir.WriteSourceDocument(map[string]any{"source_id": "source-1"}); err != nil {
 		t.Fatalf("WriteSourceDocument: %v", err)
 	}
@@ -207,6 +210,7 @@ func TestWriteTypedArtifacts(t *testing.T) {
 	for _, name := range []string{
 		ArtifactEffectiveConfig,
 		ArtifactResolvedPipeline,
+		ArtifactResolvedReferences,
 		ArtifactSourceDocument,
 		ArtifactRunManifest,
 		ArtifactRunReport,

internal/framework/contracts/composition_test.go

@@ -203,6 +203,10 @@ func (extractor compositionExtractor) SchemaVersion() string {
 	return "v1"
 }
 
+func (extractor compositionExtractor) ReferenceSlots() []contracts.ReferenceSlot {
+	return nil
+}
+
 func (extractor compositionExtractor) Validators() []contracts.Validator {
 	return []contracts.Validator{compositionValidator{}}
 }

internal/framework/contracts/contracts.go

@@ -74,10 +74,49 @@ type Chunker interface {
 	Chunk(ctx context.Context, req ChunkRequest) (ChunkResult, error)
 }
 
+const (
+	ReferenceBindingSourceConfig = "config"
+	ReferenceBindingSourceCLI    = "cli"
+)
+
+type ReferenceSlot struct {
+	Name               string   `json:"name"`
+	Description        string   `json:"description,omitempty"`
+	Required           bool     `json:"required,omitempty"`
+	AcceptedMediaTypes []string `json:"accepted_media_types,omitempty"`
+	Multiple           bool     `json:"multiple,omitempty"`
+	MaxBytes           int64    `json:"max_bytes,omitempty"`
+}
+
+type ReferenceOrigin struct {
+	Type string `json:"type"`
+	URI  string `json:"uri,omitempty"`
+}
+
+type ReferenceItem struct {
+	SlotName      string          `json:"slot_name"`
+	MediaType     string          `json:"media_type,omitempty"`
+	Content       []byte          `json:"-"`
+	Digest        string          `json:"digest,omitempty"`
+	Origin        ReferenceOrigin `json:"origin"`
+	SizeBytes     int64           `json:"size_bytes,omitempty"`
+	BindingSource string          `json:"binding_source,omitempty"`
+}
+
+type ResolvedReferenceSlot struct {
+	Slot  ReferenceSlot   `json:"slot"`
+	Items []ReferenceItem `json:"items,omitempty"`
+}
+
+type ReferenceSet struct {
+	Slots map[string]ResolvedReferenceSlot `json:"slots,omitempty"`
+}
+
 type ExtractionRequest struct {
 	Source         *source.SourceDocument `json:"-"`
 	Chunk          *SourceChunk           `json:"chunk,omitempty"`
 	AmbientContext map[string]any         `json:"ambient_context,omitempty"`
+	References     ReferenceSet           `json:"references,omitempty"`
 	LLMClient      StructuredLLMClient    `json:"-"`
 	LLMProfile     string                 `json:"llm_profile,omitempty"`
 	Options        map[string]any         `json:"options,omitempty"`
@@ -93,6 +132,7 @@ type Extractor interface {
 	Key() string
 	ArtifactType() string
 	SchemaVersion() string
+	ReferenceSlots() []ReferenceSlot
 	Validators() []Validator
 	Extract(ctx context.Context, req ExtractionRequest) (ExtractionResult, error)
 }

internal/framework/contracts/contracts_test.go

@@ -186,6 +186,71 @@ func TestFakeExtractorReceivesChunkAndAmbientContext(t *testing.T) {
 	}
 }
 
+func TestReferenceSetDataTypes(t *testing.T) {
+	references := ReferenceSet{
+		Slots: map[string]ResolvedReferenceSlot{
+			"roster": {
+				Slot: ReferenceSlot{
+					Name:               "roster",
+					Description:        "Known characters",
+					Required:           true,
+					AcceptedMediaTypes: []string{"text/plain"},
+					Multiple:           true,
+					MaxBytes:           4096,
+				},
+				Items: []ReferenceItem{
+					{
+						SlotName:  "roster",
+						MediaType: "text/plain",
+						Content:   []byte("Aria\nBryn\n"),
+						Digest:    "sha256:reference",
+						Origin: ReferenceOrigin{
+							Type: "file",
+							URI:  "file:///tmp/roster.txt",
+						},
+						SizeBytes:     10,
+						BindingSource: ReferenceBindingSourceConfig,
+					},
+				},
+			},
+		},
+	}
+
+	item := references.Slots["roster"].Items[0]
+	if item.SlotName != "roster" || item.MediaType != "text/plain" || string(item.Content) != "Aria\nBryn\n" {
+		t.Fatalf("reference item = %#v, want constructed item fields", item)
+	}
+	if item.BindingSource != ReferenceBindingSourceConfig {
+		t.Fatalf("BindingSource = %q, want %q", item.BindingSource, ReferenceBindingSourceConfig)
+	}
+}
+
+func TestReferenceItemJSONOmitsContent(t *testing.T) {
+	item := ReferenceItem{
+		SlotName:  "roster",
+		MediaType: "text/plain",
+		Content:   []byte("reference content"),
+		Digest:    "sha256:reference",
+		Origin:    ReferenceOrigin{Type: "file", URI: "file:///tmp/roster.txt"},
+	}
+
+	encoded, err := json.Marshal(item)
+	if err != nil {
+		t.Fatalf("json.Marshal() error = %v, want nil", err)
+	}
+
+	var got map[string]any
+	if err := json.Unmarshal(encoded, &got); err != nil {
+		t.Fatalf("json.Unmarshal() error = %v, want nil", err)
+	}
+	if _, ok := got["content"]; ok {
+		t.Fatalf("encoded reference item leaked content: %s", encoded)
+	}
+	if _, ok := got["Content"]; ok {
+		t.Fatalf("encoded reference item leaked Content: %s", encoded)
+	}
+}
+
 func TestFakeMergeNormalizeAndOutputContracts(t *testing.T) {
 	candidate := artifacts.ArtifactCandidate{
 		Index:         0,
@@ -359,6 +424,10 @@ func (extractor fakeExtractor) SchemaVersion() string {
 	return extractor.schemaVersion
 }
 
+func (extractor fakeExtractor) ReferenceSlots() []ReferenceSlot {
+	return nil
+}
+
 func (extractor fakeExtractor) Validators() []Validator {
 	return extractor.validators
 }

internal/framework/pipeline/default_modules_test.go

@@ -117,6 +117,8 @@ func (defaultExtractor) ArtifactType() string { return "record" }
 
 func (defaultExtractor) SchemaVersion() string { return "v1" }
 
+func (defaultExtractor) ReferenceSlots() []contracts.ReferenceSlot { return nil }
+
 func (defaultExtractor) Validators() []contracts.Validator { return nil }
 
 func (defaultExtractor) Extract(ctx context.Context, req contracts.ExtractionRequest) (contracts.ExtractionResult, error) {

internal/framework/pipeline/extractor_registry_test.go

@@ -49,6 +49,20 @@ func TestExtractorRegistryRegisterWithSpecStoresMetadata(t *testing.T) {
 		Stage:    StageExtract,
 		Provides: []string{" generic-artifact ", "source-citations", "generic-artifact", ""},
 		Requires: []string{" source-document ", "source-document", ""},
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{
+				Name:               " glossary ",
+				Description:        " Supporting terms ",
+				AcceptedMediaTypes: []string{" text/plain ", "text/markdown", "text/plain", ""},
+				MaxBytes:           1024,
+			},
+			{
+				Name:        " roster ",
+				Description: " Characters ",
+				Required:    true,
+				Multiple:    true,
+			},
+		},
 	}
 
 	if err := registry.RegisterWithSpec(spec, fakeExtractorConstructor("generic-extractor")); err != nil {
@@ -64,12 +78,28 @@ func TestExtractorRegistryRegisterWithSpecStoresMetadata(t *testing.T) {
 		Stage:    StageExtract,
 		Provides: []string{"generic-artifact", "source-citations"},
 		Requires: []string{"source-document"},
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{
+				Name:               "glossary",
+				Description:        "Supporting terms",
+				AcceptedMediaTypes: []string{"text/markdown", "text/plain"},
+				MaxBytes:           1024,
+			},
+			{
+				Name:        "roster",
+				Description: "Characters",
+				Required:    true,
+				Multiple:    true,
+			},
+		},
 	}
 	if !reflect.DeepEqual(got, want) {
 		t.Fatalf("Spec() = %#v, want %#v", got, want)
 	}
 
 	got.Provides[0] = "changed"
+	got.ReferenceSlots[0].Name = "changed"
+	got.ReferenceSlots[0].AcceptedMediaTypes[0] = "changed"
 	again, ok := registry.Spec("generic-extractor")
 	if !ok {
 		t.Fatal("Spec() after caller mutation ok = false, want true")
@@ -109,6 +139,50 @@ func TestExtractorRegistryRegisterWithSpecRejectsWrongStage(t *testing.T) {
 	}
 }
 
+func TestExtractorRegistryRejectsInvalidReferenceSlots(t *testing.T) {
+	tests := []struct {
+		name  string
+		slots []contracts.ReferenceSlot
+		want  string
+	}{
+		{
+			name:  "empty name",
+			slots: []contracts.ReferenceSlot{{Name: " "}},
+			want:  "name",
+		},
+		{
+			name: "duplicate name after trim",
+			slots: []contracts.ReferenceSlot{
+				{Name: "roster"},
+				{Name: " roster "},
+			},
+			want: "duplicated",
+		},
+		{
+			name:  "negative max bytes",
+			slots: []contracts.ReferenceSlot{{Name: "roster", MaxBytes: -1}},
+			want:  "max_bytes",
+		},
+	}
+
+	for _, test := range tests {
+		t.Run(test.name, func(t *testing.T) {
+			registry := NewExtractorRegistry()
+			err := registry.RegisterWithSpec(ModuleSpec{
+				Key:            "generic-extractor",
+				Stage:          StageExtract,
+				ReferenceSlots: test.slots,
+			}, fakeExtractorConstructor("generic-extractor"))
+			if err == nil {
+				t.Fatal("RegisterWithSpec() error = nil, want error")
+			}
+			if !strings.Contains(err.Error(), test.want) {
+				t.Fatalf("RegisterWithSpec() error = %q, want %q", err.Error(), test.want)
+			}
+		})
+	}
+}
+
 func TestExtractorRegistrySpecRejectsUnknownKey(t *testing.T) {
 	registry := NewExtractorRegistry()
 
@@ -301,6 +375,10 @@ func (extractor registryFakeExtractor) SchemaVersion() string {
 	return "v1"
 }
 
+func (extractor registryFakeExtractor) ReferenceSlots() []contracts.ReferenceSlot {
+	return nil
+}
+
 func (extractor registryFakeExtractor) Validators() []contracts.Validator {
 	return nil
 }

internal/framework/pipeline/module.go

@@ -4,6 +4,8 @@ import (
 	"fmt"
 	"sort"
 	"strings"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 )
 
 type ModuleStage string
@@ -23,6 +25,7 @@ type ModuleSpec struct {
 	Stage          ModuleStage
 	Provides       []string
 	Requires       []string
+	ReferenceSlots []contracts.ReferenceSlot
 }
 
 func defaultModuleSpec(key string, stage ModuleStage) ModuleSpec {
@@ -38,6 +41,7 @@ func normalizeModuleSpec(spec ModuleSpec) ModuleSpec {
 		Stage:          spec.Stage,
 		Provides:       normalizeCapabilities(spec.Provides),
 		Requires:       normalizeCapabilities(spec.Requires),
+		ReferenceSlots: normalizeReferenceSlots(spec.ReferenceSlots),
 	}
 }
 
@@ -72,6 +76,7 @@ func cloneModuleSpec(spec ModuleSpec) ModuleSpec {
 		Stage:          spec.Stage,
 		Provides:       append([]string(nil), spec.Provides...),
 		Requires:       append([]string(nil), spec.Requires...),
+		ReferenceSlots: cloneReferenceSlots(spec.ReferenceSlots),
 	}
 }
 
@@ -82,6 +87,12 @@ func validateModuleSpec(kind string, expectedStage ModuleStage, spec ModuleSpec)
 	if spec.Stage != expectedStage {
 		return fmt.Errorf("%s %q must use %q stage, got %q", kind, spec.Key, expectedStage, spec.Stage)
 	}
+	if spec.Stage != StageExtract && len(spec.ReferenceSlots) > 0 {
+		return fmt.Errorf("%s %q must not declare reference slots", kind, spec.Key)
+	}
+	if err := validateReferenceSlots(spec.ReferenceSlots); err != nil {
+		return fmt.Errorf("%s %q reference slots: %w", kind, spec.Key, err)
+	}
 	return nil
 }
 
@@ -97,3 +108,74 @@ func sortedRegistryKeys[C any](constructors map[string]C) []string {
 	sort.Strings(keys)
 	return keys
 }
+
+func normalizeReferenceSlots(slots []contracts.ReferenceSlot) []contracts.ReferenceSlot {
+	if len(slots) == 0 {
+		return nil
+	}
+
+	normalized := make([]contracts.ReferenceSlot, 0, len(slots))
+	for _, slot := range slots {
+		slot.Name = strings.TrimSpace(slot.Name)
+		slot.Description = strings.TrimSpace(slot.Description)
+		slot.AcceptedMediaTypes = normalizeStringSet(slot.AcceptedMediaTypes)
+		normalized = append(normalized, slot)
+	}
+	sort.SliceStable(normalized, func(i, j int) bool {
+		return normalized[i].Name < normalized[j].Name
+	})
+	return normalized
+}
+
+func normalizeStringSet(values []string) []string {
+	if len(values) == 0 {
+		return nil
+	}
+	seen := make(map[string]struct{}, len(values))
+	for _, value := range values {
+		normalized := strings.TrimSpace(value)
+		if normalized == "" {
+			continue
+		}
+		seen[normalized] = struct{}{}
+	}
+	if len(seen) == 0 {
+		return nil
+	}
+
+	out := make([]string, 0, len(seen))
+	for value := range seen {
+		out = append(out, value)
+	}
+	sort.Strings(out)
+	return out
+}
+
+func validateReferenceSlots(slots []contracts.ReferenceSlot) error {
+	seen := make(map[string]struct{}, len(slots))
+	for i, slot := range slots {
+		if slot.Name == "" {
+			return fmt.Errorf("slot[%d].name must not be empty", i)
+		}
+		if _, ok := seen[slot.Name]; ok {
+			return fmt.Errorf("slot name %q is duplicated", slot.Name)
+		}
+		seen[slot.Name] = struct{}{}
+		if slot.MaxBytes < 0 {
+			return fmt.Errorf("slot %q max_bytes must not be negative", slot.Name)
+		}
+	}
+	return nil
+}
+
+func cloneReferenceSlots(slots []contracts.ReferenceSlot) []contracts.ReferenceSlot {
+	if len(slots) == 0 {
+		return nil
+	}
+	out := make([]contracts.ReferenceSlot, 0, len(slots))
+	for _, slot := range slots {
+		slot.AcceptedMediaTypes = append([]string(nil), slot.AcceptedMediaTypes...)
+		out = append(out, slot)
+	}
+	return out
+}

internal/framework/pipeline/module_test.go

@@ -0,0 +1,25 @@
+package pipeline
+
+import (
+	"strings"
+	"testing"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+)
+
+func TestValidateModuleSpecRejectsReferenceSlotsForNonExtractors(t *testing.T) {
+	err := validateModuleSpec("chunker", StageChunk, ModuleSpec{
+		Key:   "generic",
+		Stage: StageChunk,
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{Name: "roster"},
+		},
+	})
+
+	if err == nil {
+		t.Fatal("validateModuleSpec() error = nil, want error")
+	}
+	if !strings.Contains(err.Error(), "reference slots") {
+		t.Fatalf("validateModuleSpec() error = %q, want reference slots context", err.Error())
+	}
+}

internal/framework/pipeline/profile.go

@@ -7,6 +7,8 @@ import (
 	"fmt"
 	"sort"
 	"strings"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 )
 
 const (
@@ -28,6 +30,7 @@ type ArtifactLaneProfile struct {
 	Merge      ModuleBinding     `json:"merge,omitempty"`
 	Normalize  ModuleBinding     `json:"normalize,omitempty"`
 	Validators []ModuleBinding   `json:"validators,omitempty"`
+	References map[string]string `json:"references,omitempty"`
 }
 
 type PipelineProfile struct {
@@ -36,10 +39,25 @@ type PipelineProfile struct {
 	Chunk      ModuleBinding                  `json:"chunk,omitempty"`
 	Artifacts  map[string]ArtifactLaneProfile `json:"artifacts"`
 	Output     ModuleBinding                  `json:"output,omitempty"`
+	References map[string]string              `json:"references,omitempty"`
 }
 
 type ResolveOptions struct {
 	Only               []string
+	ReferenceOverrides []ReferenceBinding
+	ReferenceUnbinds   []ReferenceUnbind
+}
+
+type ReferenceBinding struct {
+	LaneID        string `json:"lane_id,omitempty"`
+	SlotName      string `json:"slot_name"`
+	Source        string `json:"source"`
+	BindingSource string `json:"binding_source,omitempty"`
+}
+
+type ReferenceUnbind struct {
+	LaneID   string `json:"lane_id"`
+	SlotName string `json:"slot_name"`
 }
 
 type ResolvedArtifactLane struct {
@@ -48,6 +66,8 @@ type ResolvedArtifactLane struct {
 	Merge        ModuleBinding
 	Normalize    ModuleBinding
 	Validators   []ModuleBinding
+	References   []ReferenceBinding     `json:"references,omitempty"`
+	ReferenceSet contracts.ReferenceSet `json:"-"`
 }
 
 type ResolvedPipeline struct {
@@ -126,7 +146,7 @@ func ResolvePipeline(profile PipelineProfile, options ResolveOptions, catalog Mo
 
 	for _, laneID := range selectedLaneIDs {
 		laneProfile := lanesByID[laneID]
-		lane, laneCapabilities, err := resolveArtifactLane(pipelineID, laneID, laneProfile, capabilities, catalog)
+		lane, laneCapabilities, err := resolveArtifactLane(pipelineID, laneID, laneProfile, profile.References, options, capabilities, catalog)
 		if err != nil {
 			return ResolvedPipeline{}, err
 		}
@@ -150,7 +170,15 @@ func ResolvePipeline(profile PipelineProfile, options ResolveOptions, catalog Mo
 	return resolved, nil
 }
 
-func resolveArtifactLane(pipelineID, laneID string, profile ArtifactLaneProfile, inherited capabilitySet, catalog ModuleCatalog) (ResolvedArtifactLane, capabilitySet, error) {
+func resolveArtifactLane(
+	pipelineID string,
+	laneID string,
+	profile ArtifactLaneProfile,
+	pipelineReferences map[string]string,
+	options ResolveOptions,
+	inherited capabilitySet,
+	catalog ModuleCatalog,
+) (ResolvedArtifactLane, capabilitySet, error) {
 	lane := ResolvedArtifactLane{
 		ID:         laneID,
 		Extract:    resolveBinding(profile.Extract, ""),
@@ -171,6 +199,11 @@ func resolveArtifactLane(pipelineID, laneID string, profile ArtifactLaneProfile,
 	if missing, ok := capabilities.missing(extractSpec.Requires); ok {
 		return ResolvedArtifactLane{}, nil, capabilityError(pipelineID, laneID, StageExtract, lane.Extract.Module, missing)
 	}
+	references, err := resolveReferenceBindings(pipelineID, laneID, lane.Extract.Module, extractSpec.ReferenceSlots, pipelineReferences, profile.References, options)
+	if err != nil {
+		return ResolvedArtifactLane{}, nil, err
+	}
+	lane.References = references
 	capabilities.add(extractSpec.Provides...)
 
 	mergeSpec, err := mergerSpec(catalog, lane.Merge.Module)
@@ -205,6 +238,162 @@ func resolveArtifactLane(pipelineID, laneID string, profile ArtifactLaneProfile,
 	return lane, capabilities, nil
 }
 
+func resolveReferenceBindings(
+	pipelineID string,
+	laneID string,
+	extractorModule string,
+	slots []contracts.ReferenceSlot,
+	pipelineReferences map[string]string,
+	laneReferences map[string]string,
+	options ResolveOptions,
+) ([]ReferenceBinding, error) {
+	slotByName := make(map[string]contracts.ReferenceSlot, len(slots))
+	for _, slot := range slots {
+		slotByName[slot.Name] = slot
+	}
+
+	bindings := make(map[string]ReferenceBinding)
+	addBinding := func(slotName, source, bindingSource string) error {
+		slotName = strings.TrimSpace(slotName)
+		source = strings.TrimSpace(source)
+		if slotName == "" {
+			return fmt.Errorf("pipeline %q lane %q reference slot name must not be empty", pipelineID, laneID)
+		}
+		if source == "" {
+			return fmt.Errorf("pipeline %q lane %q reference slot %q source must not be empty", pipelineID, laneID, slotName)
+		}
+		if _, ok := slotByName[slotName]; !ok {
+			return fmt.Errorf("pipeline %q lane %q reference slot %q is not declared by extractor %q", pipelineID, laneID, slotName, extractorModule)
+		}
+		bindings[slotName] = ReferenceBinding{
+			LaneID:        laneID,
+			SlotName:      slotName,
+			Source:        source,
+			BindingSource: bindingSource,
+		}
+		return nil
+	}
+
+	normalizedPipelineReferences, err := normalizedReferenceMap(pipelineReferences, fmt.Sprintf("pipeline %q reference slot", pipelineID))
+	if err != nil {
+		return nil, err
+	}
+	for _, slotName := range sortedStringMapKeys(normalizedPipelineReferences) {
+		if _, ok := slotByName[slotName]; !ok {
+			continue
+		}
+		if err := addBinding(slotName, normalizedPipelineReferences[slotName], contracts.ReferenceBindingSourceConfig); err != nil {
+			return nil, err
+		}
+	}
+
+	normalizedLaneReferences, err := normalizedReferenceMap(laneReferences, fmt.Sprintf("pipeline %q lane %q reference slot", pipelineID, laneID))
+	if err != nil {
+		return nil, err
+	}
+	for _, slotName := range sortedStringMapKeys(normalizedLaneReferences) {
+		if err := addBinding(slotName, normalizedLaneReferences[slotName], contracts.ReferenceBindingSourceConfig); err != nil {
+			return nil, err
+		}
+	}
+
+	for _, override := range options.ReferenceOverrides {
+		optionLaneID := strings.TrimSpace(override.LaneID)
+		if optionLaneID == "" {
+			return nil, fmt.Errorf("pipeline %q reference override lane id must not be empty", pipelineID)
+		}
+		if optionLaneID != laneID {
+			continue
+		}
+		source := override.BindingSource
+		if strings.TrimSpace(source) == "" {
+			source = contracts.ReferenceBindingSourceCLI
+		}
+		if err := addBinding(override.SlotName, override.Source, strings.TrimSpace(source)); err != nil {
+			return nil, err
+		}
+	}
+
+	for _, unbind := range options.ReferenceUnbinds {
+		optionLaneID := strings.TrimSpace(unbind.LaneID)
+		if optionLaneID == "" {
+			return nil, fmt.Errorf("pipeline %q reference unbind lane id must not be empty", pipelineID)
+		}
+		if optionLaneID != laneID {
+			continue
+		}
+		slotName := strings.TrimSpace(unbind.SlotName)
+		if slotName == "" {
+			return nil, fmt.Errorf("pipeline %q lane %q reference unbind slot name must not be empty", pipelineID, laneID)
+		}
+		if _, ok := slotByName[slotName]; !ok {
+			return nil, fmt.Errorf("pipeline %q lane %q reference slot %q is not declared", pipelineID, laneID, slotName)
+		}
+		delete(bindings, slotName)
+	}
+
+	for _, slot := range slots {
+		if slot.Required {
+			if _, ok := bindings[slot.Name]; !ok {
+				return nil, fmt.Errorf("pipeline %q lane %q required reference slot %q is not bound", pipelineID, laneID, slot.Name)
+			}
+		}
+	}
+
+	keys := sortedReferenceBindingKeys(bindings)
+	resolved := make([]ReferenceBinding, 0, len(keys))
+	for _, slotName := range keys {
+		resolved = append(resolved, bindings[slotName])
+	}
+	return resolved, nil
+}
+
+func normalizedReferenceMap(values map[string]string, keyName string) (map[string]string, error) {
+	if len(values) == 0 {
+		return nil, nil
+	}
+	out := make(map[string]string, len(values))
+	for rawSlotName, rawSource := range values {
+		slotName := strings.TrimSpace(rawSlotName)
+		if slotName == "" {
+			return nil, fmt.Errorf("%s must not be empty", keyName)
+		}
+		if _, ok := out[slotName]; ok {
+			return nil, fmt.Errorf("%s %q is duplicated after trimming", keyName, slotName)
+		}
+		source := strings.TrimSpace(rawSource)
+		if source == "" {
+			return nil, fmt.Errorf("%s %q source must not be empty", keyName, slotName)
+		}
+		out[slotName] = source
+	}
+	return out, nil
+}
+
+func sortedStringMapKeys(values map[string]string) []string {
+	if len(values) == 0 {
+		return nil
+	}
+	keys := make([]string, 0, len(values))
+	for key := range values {
+		keys = append(keys, key)
+	}
+	sort.Strings(keys)
+	return keys
+}
+
+func sortedReferenceBindingKeys(values map[string]ReferenceBinding) []string {
+	if len(values) == 0 {
+		return nil
+	}
+	keys := make([]string, 0, len(values))
+	for key := range values {
+		keys = append(keys, key)
+	}
+	sort.Strings(keys)
+	return keys
+}
+
 func resolveBinding(binding ModuleBinding, defaultModule string) ModuleBinding {
 	module := strings.TrimSpace(binding.Module)
 	if module == "" {

internal/framework/pipeline/profile_test.go

@@ -3,6 +3,7 @@ package pipeline
 import (
 	"context"
 	"encoding/json"
+	"errors"
 	"reflect"
 	"strings"
 	"testing"
@@ -125,6 +126,137 @@ func TestResolvePipelineSelectsOnlyRequestedLanes(t *testing.T) {
 	}
 }
 
+func TestResolvePipelineAppliesReferenceBindings(t *testing.T) {
+	profile := multiLaneProfile()
+	profile.References = map[string]string{
+		" roster ":  " ./shared-roster.yml ",
+		"unclaimed": "./ignored.yml",
+	}
+	lane := profile.Artifacts["events"]
+	lane.References = map[string]string{
+		"roster": "./lane-roster.yml",
+		" lore ": " ./lore.md ",
+	}
+	profile.Artifacts["events"] = lane
+
+	catalog := newProfileCatalogWithOverride(t, ModuleSpec{
+		Key:      "event-extractor",
+		Stage:    StageExtract,
+		Requires: []string{"chunk"},
+		Provides: []string{"candidate"},
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{Name: "roster", Required: true},
+			{Name: "lore"},
+		},
+	})
+	resolved, err := ResolvePipeline(profile, ResolveOptions{Only: []string{"events", "summaries"}}, catalog)
+	if err != nil {
+		t.Fatalf("ResolvePipeline() error = %v, want nil", err)
+	}
+
+	events := resolvedLane(t, resolved.ArtifactLanes, "events")
+	want := []ReferenceBinding{
+		{LaneID: "events", SlotName: "lore", Source: "./lore.md", BindingSource: contracts.ReferenceBindingSourceConfig},
+		{LaneID: "events", SlotName: "roster", Source: "./lane-roster.yml", BindingSource: contracts.ReferenceBindingSourceConfig},
+	}
+	if !reflect.DeepEqual(events.References, want) {
+		t.Fatalf("events references = %#v, want %#v", events.References, want)
+	}
+	summaries := resolvedLane(t, resolved.ArtifactLanes, "summaries")
+	if len(summaries.References) != 0 {
+		t.Fatalf("summaries references = %#v, want none", summaries.References)
+	}
+}
+
+func TestResolvePipelineRejectsUndeclaredReferenceSlot(t *testing.T) {
+	profile := baselineProfile()
+	lane := profile.Artifacts["events"]
+	lane.References = map[string]string{"missing": "./missing.yml"}
+	profile.Artifacts["events"] = lane
+
+	_, err := ResolvePipeline(profile, ResolveOptions{}, newProfileCatalog(t))
+	if err == nil {
+		t.Fatal("ResolvePipeline() error = nil, want error")
+	}
+	assertErrorContains(t, err, "events", "missing", "not declared")
+}
+
+func TestResolvePipelineRequiresBoundReferenceSlotsForSelectedLanes(t *testing.T) {
+	catalog := newProfileCatalogWithOverride(t, ModuleSpec{
+		Key:      "event-extractor",
+		Stage:    StageExtract,
+		Requires: []string{"chunk"},
+		Provides: []string{"candidate"},
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{Name: "roster", Required: true},
+		},
+	})
+
+	if _, err := ResolvePipeline(multiLaneProfile(), ResolveOptions{Only: []string{"notes"}}, catalog); err != nil {
+		t.Fatalf("ResolvePipeline(unselected required slot) error = %v, want nil", err)
+	}
+
+	_, err := ResolvePipeline(multiLaneProfile(), ResolveOptions{Only: []string{"events"}}, catalog)
+	if err == nil {
+		t.Fatal("ResolvePipeline(selected required slot) error = nil, want error")
+	}
+	assertErrorContains(t, err, "events", "required", "roster", "not bound")
+}
+
+func TestResolvePipelineReferenceUnbindCanLeaveRequiredSlotMissing(t *testing.T) {
+	profile := baselineProfile()
+	profile.References = map[string]string{"roster": "./roster.yml"}
+	catalog := newProfileCatalogWithOverride(t, ModuleSpec{
+		Key:      "event-extractor",
+		Stage:    StageExtract,
+		Requires: []string{"chunk"},
+		Provides: []string{"candidate"},
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{Name: "roster", Required: true},
+		},
+	})
+
+	_, err := ResolvePipeline(profile, ResolveOptions{
+		ReferenceUnbinds: []ReferenceUnbind{{LaneID: "events", SlotName: "roster"}},
+	}, catalog)
+	if err == nil {
+		t.Fatal("ResolvePipeline() error = nil, want error")
+	}
+	assertErrorContains(t, err, "events", "required", "roster", "not bound")
+}
+
+func TestResolvePipelineUsesReferenceSlotsFromSpecWithoutConstructingExtractor(t *testing.T) {
+	profile := baselineProfile()
+	profile.References = map[string]string{"roster": "./roster.yml"}
+	catalog := emptyProfileCatalog()
+	for _, spec := range defaultProfileSpecs() {
+		if spec.Key != "event-extractor" {
+			registerProfileSpecs(t, catalog, spec)
+		}
+	}
+	if err := catalog.Extractors.RegisterWithSpec(ModuleSpec{
+		Key:      "event-extractor",
+		Stage:    StageExtract,
+		Requires: []string{"chunk"},
+		Provides: []string{"candidate"},
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{Name: "roster", Required: true},
+		},
+	}, func() (contracts.Extractor, error) {
+		return nil, errors.New("constructor should not run")
+	}); err != nil {
+		t.Fatalf("RegisterWithSpec() error = %v, want nil", err)
+	}
+
+	resolved, err := ResolvePipeline(profile, ResolveOptions{}, catalog)
+	if err != nil {
+		t.Fatalf("ResolvePipeline() error = %v, want nil", err)
+	}
+	if got := resolved.ArtifactLanes[0].References[0].Source; got != "./roster.yml" {
+		t.Fatalf("reference source = %q, want ./roster.yml", got)
+	}
+}
+
 func TestResolvePipelineRejectsUnknownOnlyLane(t *testing.T) {
 	_, err := ResolvePipeline(multiLaneProfile(), ResolveOptions{Only: []string{"missing"}}, newProfileCatalog(t))
 	if err == nil {
@@ -463,6 +595,17 @@ func laneIDs(lanes []ResolvedArtifactLane) []string {
 	return ids
 }
 
+func resolvedLane(t *testing.T, lanes []ResolvedArtifactLane, laneID string) ResolvedArtifactLane {
+	t.Helper()
+	for _, lane := range lanes {
+		if lane.ID == laneID {
+			return lane
+		}
+	}
+	t.Fatalf("lane %q not found in %#v", laneID, laneIDs(lanes))
+	return ResolvedArtifactLane{}
+}
+
 func assertErrorContains(t *testing.T, err error, values ...string) {
 	t.Helper()
 

internal/framework/pipeline/references.go

@@ -0,0 +1,218 @@
+package pipeline
+
+import (
+	"crypto/sha256"
+	"encoding/hex"
+	"fmt"
+	"net/url"
+	"os"
+	"path/filepath"
+	"sort"
+	"strings"
+	"unicode/utf8"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+)
+
+const (
+	referenceOriginFile = "file"
+	referenceMediaType  = "text/plain; charset=utf-8"
+)
+
+type ReferenceMaterializationOptions struct {
+	ConfigPath string
+	WorkingDir string
+}
+
+func MaterializeReferences(resolved ResolvedPipeline, catalog ModuleCatalog, options ReferenceMaterializationOptions) (ResolvedPipeline, []contracts.Warning, error) {
+	out := resolved
+	if len(resolved.ArtifactLanes) == 0 {
+		return out, nil, nil
+	}
+
+	warnings := []contracts.Warning(nil)
+	out.ArtifactLanes = make([]ResolvedArtifactLane, len(resolved.ArtifactLanes))
+	for i, lane := range resolved.ArtifactLanes {
+		materializedLane := lane
+		referenceSet, laneWarnings, err := materializeLaneReferences(resolved.ID, lane, catalog, options)
+		if err != nil {
+			return ResolvedPipeline{}, nil, err
+		}
+		materializedLane.ReferenceSet = referenceSet
+		out.ArtifactLanes[i] = materializedLane
+		warnings = append(warnings, laneWarnings...)
+	}
+	return out, warnings, nil
+}
+
+func materializeLaneReferences(
+	pipelineID string,
+	lane ResolvedArtifactLane,
+	catalog ModuleCatalog,
+	options ReferenceMaterializationOptions,
+) (contracts.ReferenceSet, []contracts.Warning, error) {
+	if len(lane.References) == 0 {
+		return contracts.ReferenceSet{}, nil, nil
+	}
+	if catalog.Extractors == nil {
+		return contracts.ReferenceSet{}, nil, fmt.Errorf("pipeline %q lane %q extract module %q: module %q is not registered", pipelineID, lane.ID, lane.Extract.Module, lane.Extract.Module)
+	}
+	spec, ok := catalog.Extractors.Spec(lane.Extract.Module)
+	if !ok {
+		return contracts.ReferenceSet{}, nil, fmt.Errorf("pipeline %q lane %q extract module %q: module %q is not registered", pipelineID, lane.ID, lane.Extract.Module, lane.Extract.Module)
+	}
+
+	slotByName := make(map[string]contracts.ReferenceSlot, len(spec.ReferenceSlots))
+	for _, slot := range spec.ReferenceSlots {
+		slotByName[slot.Name] = slot
+	}
+
+	set := contracts.ReferenceSet{Slots: make(map[string]contracts.ResolvedReferenceSlot, len(lane.References))}
+	var warnings []contracts.Warning
+	for _, binding := range lane.References {
+		slotName := strings.TrimSpace(binding.SlotName)
+		slot, ok := slotByName[slotName]
+		if !ok {
+			return contracts.ReferenceSet{}, nil, fmt.Errorf("pipeline %q lane %q reference slot %q is not declared by extractor %q", pipelineID, lane.ID, slotName, lane.Extract.Module)
+		}
+
+		path, err := referencePath(binding, options)
+		if err != nil {
+			return contracts.ReferenceSet{}, nil, fmt.Errorf("pipeline %q lane %q reference slot %q path %q: %w", pipelineID, lane.ID, slotName, binding.Source, err)
+		}
+		content, err := os.ReadFile(path)
+		if err != nil {
+			return contracts.ReferenceSet{}, nil, fmt.Errorf("pipeline %q lane %q reference slot %q read %q: %w", pipelineID, lane.ID, slotName, path, err)
+		}
+		if !utf8.Valid(content) {
+			return contracts.ReferenceSet{}, nil, fmt.Errorf("pipeline %q lane %q reference slot %q path %q must be UTF-8 text", pipelineID, lane.ID, slotName, path)
+		}
+		if slot.MaxBytes > 0 && int64(len(content)) > slot.MaxBytes {
+			return contracts.ReferenceSet{}, nil, fmt.Errorf("pipeline %q lane %q reference slot %q path %q is %d bytes, limit %d", pipelineID, lane.ID, slotName, path, len(content), slot.MaxBytes)
+		}
+		if len(content) == 0 {
+			warnings = append(warnings, contracts.Warning{
+				Scope:      fmt.Sprintf("pipeline.%s.lane.%s.reference.%s", pipelineID, lane.ID, slotName),
+				ReasonCode: "empty_reference",
+				Message:    fmt.Sprintf("reference slot %q for lane %q is bound to an empty file", slotName, lane.ID),
+			})
+		}
+
+		item := contracts.ReferenceItem{
+			SlotName:      slotName,
+			MediaType:     referenceMediaType,
+			Content:       append([]byte(nil), content...),
+			Digest:        referenceDigest(content),
+			Origin:        contracts.ReferenceOrigin{Type: referenceOriginFile, URI: fileURI(path)},
+			SizeBytes:     int64(len(content)),
+			BindingSource: strings.TrimSpace(binding.BindingSource),
+		}
+		set.Slots[slotName] = contracts.ResolvedReferenceSlot{
+			Slot:  cloneReferenceSlot(slot),
+			Items: []contracts.ReferenceItem{item},
+		}
+	}
+	return set, warnings, nil
+}
+
+func referencePath(binding ReferenceBinding, options ReferenceMaterializationOptions) (string, error) {
+	source := strings.TrimSpace(binding.Source)
+	if source == "" {
+		return "", fmt.Errorf("must not be empty")
+	}
+	if filepath.IsAbs(source) {
+		return filepath.Clean(source), nil
+	}
+
+	base := strings.TrimSpace(options.WorkingDir)
+	if strings.TrimSpace(binding.BindingSource) == contracts.ReferenceBindingSourceConfig {
+		base = filepath.Dir(strings.TrimSpace(options.ConfigPath))
+	}
+	if base == "" {
+		var err error
+		base, err = os.Getwd()
+		if err != nil {
+			return "", fmt.Errorf("resolve working directory: %w", err)
+		}
+	}
+	return filepath.Clean(filepath.Join(base, source)), nil
+}
+
+func referenceDigest(content []byte) string {
+	sum := sha256.Sum256(content)
+	return "sha256:" + hex.EncodeToString(sum[:])
+}
+
+func fileURI(path string) string {
+	absolute, err := filepath.Abs(path)
+	if err != nil {
+		absolute = path
+	}
+	absolute = filepath.ToSlash(filepath.Clean(absolute))
+	if strings.HasPrefix(absolute, "/") {
+		return "file://" + (&url.URL{Path: absolute}).EscapedPath()
+	}
+	return "file:///" + (&url.URL{Path: absolute}).EscapedPath()
+}
+
+func cloneReferenceSlot(slot contracts.ReferenceSlot) contracts.ReferenceSlot {
+	slot.AcceptedMediaTypes = append([]string(nil), slot.AcceptedMediaTypes...)
+	return slot
+}
+
+func CloneReferenceSet(in contracts.ReferenceSet) contracts.ReferenceSet {
+	if len(in.Slots) == 0 {
+		return contracts.ReferenceSet{}
+	}
+	out := contracts.ReferenceSet{Slots: make(map[string]contracts.ResolvedReferenceSlot, len(in.Slots))}
+	keys := make([]string, 0, len(in.Slots))
+	for key := range in.Slots {
+		keys = append(keys, key)
+	}
+	sort.Strings(keys)
+	for _, key := range keys {
+		slot := in.Slots[key]
+		slot.Slot = cloneReferenceSlot(slot.Slot)
+		if len(slot.Items) > 0 {
+			items := make([]contracts.ReferenceItem, len(slot.Items))
+			for i, item := range slot.Items {
+				item.Content = append([]byte(nil), item.Content...)
+				items[i] = item
+			}
+			slot.Items = items
+		}
+		out.Slots[key] = slot
+	}
+	return out
+}
+
+func ReferenceProvenance(resolved ResolvedPipeline) []artifacts.ReferenceProvenance {
+	provenance := []artifacts.ReferenceProvenance{}
+	for _, lane := range resolved.ArtifactLanes {
+		if len(lane.ReferenceSet.Slots) == 0 {
+			continue
+		}
+		slotNames := make([]string, 0, len(lane.ReferenceSet.Slots))
+		for slotName := range lane.ReferenceSet.Slots {
+			slotNames = append(slotNames, slotName)
+		}
+		sort.Strings(slotNames)
+		for _, slotName := range slotNames {
+			slot := lane.ReferenceSet.Slots[slotName]
+			for _, item := range slot.Items {
+				provenance = append(provenance, artifacts.ReferenceProvenance{
+					LaneID:        lane.ID,
+					SlotName:      item.SlotName,
+					OriginType:    item.Origin.Type,
+					OriginURI:     item.Origin.URI,
+					Digest:        item.Digest,
+					MediaType:     item.MediaType,
+					SizeBytes:     item.SizeBytes,
+					BindingSource: item.BindingSource,
+				})
+			}
+		}
+	}
+	return provenance
+}

internal/framework/pipeline/references_test.go

@@ -0,0 +1,189 @@
+package pipeline
+
+import (
+	"encoding/json"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+)
+
+func TestMaterializeReferencesResolvesPathsAndDigestsContent(t *testing.T) {
+	configDir := t.TempDir()
+	workingDir := t.TempDir()
+	configReference := filepath.Join(configDir, "config-reference.txt")
+	cliReference := filepath.Join(workingDir, "cli-reference.txt")
+	writeReferenceFile(t, configReference, []byte("config text"))
+	writeReferenceFile(t, cliReference, []byte("cli text"))
+
+	pipeline := baselineProfile()
+	pipeline.References = map[string]string{"roster": "config-reference.txt"}
+	lane := pipeline.Artifacts["events"]
+	lane.References = map[string]string{"glossary": "cli-reference.txt"}
+	pipeline.Artifacts["events"] = lane
+	catalog := referenceCatalog(t, []contracts.ReferenceSlot{
+		{Name: "roster"},
+		{Name: "glossary"},
+	})
+	resolved, err := ResolvePipeline(pipeline, ResolveOptions{
+		ReferenceOverrides: []ReferenceBinding{
+			{LaneID: "events", SlotName: "glossary", Source: "cli-reference.txt", BindingSource: contracts.ReferenceBindingSourceCLI},
+		},
+	}, catalog)
+	if err != nil {
+		t.Fatalf("ResolvePipeline() error = %v, want nil", err)
+	}
+
+	first, warnings, err := MaterializeReferences(resolved, catalog, ReferenceMaterializationOptions{
+		ConfigPath: filepath.Join(configDir, "config.yml"),
+		WorkingDir: workingDir,
+	})
+	if err != nil {
+		t.Fatalf("MaterializeReferences() error = %v, want nil", err)
+	}
+	if len(warnings) != 0 {
+		t.Fatalf("warnings = %#v, want none", warnings)
+	}
+	second, _, err := MaterializeReferences(resolved, catalog, ReferenceMaterializationOptions{
+		ConfigPath: filepath.Join(configDir, "config.yml"),
+		WorkingDir: workingDir,
+	})
+	if err != nil {
+		t.Fatalf("MaterializeReferences(second) error = %v, want nil", err)
+	}
+
+	referenceSet := first.ArtifactLanes[0].ReferenceSet
+	roster := referenceSet.Slots["roster"].Items[0]
+	if string(roster.Content) != "config text" {
+		t.Fatalf("roster content = %q, want config text", roster.Content)
+	}
+	if roster.Digest != referenceDigest([]byte("config text")) || roster.Digest != second.ArtifactLanes[0].ReferenceSet.Slots["roster"].Items[0].Digest {
+		t.Fatalf("roster digest = %q, want stable digest", roster.Digest)
+	}
+	if roster.BindingSource != contracts.ReferenceBindingSourceConfig {
+		t.Fatalf("roster binding source = %q, want config", roster.BindingSource)
+	}
+	if roster.MediaType != referenceMediaType || roster.Origin.Type != referenceOriginFile || roster.SizeBytes != int64(len("config text")) {
+		t.Fatalf("roster metadata = %#v, want text file metadata", roster)
+	}
+	if !strings.Contains(roster.Origin.URI, "config-reference.txt") {
+		t.Fatalf("roster origin URI = %q, want config reference path", roster.Origin.URI)
+	}
+
+	glossary := referenceSet.Slots["glossary"].Items[0]
+	if string(glossary.Content) != "cli text" {
+		t.Fatalf("glossary content = %q, want cli text", glossary.Content)
+	}
+	if glossary.BindingSource != contracts.ReferenceBindingSourceCLI {
+		t.Fatalf("glossary binding source = %q, want cli", glossary.BindingSource)
+	}
+	if !strings.Contains(glossary.Origin.URI, "cli-reference.txt") {
+		t.Fatalf("glossary origin URI = %q, want cli reference path", glossary.Origin.URI)
+	}
+
+	provenance := ReferenceProvenance(first)
+	if len(provenance) != 2 {
+		t.Fatalf("ReferenceProvenance() = %#v, want two entries", provenance)
+	}
+	if provenance[0].LaneID != "events" || provenance[0].SlotName != "glossary" || provenance[0].Digest != glossary.Digest {
+		t.Fatalf("ReferenceProvenance()[0] = %#v, want sorted glossary provenance", provenance[0])
+	}
+	if provenance[1].LaneID != "events" || provenance[1].SlotName != "roster" || provenance[1].Digest != roster.Digest {
+		t.Fatalf("ReferenceProvenance()[1] = %#v, want roster provenance", provenance[1])
+	}
+
+	encoded, err := json.Marshal(first)
+	if err != nil {
+		t.Fatalf("json.Marshal(materialized) error = %v, want nil", err)
+	}
+	if strings.Contains(string(encoded), "config text") || strings.Contains(string(encoded), "cli text") {
+		t.Fatalf("materialized pipeline JSON contains reference content: %s", encoded)
+	}
+}
+
+func TestMaterializeReferencesRejectsNonUTF8Content(t *testing.T) {
+	configDir := t.TempDir()
+	path := filepath.Join(configDir, "bad.txt")
+	writeReferenceFile(t, path, []byte{0xff, 0xfe})
+
+	resolved := resolvedPipelineWithReference(t, "roster", "bad.txt", contracts.ReferenceBindingSourceConfig, contracts.ReferenceSlot{Name: "roster"})
+	_, _, err := MaterializeReferences(resolved, referenceCatalog(t, []contracts.ReferenceSlot{{Name: "roster"}}), ReferenceMaterializationOptions{
+		ConfigPath: filepath.Join(configDir, "config.yml"),
+	})
+	if err == nil || !strings.Contains(err.Error(), "UTF-8") || !strings.Contains(err.Error(), "roster") || !strings.Contains(err.Error(), path) {
+		t.Fatalf("error = %v, want UTF-8 path error", err)
+	}
+}
+
+func TestMaterializeReferencesWarnsForEmptyFiles(t *testing.T) {
+	configDir := t.TempDir()
+	path := filepath.Join(configDir, "empty.txt")
+	writeReferenceFile(t, path, nil)
+
+	resolved := resolvedPipelineWithReference(t, "roster", "empty.txt", contracts.ReferenceBindingSourceConfig, contracts.ReferenceSlot{Name: "roster"})
+	materialized, warnings, err := MaterializeReferences(resolved, referenceCatalog(t, []contracts.ReferenceSlot{{Name: "roster"}}), ReferenceMaterializationOptions{
+		ConfigPath: filepath.Join(configDir, "config.yml"),
+	})
+	if err != nil {
+		t.Fatalf("MaterializeReferences() error = %v, want nil", err)
+	}
+	if len(warnings) != 1 || warnings[0].ReasonCode != "empty_reference" {
+		t.Fatalf("warnings = %#v, want empty reference warning", warnings)
+	}
+	item := materialized.ArtifactLanes[0].ReferenceSet.Slots["roster"].Items[0]
+	if item.SizeBytes != 0 || item.Digest != referenceDigest(nil) {
+		t.Fatalf("empty item = %#v, want zero size and empty digest", item)
+	}
+}
+
+func TestMaterializeReferencesEnforcesMaxBytes(t *testing.T) {
+	configDir := t.TempDir()
+	path := filepath.Join(configDir, "large.txt")
+	writeReferenceFile(t, path, []byte("too large"))
+
+	slot := contracts.ReferenceSlot{Name: "roster", MaxBytes: 3}
+	resolved := resolvedPipelineWithReference(t, "roster", "large.txt", contracts.ReferenceBindingSourceConfig, slot)
+	_, _, err := MaterializeReferences(resolved, referenceCatalog(t, []contracts.ReferenceSlot{slot}), ReferenceMaterializationOptions{
+		ConfigPath: filepath.Join(configDir, "config.yml"),
+	})
+	if err == nil || !strings.Contains(err.Error(), "9 bytes") || !strings.Contains(err.Error(), "limit 3") || !strings.Contains(err.Error(), "roster") {
+		t.Fatalf("error = %v, want max bytes error", err)
+	}
+}
+
+func resolvedPipelineWithReference(t *testing.T, slotName, source, bindingSource string, slot contracts.ReferenceSlot) ResolvedPipeline {
+	t.Helper()
+	profile := baselineProfile()
+	lane := profile.Artifacts["events"]
+	lane.References = map[string]string{slotName: source}
+	profile.Artifacts["events"] = lane
+	catalog := referenceCatalog(t, []contracts.ReferenceSlot{slot})
+	resolved, err := ResolvePipeline(profile, ResolveOptions{}, catalog)
+	if err != nil {
+		t.Fatalf("ResolvePipeline() error = %v, want nil", err)
+	}
+	if bindingSource != contracts.ReferenceBindingSourceConfig {
+		resolved.ArtifactLanes[0].References[0].BindingSource = bindingSource
+	}
+	return resolved
+}
+
+func referenceCatalog(t *testing.T, slots []contracts.ReferenceSlot) ModuleCatalog {
+	t.Helper()
+	return newProfileCatalogWithOverride(t, ModuleSpec{
+		Key:            "event-extractor",
+		Stage:          StageExtract,
+		Requires:       []string{"chunk"},
+		Provides:       []string{"candidate"},
+		ReferenceSlots: slots,
+	})
+}
+
+func writeReferenceFile(t *testing.T, path string, content []byte) {
+	t.Helper()
+	if err := os.WriteFile(path, content, 0o644); err != nil {
+		t.Fatalf("write reference %q: %v", path, err)
+	}
+}

internal/framework/pipeline/registry_integration_test.go

@@ -149,6 +149,10 @@ func (extractor integrationExtractor) SchemaVersion() string {
 	return "v1"
 }
 
+func (extractor integrationExtractor) ReferenceSlots() []contracts.ReferenceSlot {
+	return nil
+}
+
 func (extractor integrationExtractor) Validators() []contracts.Validator {
 	return extractor.validators
 }

internal/framework/pipeline/runner.go

@@ -41,6 +41,7 @@ type RunInput struct {
 	StartedAt   time.Time
 	LLMProfiles []artifacts.LLMProfileManifest
 	Metadata    map[string]any
+	Warnings    []contracts.Warning
 }
 
 type RunOutput struct {
@@ -63,6 +64,7 @@ func (r *Runner) Run(ctx context.Context, input RunInput) (RunOutput, error) {
 		return output, err
 	}
 
+	output.Warnings = append(output.Warnings, cloneWarnings(input.Warnings)...)
 	output.Manifest = manifestFromPipeline(input)
 
 	adapter, err := r.registries.Inputs.Build(input.Pipeline.Input.Module)
@@ -184,6 +186,7 @@ func (r *Runner) runLane(ctx context.Context, input RunInput, doc *source.Source
 		result, err := extractor.Extract(ctx, contracts.ExtractionRequest{
 			Source:     doc,
 			Chunk:      &chunk,
+			References: CloneReferenceSet(lane.ReferenceSet),
 			LLMClient:  input.LLMClient,
 			LLMProfile: lane.Extract.LLMProfile,
 			Options:    cloneOptions(lane.Extract.Options),
@@ -353,8 +356,12 @@ func manifestFromPipeline(input RunInput) artifacts.RunManifest {
 		ArtifactLanes:  make([]artifacts.ArtifactLaneManifest, 0, len(pipeline.ArtifactLanes)),
 		RunID:          runID,
 		StartedAt:      timePtr(startedAt),
+		References:     ReferenceProvenance(pipeline),
 		LLMProfiles:    cloneLLMProfiles(input.LLMProfiles),
 	}
+	// The runner does not currently maintain a cache or idempotency key. Reference
+	// digests are recorded in manifest provenance and intentionally kept separate
+	// from source_digests.
 
 	for _, lane := range pipeline.ArtifactLanes {
 		laneManifest := artifacts.ArtifactLaneManifest{
@@ -500,6 +507,13 @@ func cloneLLMProfiles(profiles []artifacts.LLMProfileManifest) []artifacts.LLMPr
 	return append([]artifacts.LLMProfileManifest(nil), profiles...)
 }
 
+func cloneWarnings(warnings []contracts.Warning) []contracts.Warning {
+	if len(warnings) == 0 {
+		return nil
+	}
+	return append([]contracts.Warning(nil), warnings...)
+}
+
 func timePtr(t time.Time) *time.Time {
 	return &t
 }

internal/framework/pipeline/runner_test.go

@@ -559,6 +559,60 @@ func TestRunPassesModuleBindingConfigToStageRequests(t *testing.T) {
 	}
 }
 
+func TestRunPassesLaneReferencesToExtractorRequests(t *testing.T) {
+	modules := defaultRunnerModules()
+	pipeline := resolvedPipeline()
+	pipeline.ArtifactLanes[0].ReferenceSet = contracts.ReferenceSet{
+		Slots: map[string]contracts.ResolvedReferenceSlot{
+			"roster": {
+				Slot: contracts.ReferenceSlot{Name: "roster"},
+				Items: []contracts.ReferenceItem{
+					{
+						SlotName:      "roster",
+						MediaType:     "text/plain; charset=utf-8",
+						Content:       []byte("reference text"),
+						Digest:        "sha256:test",
+						Origin:        contracts.ReferenceOrigin{Type: "file", URI: "file:///tmp/reference.txt"},
+						SizeBytes:     int64(len("reference text")),
+						BindingSource: contracts.ReferenceBindingSourceConfig,
+					},
+				},
+			},
+		},
+	}
+
+	_, err := New(newRunnerRegistries(t, modules)).Run(context.Background(), RunInput{Pipeline: pipeline})
+	if err != nil {
+		t.Fatalf("Run() error = %v, want nil", err)
+	}
+
+	req := modules.extractors["extract-alpha"].requests[0]
+	item := req.References.Slots["roster"].Items[0]
+	if string(item.Content) != "reference text" {
+		t.Fatalf("reference content = %q, want reference text", item.Content)
+	}
+	item.Content[0] = 'R'
+	if got := string(pipeline.ArtifactLanes[0].ReferenceSet.Slots["roster"].Items[0].Content); got != "reference text" {
+		t.Fatalf("runner mutated reference set content = %q", got)
+	}
+}
+
+func TestRunIncludesInputWarnings(t *testing.T) {
+	modules := defaultRunnerModules()
+	warning := contracts.Warning{Scope: "reference", ReasonCode: "empty_reference", Message: "empty reference"}
+
+	output, err := New(newRunnerRegistries(t, modules)).Run(context.Background(), RunInput{
+		Pipeline: resolvedPipeline(),
+		Warnings: []contracts.Warning{warning},
+	})
+	if err != nil {
+		t.Fatalf("Run() error = %v, want nil", err)
+	}
+	if len(output.Warnings) != 1 || output.Warnings[0] != warning {
+		t.Fatalf("warnings = %#v, want input warning", output.Warnings)
+	}
+}
+
 func TestRunRecordsTopLevelModuleMetadataForSingletonModules(t *testing.T) {
 	modules := defaultRunnerModules()
 	modules.input.manifestMetadata = map[string]any{
@@ -906,7 +960,27 @@ func TestRunReturnsFailedManifestWhenOutputEncoderFails(t *testing.T) {
 }
 
 func TestRunManifestIncludesPipelineAndLaneDetails(t *testing.T) {
-	output, err := New(newRunnerRegistries(t, nil)).Run(context.Background(), RunInput{Pipeline: resolvedPipelineWithValidators("configured")})
+	resolved := resolvedPipelineWithValidators("configured")
+	resolved.ArtifactLanes[0].ReferenceSet = contracts.ReferenceSet{
+		Slots: map[string]contracts.ResolvedReferenceSlot{
+			"roster": {
+				Slot: contracts.ReferenceSlot{Name: "roster"},
+				Items: []contracts.ReferenceItem{
+					{
+						SlotName:      "roster",
+						MediaType:     "text/plain; charset=utf-8",
+						Content:       []byte("reference content"),
+						Digest:        "sha256:reference",
+						Origin:        contracts.ReferenceOrigin{Type: "file", URI: "file:///tmp/roster.txt"},
+						SizeBytes:     int64(len("reference content")),
+						BindingSource: contracts.ReferenceBindingSourceConfig,
+					},
+				},
+			},
+		},
+	}
+
+	output, err := New(newRunnerRegistries(t, nil)).Run(context.Background(), RunInput{Pipeline: resolved})
 	if err != nil {
 		t.Fatalf("Run() error = %v, want nil", err)
 	}
@@ -921,6 +995,16 @@ func TestRunManifestIncludesPipelineAndLaneDetails(t *testing.T) {
 	if !reflect.DeepEqual(manifest.SourceDigests, []string{"sha256:source"}) {
 		t.Fatalf("SourceDigests = %#v, want source digest", manifest.SourceDigests)
 	}
+	if len(manifest.References) != 1 {
+		t.Fatalf("References = %#v, want one reference provenance entry", manifest.References)
+	}
+	reference := manifest.References[0]
+	if reference.LaneID != "alpha" || reference.SlotName != "roster" || reference.Digest != "sha256:reference" {
+		t.Fatalf("reference provenance = %#v, want lane slot digest", reference)
+	}
+	if reference.OriginType != "file" || reference.OriginURI != "file:///tmp/roster.txt" || reference.MediaType != "text/plain; charset=utf-8" || reference.SizeBytes != int64(len("reference content")) || reference.BindingSource != contracts.ReferenceBindingSourceConfig {
+		t.Fatalf("reference provenance = %#v, want origin/media/size/source", reference)
+	}
 	if manifest.ValidationStatus != "approved" {
 		t.Fatalf("ValidationStatus = %q, want approved", manifest.ValidationStatus)
 	}
@@ -1269,6 +1353,10 @@ func (extractor *runnerExtractor) SchemaVersion() string {
 	return extractor.schemaVersion
 }
 
+func (extractor *runnerExtractor) ReferenceSlots() []contracts.ReferenceSlot {
+	return nil
+}
+
 func (extractor *runnerExtractor) ManifestMetadata() map[string]any {
 	return extractor.manifestMetadata
 }

internal/framework/pipeline/walking_skeleton_test.go

@@ -252,6 +252,10 @@ func (extractor walkingSkeletonExtractor) SchemaVersion() string {
 	return "v1"
 }
 
+func (extractor walkingSkeletonExtractor) ReferenceSlots() []contracts.ReferenceSlot {
+	return nil
+}
+
 func (extractor walkingSkeletonExtractor) Validators() []contracts.Validator {
 	return nil
 }

internal/framework/prompt/registry.go

@@ -7,9 +7,13 @@ import (
 	"fmt"
 	"io/fs"
 	"path"
+	"reflect"
 	"sort"
 	"strings"
 	"text/template"
+	"text/template/parse"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 )
 
 //go:embed assets/**
@@ -48,6 +52,7 @@ type Definition struct {
 	EmbeddedPath   string
 	SystemPath     string
 	UserPath       string
+	ReferenceSlots []contracts.ReferenceSlot
 }
 
 // Bundle is a compiled system/user prompt pair.
@@ -55,6 +60,7 @@ type Bundle struct {
 	systemTmpl     *template.Template
 	userTmpl       *template.Template
 	metadata       Metadata
+	referenceSlots map[string]contracts.ReferenceSlot
 }
 
 // Metadata returns metadata for the compiled prompt bundle.
@@ -169,6 +175,8 @@ func LoadBundle(fsys fs.FS, def Definition) (*Bundle, error) {
 
 	funcs := template.FuncMap{
 		"hardening":    func() string { return sharedHardening },
+		"reference":    func(string) (string, error) { return "", nil },
+		"hasreference": func(string) (bool, error) { return false, nil },
 	}
 	systemTmpl, err := template.New(path.Base(systemPath)).Option("missingkey=error").Funcs(funcs).Parse(systemSource)
 	if err != nil {
@@ -178,6 +186,13 @@ func LoadBundle(fsys fs.FS, def Definition) (*Bundle, error) {
 	if err != nil {
 		return nil, fmt.Errorf("parse embedded user prompt %q: %w", userPath, err)
 	}
+	referenceSlots := referenceSlotMap(def.ReferenceSlots)
+	if err := validateTemplateReferenceSlots(systemTmpl, referenceSlots); err != nil {
+		return nil, fmt.Errorf("validate embedded system prompt %q: %w", systemPath, err)
+	}
+	if err := validateTemplateReferenceSlots(userTmpl, referenceSlots); err != nil {
+		return nil, fmt.Errorf("validate embedded user prompt %q: %w", userPath, err)
+	}
 
 	hashInput := systemSource + "\n\n" + userSource
 	hash := sha256.Sum256([]byte(hashInput))
@@ -193,9 +208,124 @@ func LoadBundle(fsys fs.FS, def Definition) (*Bundle, error) {
 		systemTmpl:     systemTmpl,
 		userTmpl:       userTmpl,
 		metadata:       metadata,
+		referenceSlots: referenceSlots,
 	}, nil
 }
 
+func referenceSlotMap(slots []contracts.ReferenceSlot) map[string]contracts.ReferenceSlot {
+	if len(slots) == 0 {
+		return nil
+	}
+	out := make(map[string]contracts.ReferenceSlot, len(slots))
+	for _, slot := range slots {
+		name := strings.TrimSpace(slot.Name)
+		if name == "" {
+			continue
+		}
+		slot.Name = name
+		slot.AcceptedMediaTypes = append([]string(nil), slot.AcceptedMediaTypes...)
+		out[name] = slot
+	}
+	return out
+}
+
+func validateTemplateReferenceSlots(tmpl *template.Template, declared map[string]contracts.ReferenceSlot) error {
+	if tmpl == nil || tmpl.Tree == nil || tmpl.Tree.Root == nil {
+		return nil
+	}
+	return validateReferenceNodes(tmpl.Tree.Root, declared)
+}
+
+func validateReferenceNodes(node parse.Node, declared map[string]contracts.ReferenceSlot) error {
+	if node == nil || reflect.ValueOf(node).IsNil() {
+		return nil
+	}
+	switch typed := node.(type) {
+	case *parse.ListNode:
+		for _, child := range typed.Nodes {
+			if err := validateReferenceNodes(child, declared); err != nil {
+				return err
+			}
+		}
+	case *parse.ActionNode:
+		return validateReferencePipeline(typed.Pipe, declared)
+	case *parse.IfNode:
+		if err := validateReferencePipeline(typed.Pipe, declared); err != nil {
+			return err
+		}
+		if err := validateReferenceNodes(typed.List, declared); err != nil {
+			return err
+		}
+		return validateReferenceNodes(typed.ElseList, declared)
+	case *parse.RangeNode:
+		if err := validateReferencePipeline(typed.Pipe, declared); err != nil {
+			return err
+		}
+		if err := validateReferenceNodes(typed.List, declared); err != nil {
+			return err
+		}
+		return validateReferenceNodes(typed.ElseList, declared)
+	case *parse.WithNode:
+		if err := validateReferencePipeline(typed.Pipe, declared); err != nil {
+			return err
+		}
+		if err := validateReferenceNodes(typed.List, declared); err != nil {
+			return err
+		}
+		return validateReferenceNodes(typed.ElseList, declared)
+	case *parse.TemplateNode:
+		return nil
+	}
+	return nil
+}
+
+func validateReferencePipeline(pipe *parse.PipeNode, declared map[string]contracts.ReferenceSlot) error {
+	if pipe == nil {
+		return nil
+	}
+	for _, cmd := range pipe.Cmds {
+		if err := validateReferenceCommand(cmd, declared); err != nil {
+			return err
+		}
+	}
+	return nil
+}
+
+func validateReferenceCommand(cmd *parse.CommandNode, declared map[string]contracts.ReferenceSlot) error {
+	if cmd == nil || len(cmd.Args) == 0 {
+		return nil
+	}
+	for _, arg := range cmd.Args[1:] {
+		if nested, ok := arg.(*parse.PipeNode); ok {
+			if err := validateReferencePipeline(nested, declared); err != nil {
+				return err
+			}
+		}
+	}
+	identifier, ok := cmd.Args[0].(*parse.IdentifierNode)
+	if !ok {
+		return nil
+	}
+	if identifier.Ident != "reference" && identifier.Ident != "hasreference" {
+		return nil
+	}
+	if len(cmd.Args) != 2 {
+		return fmt.Errorf("%s requires one string slot name", identifier.Ident)
+	}
+	slotArg, ok := cmd.Args[1].(*parse.StringNode)
+	if !ok {
+		return fmt.Errorf("%s requires a string literal slot name", identifier.Ident)
+	}
+	slotName := strings.TrimSpace(slotArg.Text)
+	if slotName == "" {
+		return fmt.Errorf("%s slot name must not be empty", identifier.Ident)
+	}
+	if _, ok := declared[slotName]; !ok {
+		return fmt.Errorf("%s slot %q is not declared", identifier.Ident, slotName)
+	}
+	return nil
+}
+
 func readPromptAsset(fsys fs.FS, assetPath string) (string, error) {
 	if strings.TrimSpace(assetPath) == "" {
 		return "", fmt.Errorf("prompt asset path must not be empty")

internal/framework/prompt/render.go

@@ -4,6 +4,9 @@ import (
 	"bytes"
 	"fmt"
 	"strings"
+	"text/template"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 )
 
 // RenderUserSystem renders the system and user prompt pair for promptID.
@@ -16,20 +19,105 @@ func RenderUserSystem(promptID string, data any) (system string, user string, me
 	return compiled.RenderUserSystem(data)
 }
 
+// RenderUserSystemWithReferences renders the system and user prompt pair for promptID with reference template functions.
+func RenderUserSystemWithReferences(promptID string, data any, references contracts.ReferenceSet) (system string, user string, metadata Metadata, err error) {
+	trimmedID := strings.TrimSpace(promptID)
+	compiled, ok := promptRegistry[trimmedID]
+	if !ok {
+		return "", "", Metadata{}, fmt.Errorf("unknown prompt id %q", promptID)
+	}
+	return compiled.RenderUserSystemWithReferences(data, references)
+}
+
 // RenderUserSystem renders the bundle's system and user prompts.
 func (b *Bundle) RenderUserSystem(data any) (system string, user string, metadata Metadata, err error) {
+	return b.RenderUserSystemWithReferences(data, contracts.ReferenceSet{})
+}
+
+// RenderUserSystemWithReferences renders the bundle's system and user prompts with reference template functions.
+func (b *Bundle) RenderUserSystemWithReferences(data any, references contracts.ReferenceSet) (system string, user string, metadata Metadata, err error) {
 	if b == nil {
 		return "", "", Metadata{}, fmt.Errorf("prompt bundle must not be nil")
 	}
+	systemTmpl, userTmpl, err := b.renderTemplates(references)
+	if err != nil {
+		return "", "", Metadata{}, err
+	}
 	var systemBuf bytes.Buffer
-	if err := b.systemTmpl.Execute(&systemBuf, data); err != nil {
+	if err := systemTmpl.Execute(&systemBuf, data); err != nil {
 		return "", "", Metadata{}, fmt.Errorf("render system prompt %q: %w", b.metadata.PromptID, err)
 	}
 
 	var userBuf bytes.Buffer
-	if err := b.userTmpl.Execute(&userBuf, data); err != nil {
+	if err := userTmpl.Execute(&userBuf, data); err != nil {
 		return "", "", Metadata{}, fmt.Errorf("render user prompt %q: %w", b.metadata.PromptID, err)
 	}
 
 	return strings.TrimSpace(systemBuf.String()), strings.TrimSpace(userBuf.String()), b.metadata, nil
 }
+
+func (b *Bundle) renderTemplates(references contracts.ReferenceSet) (*template.Template, *template.Template, error) {
+	funcs := b.referenceFuncs(references)
+	systemTmpl, err := b.systemTmpl.Clone()
+	if err != nil {
+		return nil, nil, fmt.Errorf("clone system prompt %q: %w", b.metadata.PromptID, err)
+	}
+	userTmpl, err := b.userTmpl.Clone()
+	if err != nil {
+		return nil, nil, fmt.Errorf("clone user prompt %q: %w", b.metadata.PromptID, err)
+	}
+	systemTmpl.Funcs(funcs)
+	userTmpl.Funcs(funcs)
+	return systemTmpl, userTmpl, nil
+}
+
+func (b *Bundle) referenceFuncs(references contracts.ReferenceSet) template.FuncMap {
+	return template.FuncMap{
+		"hardening": func() string { return sharedHardening },
+		"hasreference": func(slotName string) (bool, error) {
+			items, _, err := b.referenceItems(slotName, references)
+			if err != nil {
+				return false, err
+			}
+			for _, item := range items {
+				if len(item.Content) > 0 {
+					return true, nil
+				}
+			}
+			return false, nil
+		},
+		"reference": func(slotName string) (string, error) {
+			items, slot, err := b.referenceItems(slotName, references)
+			if err != nil {
+				return "", err
+			}
+			if len(items) == 0 {
+				return "", nil
+			}
+			if len(items) > 1 && !slot.Multiple {
+				return "", fmt.Errorf("reference slot %q has %d bound items but does not allow multiple", slot.Name, len(items))
+			}
+			parts := make([]string, 0, len(items))
+			for _, item := range items {
+				parts = append(parts, string(item.Content))
+			}
+			return strings.Join(parts, "\n"), nil
+		},
+	}
+}
+
+func (b *Bundle) referenceItems(slotName string, references contracts.ReferenceSet) ([]contracts.ReferenceItem, contracts.ReferenceSlot, error) {
+	slotName = strings.TrimSpace(slotName)
+	slot, ok := b.referenceSlots[slotName]
+	if !ok {
+		return nil, contracts.ReferenceSlot{}, fmt.Errorf("reference slot %q is not declared", slotName)
+	}
+	if len(references.Slots) == 0 {
+		return nil, slot, nil
+	}
+	resolved, ok := references.Slots[slotName]
+	if !ok {
+		return nil, slot, nil
+	}
+	return append([]contracts.ReferenceItem(nil), resolved.Items...), slot, nil
+}

internal/framework/prompt/render_test.go

@@ -1,8 +1,13 @@
 package prompt
 
 import (
+	"crypto/sha256"
+	"encoding/hex"
 	"strings"
 	"testing"
+	"testing/fstest"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 )
 
 func TestRenderUserSystemReturnsTextAndMetadata(t *testing.T) {
@@ -64,3 +69,175 @@ func TestRenderUserSystemIncludesHardeningText(t *testing.T) {
 		t.Fatalf("expected rendered system prompt to include hardening text: %q", system)
 	}
 }
+
+func TestRenderUserSystemWithReferencesRendersDeclaredSlots(t *testing.T) {
+	bundle := loadReferenceBundle(t,
+		[]contracts.ReferenceSlot{{Name: "roster"}, {Name: "glossary"}},
+		`System has roster={{ hasreference "roster" }} has glossary={{ hasreference "glossary" }}`,
+		`Roster={{ reference "roster" }} Glossary={{ reference "glossary" }}`,
+	)
+	references := contracts.ReferenceSet{Slots: map[string]contracts.ResolvedReferenceSlot{
+		"roster": {
+			Slot: contracts.ReferenceSlot{Name: "roster"},
+			Items: []contracts.ReferenceItem{
+				{SlotName: "roster", Content: []byte("Aria")},
+			},
+		},
+	}}
+
+	system, user, _, err := bundle.RenderUserSystemWithReferences(map[string]any{}, references)
+	if err != nil {
+		t.Fatalf("RenderUserSystemWithReferences: %v", err)
+	}
+	if !strings.Contains(system, "has roster=true") || !strings.Contains(system, "has glossary=false") {
+		t.Fatalf("system = %q, want reference presence flags", system)
+	}
+	if !strings.Contains(user, "Roster=Aria") || !strings.Contains(user, "Glossary=") {
+		t.Fatalf("user = %q, want rendered and empty optional references", user)
+	}
+}
+
+func TestRenderUserSystemReferenceHasReferenceRequiresContent(t *testing.T) {
+	bundle := loadReferenceBundle(t,
+		[]contracts.ReferenceSlot{{Name: "roster"}},
+		`System`,
+		`{{ hasreference "roster" }} {{ reference "roster" }}`,
+	)
+	references := contracts.ReferenceSet{Slots: map[string]contracts.ResolvedReferenceSlot{
+		"roster": {
+			Slot: contracts.ReferenceSlot{Name: "roster"},
+			Items: []contracts.ReferenceItem{
+				{SlotName: "roster", Content: nil},
+			},
+		},
+	}}
+
+	_, user, _, err := bundle.RenderUserSystemWithReferences(map[string]any{}, references)
+	if err != nil {
+		t.Fatalf("RenderUserSystemWithReferences: %v", err)
+	}
+	if user != "false" {
+		t.Fatalf("user = %q, want false with empty reference content", user)
+	}
+}
+
+func TestLoadBundleRejectsUndeclaredReferenceSlots(t *testing.T) {
+	_, err := LoadBundle(referenceBundleFS(`System`, `{{ reference "roster" }}`), referenceBundleDefinition(nil))
+	if err == nil || !strings.Contains(err.Error(), "roster") || !strings.Contains(err.Error(), "not declared") {
+		t.Fatalf("LoadBundle() error = %v, want undeclared reference slot error", err)
+	}
+}
+
+func TestLoadBundleRejectsDynamicReferenceSlotNames(t *testing.T) {
+	_, err := LoadBundle(referenceBundleFS(`System`, `{{ reference .SlotName }}`), referenceBundleDefinition([]contracts.ReferenceSlot{{Name: "roster"}}))
+	if err == nil || !strings.Contains(err.Error(), "string literal") {
+		t.Fatalf("LoadBundle() error = %v, want string literal error", err)
+	}
+}
+
+func TestLoadBundleRejectsNestedUndeclaredReferenceSlots(t *testing.T) {
+	_, err := LoadBundle(referenceBundleFS(`System`, `{{ printf "%s" (reference "roster") }}`), referenceBundleDefinition(nil))
+	if err == nil || !strings.Contains(err.Error(), "roster") || !strings.Contains(err.Error(), "not declared") {
+		t.Fatalf("LoadBundle() error = %v, want nested undeclared reference slot error", err)
+	}
+}
+
+func TestRenderUserSystemRejectsMultipleReferenceItemsUnlessDeclared(t *testing.T) {
+	bundle := loadReferenceBundle(t,
+		[]contracts.ReferenceSlot{{Name: "roster"}},
+		`System`,
+		`{{ reference "roster" }}`,
+	)
+	references := contracts.ReferenceSet{Slots: map[string]contracts.ResolvedReferenceSlot{
+		"roster": {
+			Slot: contracts.ReferenceSlot{Name: "roster"},
+			Items: []contracts.ReferenceItem{
+				{SlotName: "roster", Content: []byte("Aria")},
+				{SlotName: "roster", Content: []byte("Bryn")},
+			},
+		},
+	}}
+
+	_, _, _, err := bundle.RenderUserSystemWithReferences(map[string]any{}, references)
+	if err == nil || !strings.Contains(err.Error(), "does not allow multiple") {
+		t.Fatalf("RenderUserSystemWithReferences() error = %v, want multiple item error", err)
+	}
+}
+
+func TestRenderUserSystemRendersMultipleReferenceItemsDeterministicallyWhenDeclared(t *testing.T) {
+	bundle := loadReferenceBundle(t,
+		[]contracts.ReferenceSlot{{Name: "roster", Multiple: true}},
+		`System`,
+		`{{ reference "roster" }}`,
+	)
+	references := contracts.ReferenceSet{Slots: map[string]contracts.ResolvedReferenceSlot{
+		"roster": {
+			Slot: contracts.ReferenceSlot{Name: "roster", Multiple: true},
+			Items: []contracts.ReferenceItem{
+				{SlotName: "roster", Content: []byte("Aria")},
+				{SlotName: "roster", Content: []byte("Bryn")},
+			},
+		},
+	}}
+
+	_, first, _, err := bundle.RenderUserSystemWithReferences(map[string]any{}, references)
+	if err != nil {
+		t.Fatalf("RenderUserSystemWithReferences(first): %v", err)
+	}
+	_, second, _, err := bundle.RenderUserSystemWithReferences(map[string]any{}, references)
+	if err != nil {
+		t.Fatalf("RenderUserSystemWithReferences(second): %v", err)
+	}
+	if first != "Aria\nBryn" || first != second {
+		t.Fatalf("rendered references = %q/%q, want deterministic item order", first, second)
+	}
+}
+
+func TestPromptMetadataHashIgnoresRenderedReferenceContent(t *testing.T) {
+	systemSource := `System`
+	userSource := `{{ reference "roster" }}`
+	bundle := loadReferenceBundle(t, []contracts.ReferenceSlot{{Name: "roster"}}, systemSource, userSource)
+	references := contracts.ReferenceSet{Slots: map[string]contracts.ResolvedReferenceSlot{
+		"roster": {
+			Slot:  contracts.ReferenceSlot{Name: "roster"},
+			Items: []contracts.ReferenceItem{{SlotName: "roster", Content: []byte("Aria")}},
+		},
+	}}
+
+	_, _, metadata, err := bundle.RenderUserSystemWithReferences(map[string]any{}, references)
+	if err != nil {
+		t.Fatalf("RenderUserSystemWithReferences: %v", err)
+	}
+	hash := sha256.Sum256([]byte(systemSource + "\n\n" + userSource))
+	want := "sha256:" + hex.EncodeToString(hash[:])
+	if metadata.SHA256 != want {
+		t.Fatalf("metadata.SHA256 = %q, want template source hash %q", metadata.SHA256, want)
+	}
+}
+
+func loadReferenceBundle(t *testing.T, slots []contracts.ReferenceSlot, systemSource string, userSource string) *Bundle {
+	t.Helper()
+	bundle, err := LoadBundle(referenceBundleFS(systemSource, userSource), referenceBundleDefinition(slots))
+	if err != nil {
+		t.Fatalf("LoadBundle() error = %v, want nil", err)
+	}
+	return bundle
+}
+
+func referenceBundleDefinition(slots []contracts.ReferenceSlot) Definition {
+	return Definition{
+		PromptID:       "test.references",
+		Version:        VersionV1,
+		EmbeddedPath:   "assets/test/references",
+		SystemPath:     "assets/test/references/system.md",
+		UserPath:       "assets/test/references/user.md",
+		ReferenceSlots: slots,
+	}
+}
+
+func referenceBundleFS(systemSource string, userSource string) fstest.MapFS {
+	return fstest.MapFS{
+		"assets/test/references/system.md": {Data: []byte(systemSource)},
+		"assets/test/references/user.md":   {Data: []byte(userSource)},
+	}
+}

internal/modules/extract/dnd/spells/assets/prompts/system.md

@@ -6,4 +6,9 @@ Extract only spell casts that are supported by the provided source text. Do not
 infer spells from general D&D knowledge or from table chatter that does not
 identify a spell being cast.
 
+Reference material, when present, is supporting context only. Use it only to
+disambiguate names, aliases, speakers, campaign terms, or spell names already
+present in the source text. Do not extract a spell cast solely because it appears
+in reference material.
+
 Source references must use the source-unit IDs exactly as provided.

internal/modules/extract/dnd/spells/assets/prompts/user.md

@@ -16,6 +16,19 @@ Source units:
 {{ end }}
 {{ end }}
 
+{{ if hasreference "roster" }}
+Roster reference material:
+{{ reference "roster" }}
+
+{{ end }}
+{{ if hasreference "glossary" }}
+Glossary reference material:
+{{ reference "glossary" }}
+
+{{ end }}
 Return only D&D spell-cast artifacts. For each spell cast, identify the in-world
 caster, spell name, effect, narrative description, and source references using
 source_id, start_unit_id, and end_unit_id.
+
+Use roster and glossary reference material only to clarify source text. Do not
+return spells, casters, or effects that are mentioned only in reference material.

internal/modules/extract/dnd/spells/extractor.go

@@ -25,6 +25,19 @@ var providedCapabilities = []string{
 	"dnd.spell_casts",
 }
 
+var referenceSlots = []contracts.ReferenceSlot{
+	{
+		Name:               "glossary",
+		Description:        "Optional campaign glossary reference material used only for disambiguation.",
+		AcceptedMediaTypes: []string{"text/plain; charset=utf-8"},
+	},
+	{
+		Name:               "roster",
+		Description:        "Optional campaign roster or player-character reference material used only for disambiguation.",
+		AcceptedMediaTypes: []string{"text/plain; charset=utf-8"},
+	},
+}
+
 var _ contracts.Extractor = (*Extractor)(nil)
 
 type Extractor struct{}
@@ -45,6 +58,10 @@ func (e *Extractor) SchemaVersion() string {
 	return SchemaVersion
 }
 
+func (e *Extractor) ReferenceSlots() []contracts.ReferenceSlot {
+	return cloneReferenceSlots(referenceSlots)
+}
+
 func (e *Extractor) ManifestMetadata() map[string]any {
 	promptMetadata := spellsPromptBundle.Metadata()
 	metadata := map[string]any{
@@ -140,6 +157,7 @@ func ModuleSpec() pipeline.ModuleSpec {
 		Stage:          pipeline.StageExtract,
 		Requires:       append([]string(nil), requiredCapabilities...),
 		Provides:       append([]string(nil), providedCapabilities...),
+		ReferenceSlots: cloneReferenceSlots(referenceSlots),
 	}
 }
 
@@ -161,3 +179,15 @@ func spellCastPayload(spellCast spellCastResponse) (json.RawMessage, error) {
 func extractorErrorf(format string, args ...any) error {
 	return fmt.Errorf("dnd spells extractor: "+format, args...)
 }
+
+func cloneReferenceSlots(slots []contracts.ReferenceSlot) []contracts.ReferenceSlot {
+	if len(slots) == 0 {
+		return nil
+	}
+	out := make([]contracts.ReferenceSlot, len(slots))
+	for i, slot := range slots {
+		slot.AcceptedMediaTypes = append([]string(nil), slot.AcceptedMediaTypes...)
+		out[i] = slot
+	}
+	return out
+}

internal/modules/extract/dnd/spells/extractor_test.go

@@ -116,6 +116,56 @@ func TestExtractorManifestMetadataIncludesPromptAndSchemaProvenance(t *testing.T
 	}
 }
 
+func TestExtractIncludesReferencesInPrompt(t *testing.T) {
+	client := &fakeSpellsLLMClient{response: extractionResponse{SpellCasts: []spellCastResponse{}}}
+	req := extractionRequestWithClient(client)
+	req.References = contracts.ReferenceSet{
+		Slots: map[string]contracts.ResolvedReferenceSlot{
+			"roster": {
+				Slot: contracts.ReferenceSlot{Name: "roster"},
+				Items: []contracts.ReferenceItem{
+					{SlotName: "roster", Content: []byte("Aria Brightmantle: party cleric")},
+				},
+			},
+			"glossary": {
+				Slot: contracts.ReferenceSlot{Name: "glossary"},
+				Items: []contracts.ReferenceItem{
+					{SlotName: "glossary", Content: []byte("Brightmantle: local temple name")},
+				},
+			},
+		},
+	}
+
+	if _, err := New().Extract(context.Background(), req); err != nil {
+		t.Fatalf("Extract() error = %v, want nil", err)
+	}
+
+	if len(client.requests) != 1 {
+		t.Fatalf("LLM calls = %d, want 1", len(client.requests))
+	}
+	system := client.requests[0].Messages[0].Content
+	for _, want := range []string{
+		"Reference material, when present, is supporting context only.",
+		"in reference material.",
+	} {
+		if !strings.Contains(system, want) {
+			t.Fatalf("system prompt = %q, want substring %q", system, want)
+		}
+	}
+	user := client.requests[0].Messages[1].Content
+	for _, want := range []string{
+		"Roster reference material:",
+		"Aria Brightmantle: party cleric",
+		"Glossary reference material:",
+		"Brightmantle: local temple name",
+		"mentioned only in reference material.",
+	} {
+		if !strings.Contains(user, want) {
+			t.Fatalf("user prompt = %q, want substring %q", user, want)
+		}
+	}
+}
+
 func TestExtractReturnsNoCandidatesForEmptyResponse(t *testing.T) {
 	client := &fakeSpellsLLMClient{response: extractionResponse{SpellCasts: []spellCastResponse{}}}
 

internal/modules/extract/dnd/spells/prompt.go

@@ -37,6 +37,7 @@ func mustLoadPromptBundle() *prompt.Bundle {
 		EmbeddedPath:   "assets/prompts",
 		SystemPath:     "assets/prompts/system.md",
 		UserPath:       "assets/prompts/user.md",
+		ReferenceSlots: cloneReferenceSlots(referenceSlots),
 	})
 	if err != nil {
 		panic(err)
@@ -74,7 +75,7 @@ func renderPrompt(req contracts.ExtractionRequest) (system string, user string,
 	if err != nil {
 		return "", "", prompt.Metadata{}, err
 	}
-	system, user, metadata, err = spellsPromptBundle.RenderUserSystem(data)
+	system, user, metadata, err = spellsPromptBundle.RenderUserSystemWithReferences(data, req.References)
 	if err != nil {
 		return "", "", prompt.Metadata{}, fmt.Errorf("dnd spells prompt: %w", err)
 	}

internal/modules/extract/dnd/spells/prompt_test.go

@@ -101,6 +101,50 @@ func TestRenderPromptIncludesSourceContext(t *testing.T) {
 	if metadata.EmbeddedPath != "assets/prompts" {
 		t.Fatalf("metadata.EmbeddedPath = %q, want assets/prompts", metadata.EmbeddedPath)
 	}
+	if strings.Contains(user, "Roster reference material") || strings.Contains(user, "Glossary reference material") {
+		t.Fatalf("user prompt = %q, want no optional reference sections without bindings", user)
+	}
+}
+
+func TestRenderPromptIncludesBoundReferences(t *testing.T) {
+	req := promptExtractionRequest()
+	req.References = contracts.ReferenceSet{
+		Slots: map[string]contracts.ResolvedReferenceSlot{
+			"roster": {
+				Slot: contracts.ReferenceSlot{Name: "roster"},
+				Items: []contracts.ReferenceItem{
+					{SlotName: "roster", Content: []byte("Aria: cleric, also known as Sister Aria")},
+				},
+			},
+			"glossary": {
+				Slot: contracts.ReferenceSlot{Name: "glossary"},
+				Items: []contracts.ReferenceItem{
+					{SlotName: "glossary", Content: []byte("Cure Wounds: healing spell")},
+				},
+			},
+		},
+	}
+
+	_, user, metadata, err := renderPrompt(req)
+	if err != nil {
+		t.Fatalf("renderPrompt() error = %v, want nil", err)
+	}
+
+	for _, want := range []string{
+		"Roster reference material:",
+		"Aria: cleric, also known as Sister Aria",
+		"Glossary reference material:",
+		"Cure Wounds: healing spell",
+		"Use roster and glossary reference material only to clarify source text.",
+		"mentioned only in reference material.",
+	} {
+		if !strings.Contains(user, want) {
+			t.Fatalf("user prompt = %q, want substring %q", user, want)
+		}
+	}
+	if metadata.SHA256 != spellsPromptBundle.Metadata().SHA256 {
+		t.Fatalf("metadata.SHA256 = %q, want template hash %q", metadata.SHA256, spellsPromptBundle.Metadata().SHA256)
+	}
 }
 
 func TestBuildPromptDataRejectsMissingSourceContext(t *testing.T) {

internal/modules/extract/dnd/spells/registry_test.go

@@ -5,6 +5,7 @@ import (
 	"strings"
 	"testing"
 
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
 )
 
@@ -36,6 +37,18 @@ func TestModuleSpec(t *testing.T) {
 		Provides: []string{
 			"dnd.spell_casts",
 		},
+		ReferenceSlots: []contracts.ReferenceSlot{
+			{
+				Name:               "glossary",
+				Description:        "Optional campaign glossary reference material used only for disambiguation.",
+				AcceptedMediaTypes: []string{"text/plain; charset=utf-8"},
+			},
+			{
+				Name:               "roster",
+				Description:        "Optional campaign roster or player-character reference material used only for disambiguation.",
+				AcceptedMediaTypes: []string{"text/plain; charset=utf-8"},
+			},
+		},
 	}
 	if !reflect.DeepEqual(got, want) {
 		t.Fatalf("ModuleSpec() = %#v, want %#v", got, want)
@@ -43,6 +56,7 @@ func TestModuleSpec(t *testing.T) {
 
 	got.Requires[0] = "changed"
 	got.Provides[0] = "changed"
+	got.ReferenceSlots[0].AcceptedMediaTypes[0] = "changed"
 	again := ModuleSpec()
 	if !reflect.DeepEqual(again, want) {
 		t.Fatalf("ModuleSpec() after caller mutation = %#v, want %#v", again, want)
@@ -82,6 +96,15 @@ func TestRegisterStoresModuleSpec(t *testing.T) {
 	}
 }
 
+func TestRuntimeReferenceSlotsMatchModuleSpec(t *testing.T) {
+	extractor := New()
+	spec := ModuleSpec()
+
+	if !reflect.DeepEqual(extractor.ReferenceSlots(), spec.ReferenceSlots) {
+		t.Fatalf("ReferenceSlots() = %#v, want spec slots %#v", extractor.ReferenceSlots(), spec.ReferenceSlots)
+	}
+}
+
 func TestRegisterNilRegistryReturnsError(t *testing.T) {
 	err := Register(nil)
 	if err == nil {

internal/modules/extract/dnd/spells/runner_test.go

@@ -110,6 +110,96 @@ func TestRunnerProcessesSeriatimInputWithDNDSpellsExtractor(t *testing.T) {
 	}
 }
 
+func TestRunnerPassesRosterAndGlossaryReferencesToDNDSpellsPrompt(t *testing.T) {
+	raw := readDNDSpellsFixture(t)
+	expectedDoc := parseDNDSpellsFixture(t, raw)
+	resolved := resolveDNDSpellsPipeline(t)
+	resolved.ResolvedPipeline.ArtifactLanes[0].ReferenceSet = dndSpellsReferenceSet(
+		"Aria: party cleric\nBorin: fighter",
+		"Fire Bolt: evocation cantrip",
+	)
+	llmClient := &fakeSpellsLLMClient{
+		response: extractionResponse{
+			SpellCasts: []spellCastResponse{
+				{
+					Caster:               "Borin",
+					Spell:                "Fire Bolt",
+					Effect:               "Scorches the wight.",
+					NarrativeDescription: "Borin hurls fire at the wight.",
+					SourceRefs: []source.SourceRef{
+						{SourceID: expectedDoc.ID, StartUnitID: "seg-003", EndUnitID: "seg-003"},
+					},
+				},
+			},
+		},
+	}
+
+	output, err := pipeline.New(dndSpellsRunnerRegistries(t)).Run(context.Background(), pipeline.RunInput{
+		Pipeline:  resolved.ResolvedPipeline,
+		RawInput:  raw,
+		LLMClient: llmClient,
+	})
+	if err != nil {
+		t.Fatalf("Run() error = %v, want nil", err)
+	}
+
+	if len(output.Approved) != 1 {
+		t.Fatalf("len(Approved) = %d, want 1", len(output.Approved))
+	}
+	if len(output.Manifest.References) != 2 {
+		t.Fatalf("manifest references = %#v, want roster and glossary provenance", output.Manifest.References)
+	}
+	if len(llmClient.requests) != 1 {
+		t.Fatalf("LLM calls = %d, want 1", len(llmClient.requests))
+	}
+	user := llmClient.requests[0].Messages[1].Content
+	for _, want := range []string{
+		"Roster reference material:",
+		"Aria: party cleric",
+		"Glossary reference material:",
+		"Fire Bolt: evocation cantrip",
+	} {
+		if !strings.Contains(user, want) {
+			t.Fatalf("user prompt = %q, want substring %q", user, want)
+		}
+	}
+}
+
+func TestRunnerDoesNotExtractSpellMentionedOnlyInRoster(t *testing.T) {
+	raw := readDNDSpellsFixture(t)
+	resolved := resolveDNDSpellsPipeline(t)
+	resolved.ResolvedPipeline.ArtifactLanes[0].ReferenceSet = dndSpellsReferenceSet(
+		"Mira: wizard who can cast Lightning Bolt",
+		"",
+	)
+	llmClient := &fakeSpellsLLMClient{
+		response: extractionResponse{SpellCasts: []spellCastResponse{}},
+	}
+
+	output, err := pipeline.New(dndSpellsRunnerRegistries(t)).Run(context.Background(), pipeline.RunInput{
+		Pipeline:  resolved.ResolvedPipeline,
+		RawInput:  raw,
+		LLMClient: llmClient,
+	})
+	if err != nil {
+		t.Fatalf("Run() error = %v, want nil", err)
+	}
+
+	if len(output.Approved) != 0 {
+		t.Fatalf("approved artifacts = %#v, want no roster-only spell casts", output.Approved)
+	}
+	if len(llmClient.requests) != 1 {
+		t.Fatalf("LLM calls = %d, want 1", len(llmClient.requests))
+	}
+	user := llmClient.requests[0].Messages[1].Content
+	if !strings.Contains(user, "Lightning Bolt") {
+		t.Fatalf("user prompt = %q, want roster-only spell in reference section", user)
+	}
+	if output.Manifest.ValidationStatus != "approved" {
+		t.Fatalf("ValidationStatus = %q, want approved empty extraction", output.Manifest.ValidationStatus)
+	}
+}
+
 func TestRunnerRejectsDNDSpellCastWithInvalidSourceRef(t *testing.T) {
 	raw := readDNDSpellsFixture(t)
 	resolved := resolveDNDSpellsPipeline(t)
@@ -155,6 +245,43 @@ func TestRunnerRejectsDNDSpellCastWithInvalidSourceRef(t *testing.T) {
 	}
 }
 
+func dndSpellsReferenceSet(roster string, glossary string) contracts.ReferenceSet {
+	slots := make(map[string]contracts.ResolvedReferenceSlot)
+	if strings.TrimSpace(roster) != "" {
+		slots["roster"] = contracts.ResolvedReferenceSlot{
+			Slot: contracts.ReferenceSlot{Name: "roster"},
+			Items: []contracts.ReferenceItem{
+				{
+					SlotName:      "roster",
+					MediaType:     "text/plain; charset=utf-8",
+					Content:       []byte(roster),
+					Digest:        "sha256:roster",
+					Origin:        contracts.ReferenceOrigin{Type: "file", URI: "file:///tmp/roster.txt"},
+					SizeBytes:     int64(len(roster)),
+					BindingSource: contracts.ReferenceBindingSourceConfig,
+				},
+			},
+		}
+	}
+	if strings.TrimSpace(glossary) != "" {
+		slots["glossary"] = contracts.ResolvedReferenceSlot{
+			Slot: contracts.ReferenceSlot{Name: "glossary"},
+			Items: []contracts.ReferenceItem{
+				{
+					SlotName:      "glossary",
+					MediaType:     "text/plain; charset=utf-8",
+					Content:       []byte(glossary),
+					Digest:        "sha256:glossary",
+					Origin:        contracts.ReferenceOrigin{Type: "file", URI: "file:///tmp/glossary.txt"},
+					SizeBytes:     int64(len(glossary)),
+					BindingSource: contracts.ReferenceBindingSourceConfig,
+				},
+			},
+		}
+	}
+	return contracts.ReferenceSet{Slots: slots}
+}
+
 func TestRunnerFailsWhenDNDSpellsExtractorReturnsMalformedOutput(t *testing.T) {
 	raw := readDNDSpellsFixture(t)
 	resolved := resolveDNDSpellsPipeline(t)

internal/modules/extract/dnd/spells/validator.go

@@ -20,6 +20,7 @@ const (
 	reasonMissingRequiredField = "missing_required_field"
 	reasonMissingSourceRef     = "missing_source_ref"
 	reasonInvalidSourceRef     = "invalid_source_ref"
+	reasonSpellNotNearSource   = "spell_not_near_source"
 )
 
 var _ contracts.Validator = ShapeValidator{}
@@ -54,12 +55,15 @@ func (validator SourceRefValidator) Validate(ctx context.Context, req contracts.
 	}
 
 	decisions := make([]contracts.ValidationDecision, 0, len(req.Candidates))
+	var warnings []contracts.Warning
 	for _, candidate := range req.Candidates {
 		decisions = append(decisions, validateSourceRefs(req.Source, candidate))
+		warnings = append(warnings, sourceRelatednessWarnings(req.Source, candidate)...)
 	}
 	return contracts.ValidationResult{
 		ValidatorName: validator.Name(),
 		Decisions:     decisions,
+		Warnings:      warnings,
 	}, nil
 }
 
@@ -88,6 +92,66 @@ func validateSourceRefs(doc *source.SourceDocument, candidate artifacts.Artifact
 	return validate.Approved(candidate.Index)
 }
 
+func sourceRelatednessWarnings(doc *source.SourceDocument, candidate artifacts.ArtifactCandidate) []contracts.Warning {
+	if doc == nil || len(candidate.SourceRefs) == 0 {
+		return nil
+	}
+	var payload SpellCast
+	if err := json.Unmarshal(candidate.Payload, &payload); err != nil {
+		return nil
+	}
+	spell := strings.TrimSpace(payload.Spell)
+	if spell == "" {
+		return nil
+	}
+
+	needle := strings.ToLower(spell)
+	for _, ref := range candidate.SourceRefs {
+		text, ok := sourceRefText(doc, ref)
+		if !ok {
+			continue
+		}
+		if strings.Contains(strings.ToLower(text), needle) {
+			return nil
+		}
+	}
+
+	return []contracts.Warning{
+		{
+			Scope:      fmt.Sprintf("candidate.%d", candidate.Index),
+			ReasonCode: reasonSpellNotNearSource,
+			Message:    fmt.Sprintf("spell %q was not found in the cited source text", spell),
+		},
+	}
+}
+
+func sourceRefText(doc *source.SourceDocument, ref source.SourceRef) (string, bool) {
+	if err := source.ValidateRef(doc, ref); err != nil {
+		return "", false
+	}
+	start := -1
+	end := -1
+	for i, unit := range doc.Units {
+		if unit.ID == ref.StartUnitID {
+			start = i
+		}
+		if unit.ID == ref.EndUnitID {
+			end = i
+		}
+	}
+	if start < 0 || end < start {
+		return "", false
+	}
+	var b strings.Builder
+	for i := start; i <= end; i++ {
+		if b.Len() > 0 {
+			b.WriteString("\n")
+		}
+		b.WriteString(doc.Units[i].Text)
+	}
+	return b.String(), true
+}
+
 func requiredSpellCastFields(payload SpellCast) []struct {
 	name  string
 	value string

internal/modules/extract/dnd/spells/validator_test.go

@@ -51,6 +51,9 @@ func TestValidatorsApproveValidCandidate(t *testing.T) {
 		t.Fatalf("SourceRefValidator.Validate() error = %v, want nil", err)
 	}
 	assertSingleDecision(t, sourceRefResult, sourceRefValidatorName, 7, true, validate.ReasonApproved)
+	if len(sourceRefResult.Warnings) != 0 {
+		t.Fatalf("warnings = %#v, want none", sourceRefResult.Warnings)
+	}
 }
 
 func TestShapeValidatorRejectsMalformedPayload(t *testing.T) {
@@ -167,6 +170,29 @@ func TestSourceRefValidatorRejectsInvalidRefs(t *testing.T) {
 	}
 }
 
+func TestSourceRefValidatorWarnsWhenSpellNameIsNotInCitedSource(t *testing.T) {
+	candidate := validSpellCandidate(31)
+	payload := validSpellPayload()
+	payload.Spell = "Shield"
+	candidate.Payload = mustSpellPayload(t, payload)
+
+	result, err := SourceRefValidator{}.Validate(context.Background(), contracts.ValidationRequest{
+		Source:     promptSourceDocument(),
+		Candidates: []artifacts.ArtifactCandidate{candidate},
+	})
+	if err != nil {
+		t.Fatalf("SourceRefValidator.Validate() error = %v, want nil", err)
+	}
+	assertSingleDecision(t, result, sourceRefValidatorName, 31, true, validate.ReasonApproved)
+	if len(result.Warnings) != 1 {
+		t.Fatalf("warnings = %#v, want one relatedness warning", result.Warnings)
+	}
+	warning := result.Warnings[0]
+	if warning.ReasonCode != reasonSpellNotNearSource || !strings.Contains(warning.Message, "Shield") {
+		t.Fatalf("warning = %#v, want spell relatedness warning", warning)
+	}
+}
+
 func TestSourceRefValidatorRequiresSourceDocument(t *testing.T) {
 	_, err := SourceRefValidator{}.Validate(context.Background(), contracts.ValidationRequest{
 		Candidates: []artifacts.ArtifactCandidate{validSpellCandidate(19)},

internal/modules/input/seriatim/config_test.go

@@ -221,6 +221,8 @@ func (fakeExtractor) ArtifactType() string { return "fake" }
 
 func (fakeExtractor) SchemaVersion() string { return "v1" }
 
+func (fakeExtractor) ReferenceSlots() []contracts.ReferenceSlot { return nil }
+
 func (fakeExtractor) Validators() []contracts.Validator { return nil }
 
 func (fakeExtractor) Extract(ctx context.Context, req contracts.ExtractionRequest) (contracts.ExtractionResult, error) {

internal/modules/input/seriatim/runner_test.go

@@ -186,6 +186,10 @@ func (e *runnerSeriatimExtractor) SchemaVersion() string {
 	return "v1"
 }
 
+func (e *runnerSeriatimExtractor) ReferenceSlots() []contracts.ReferenceSlot {
+	return nil
+}
+
 func (e *runnerSeriatimExtractor) Validators() []contracts.Validator {
 	return nil
 }

internal/modules/output/json/encoder_test.go

@@ -142,6 +142,42 @@ func TestEncodePrettyPrintsJSON(t *testing.T) {
 	}
 }
 
+func TestEncodeIncludesManifestReferences(t *testing.T) {
+	result, err := New().Encode(context.Background(), contracts.OutputRequest{
+		Manifest: artifacts.RunManifest{
+			RunID: "run-1",
+			References: []artifacts.ReferenceProvenance{
+				{
+					LaneID:        "events",
+					SlotName:      "roster",
+					OriginType:    "file",
+					OriginURI:     "file:///tmp/roster.txt",
+					Digest:        "sha256:reference",
+					MediaType:     "text/plain; charset=utf-8",
+					SizeBytes:     12,
+					BindingSource: "config",
+				},
+			},
+		},
+	})
+	if err != nil {
+		t.Fatalf("Encode() error = %v, want nil", err)
+	}
+
+	manifest := decodeObject(t, fileBytes(t, result.Files, "manifest.json"))
+	references := manifest["references"].([]any)
+	if len(references) != 1 {
+		t.Fatalf("references = %#v, want one entry", references)
+	}
+	reference := references[0].(map[string]any)
+	if reference["lane_id"] != "events" || reference["slot_name"] != "roster" || reference["digest"] != "sha256:reference" {
+		t.Fatalf("reference manifest = %#v, want lane slot digest", reference)
+	}
+	if _, ok := reference["content"]; ok {
+		t.Fatalf("reference manifest = %#v, want no content field", reference)
+	}
+}
+
 func TestEncodeRejectsArtifactTypeWithoutSafeFileName(t *testing.T) {
 	_, err := New().Encode(context.Background(), contracts.OutputRequest{
 		Approved: []artifacts.Artifact{artifact("///", "unsafe")},