Mark MVP implementation complete in roadmap

docs/roadmap/mvp.md

@@ -2,12 +2,12 @@
 
 ## Status
 
-This is the active roadmap for reaching the first functional Notarius MVP.
+The first functional Notarius MVP implementation is complete enough to start the
+deferred documentation pass.
 
 The previous numbered checkpoint roadmaps have been implemented and retired.
-This document captures the remaining work needed to turn the implemented
-architecture into a usable MVP, with the current architectural review findings
-folded in as first-class work.
+This document now records the implemented MVP scope and the remaining
+release/documentation work before alpha `0.1.0`.
 
 Implementation staging belongs in [`implementation.md`](implementation.md).
 
@@ -36,163 +36,71 @@ The MVP remains intentionally narrow:
 - config-driven pipeline profiles;
 - OpenAI-compatible structured LLM execution through the existing LLM client.
 
-## MVP Work Areas
+## Implemented MVP Behavior
 
-### Framework/Domain Asset Boundaries
+The MVP now includes:
 
-This is the highest-priority remaining architecture correction.
+- framework/domain asset boundaries: D&D spell prompt and response schema assets
+  are owned by `internal/modules/extract/dnd/spells`, while framework prompt and
+  LLM packages provide only generic primitives;
+- production CLI wiring that registers `seriatim`, `dnd/spells`, and the
+  default `generic`, `appendorder`, `noop`, and `json` modules;
+- a config-driven `notarius run` command that reads Seriatim input, resolves a
+  configured pipeline, invokes the runner, and writes durable output plus
+  diagnostics;
+- fixture-driven CLI acceptance coverage using maintained example config and
+  transcript fixtures with a fake LLM path, so `go test ./...` exercises the MVP
+  without network access.
 
-Framework packages must remain source-agnostic and domain-agnostic. D&D spell
-prompt assets, response schema assets, prompt IDs, response schema keys, and
-domain-specific prompt/schema tests should not live in `internal/framework/llm`
-or `internal/framework/prompt`.
-
-Target state:
-
-- `internal/framework/llm` provides generic structured-output client,
-  scheduler, schema metadata, schema loading, and schema lookup/registration
-  primitives.
-- `internal/framework/prompt` provides generic prompt metadata, prompt loading,
-  rendering, hardening, and lookup/registration primitives.
-- `internal/modules/extract/dnd/spells` owns the D&D spell prompt assets,
-  response schema assets, stable prompt ID, stable response schema key, and
-  module-specific prompt/schema tests.
-- Framework tests use placeholder/test assets only.
-- The D&D spells extractor depends on generic framework APIs, not
-  framework-owned D&D constants.
-
-This work should not change the external artifact shape or module key. It is an
-ownership and package-boundary correction.
-
-### Production Application Catalog Wiring
-
-The implemented modules and registries are currently exercised mostly through
-tests that inject catalogs. The MVP needs a production assembly point that
-builds the catalog and stage registries used by real CLI commands.
-
-Target state:
-
-- a small app-level package or CLI wiring function constructs the production
-  `pipeline.ModuleCatalog`;
-- production wiring registers `seriatim`;
-- production wiring registers `dnd/spells`;
-- production wiring registers the default `generic`, `appendorder`, `noop`, and
-  `json` modules;
-- `notarius config validate --pipeline ...` validates real configured
-  pipelines without test-only catalog injection;
-- `notarius pipelines list` reports production-registered modules where useful
-  for discoverability.
-
-The production wiring should not move domain behavior into the CLI. The CLI may
-compose modules, but module packages should continue to own their own behavior
-and metadata.
-
-### Default Production Stage Modules
-
-Pipeline defaults are already part of the architecture:
+The production pipeline defaults are:
 
 - `chunk: generic`;
 - `merge: appendorder`;
 - `normalize: noop`;
 - `output: json`.
 
-The MVP should make those defaults real production modules rather than
-test-only conveniences.
-
-Target state:
-
-- `generic` chunking creates ordered chunks over generic source units and is
-  configurable enough for transcript MVP use;
-- `appendorder` merge serializes artifact candidates in deterministic source
-  and chunk order;
-- `noop` normalize passes merged artifacts through unchanged while preserving
-  diagnostics;
-- `json` output encodes approved artifacts, rejected artifacts, warnings,
-  manifest data, and relevant run metadata in a durable JSON shape;
-- each default module declares module specs and capabilities compatible with
-  pipeline validation;
-- default modules are registered by production app wiring.
-
-If a default module remains implemented in `internal/framework/pipeline`, its
-production registration still needs to be explicit and discoverable. If its
-logic grows beyond a small generic helper, move it under `internal/modules`.
-
-### `notarius run`
-
-The MVP needs a functional run command that drives the already-implemented
-pipeline runner.
-
-Target state:
-
-- command shape:
+The implemented command shape is:
 
 ```sh
 notarius run <pipeline-id> --input path/to/source.json
 notarius run <pipeline-id> --input path/to/source.json --only spells
 ```
 
-- required flags and arguments produce clear usage errors;
-- `--config` selects the config file;
-- `--only` filters artifact lanes without changing structural pipeline config;
-- operational overrides may cover output directory, work directory,
-  concurrency, and LLM profile/model settings where already supported by config;
-- structural stage selection remains config-driven;
-- the command parses input through the configured input adapter;
-- the command constructs the configured LLM client and scheduler;
-- the command invokes the pipeline runner;
-- the command writes durable output and diagnostics;
-- failures return stable non-zero exit codes and useful error messages.
+Current output and diagnostics behavior:
 
-The command should be covered by fixture-driven CLI tests with fake LLM behavior
-where network calls would otherwise be required.
+- output is written under `<output-root>/<run-id>/`, defaulting to
+  `./notarius-output`;
+- JSON output includes a manifest, grouped approved artifacts, rejected
+  artifacts, and warnings;
+- artifact records include generic source references;
+- output-stage warnings remain out-of-band from artifact payloads and are
+  captured for CLI reporting and diagnostics;
+- run manifest data includes source digest, resolved pipeline digest, LLM
+  profile/model metadata, prompt/schema identifiers, and validation status;
+- diagnostics redact secrets and include invocation metadata, redacted effective
+  config, resolved pipeline, manifest, warnings, run report, and error logs.
 
-### MVP Output And Diagnostics Behavior
+Maintained MVP fixtures:
 
-The MVP should produce inspectable files that are stable enough for downstream
-experiments, without pretending to be a final public artifact contract.
+- `examples/dnd-spells.config.yml`;
+- `examples/seriatim-minimal-transcript.json`;
+- `internal/cli/testdata/invalid-seriatim-empty-segments.json`.
 
-Target state:
-
-- output path behavior is deterministic and documented in code/tests;
-- JSON output includes approved artifacts grouped or ordered predictably;
-- each artifact includes its generic source references;
-- rejected artifacts and validation decisions remain inspectable;
-- output-stage warnings remain out-of-band from the durable artifact payload but
-  are captured for CLI reporting and diagnostics;
-- run manifest data includes source digest, resolved pipeline digest, relevant
-  model/profile information, prompt/schema identifiers, and validation status;
-- diagnostics redact secrets and include the resolved effective configuration
-  needed to debug a run.
-
-### MVP Fixtures And Acceptance Tests
-
-The MVP should be continuously testable without external services.
-
-Target state:
-
-- maintained Seriatim transcript fixture for the D&D spells MVP;
-- maintained minimal config fixture for the MVP pipeline;
-- fake LLM path for deterministic CLI and runner tests;
-- config validation tests using the production catalog;
-- `notarius run` fixture test from input file to output JSON;
-- failure tests for missing config, unknown pipeline, invalid input,
-  invalid lane selection, LLM failure, and validation rejection;
-- `go test ./...` is sufficient to exercise the MVP path without network
-  access.
-
-### Documentation Pass Preparation
+## Remaining Release And Documentation Work
 
 The full documentation pass is intentionally deferred until MVP functionality
 exists. It should happen before tagging alpha `0.1.0`.
 
-The MVP implementation should still leave clear hooks for the documentation
-rewrite:
+Remaining work before alpha `0.1.0`:
 
-- command behavior should be stable enough to document in `docs/cli.md`;
-- config behavior should be stable enough to document in `docs/config.md`;
-- output behavior should be stable enough to document in integration docs;
-- examples should be generated from or validated against maintained fixtures
-  where practical.
+- move implemented CLI behavior into `docs/cli.md`;
+- move implemented config behavior into `docs/config.md`;
+- document run output and diagnostics behavior in canonical docs;
+- update integration docs for Seriatim input, D&D spell artifacts, and JSON
+  output where needed;
+- update `README.md` with a shortest useful command based on the maintained
+  examples;
+- keep examples validated by tests.
 
 ## Out Of Scope For MVP
 
@@ -234,9 +142,9 @@ rewrite:
 
 ## Deferred Documentation Pass
 
-After MVP behavior is implemented and before alpha `0.1.0`, complete a full
-documentation pass/rewrite. That pass should move implemented behavior out of
-roadmap documents and into canonical docs required by
+Before alpha `0.1.0`, complete a full documentation pass/rewrite. That pass
+should move implemented behavior out of roadmap documents and into canonical
+docs required by
 [`../policy/documentation.md`](../policy/documentation.md), including at least:
 
 - `README.md`;

examples/dnd-spells.config.yml

@@ -0,0 +1,16 @@
+version: 1
+llm_profiles:
+  default:
+    provider: openai-compatible
+    base_url: http://127.0.0.1:1
+    model: fake-model
+pipelines:
+  dnd-session:
+    input: seriatim
+    chunk:
+      module: generic
+      options:
+        max_units: 50
+    artifacts:
+      spells:
+        extract: dnd/spells

examples/seriatim-minimal-transcript.json

@@ -0,0 +1,22 @@
+{
+  "metadata": {
+    "id": "session-alpha",
+    "title": "Synthetic D&D spell session"
+  },
+  "segments": [
+    {
+      "id": "seg-001",
+      "start": 0,
+      "end": 4,
+      "speaker": "Aria",
+      "text": "Aria raises her holy symbol and casts Cure Wounds."
+    },
+    {
+      "id": "seg-002",
+      "start": 4,
+      "end": 8,
+      "speaker": "DM",
+      "text": "The bandit mage casts Shield as the blow lands."
+    }
+  ]
+}

internal/cli/catalog.go

@@ -0,0 +1,172 @@
+package cli
+
+import (
+	"context"
+	"fmt"
+	"strings"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
+	"gitea.maximumdirect.net/eric/notarius/internal/core/config"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/llm"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/chunk/generic"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/extract/dnd/spells"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/input/seriatim"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/merge/appendorder"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/normalize/noop"
+	jsonoutput "gitea.maximumdirect.net/eric/notarius/internal/modules/output/json"
+)
+
+func productionRegistries() (pipeline.Registries, error) {
+	registries := pipeline.Registries{
+		Inputs:      pipeline.NewInputAdapterRegistry(),
+		Chunkers:    pipeline.NewChunkerRegistry(),
+		Extractors:  pipeline.NewExtractorRegistry(),
+		Mergers:     pipeline.NewMergerRegistry(),
+		Normalizers: pipeline.NewNormalizerRegistry(),
+		Validators:  pipeline.NewValidatorRegistry(),
+		Outputs:     pipeline.NewOutputEncoderRegistry(),
+	}
+	if err := seriatim.Register(registries.Inputs); err != nil {
+		return pipeline.Registries{}, fmt.Errorf("register seriatim input: %w", err)
+	}
+	if err := generic.Register(registries.Chunkers); err != nil {
+		return pipeline.Registries{}, fmt.Errorf("register generic chunker: %w", err)
+	}
+	if err := spells.Register(registries.Extractors); err != nil {
+		return pipeline.Registries{}, fmt.Errorf("register dnd spells extractor: %w", err)
+	}
+	if err := appendorder.Register(registries.Mergers); err != nil {
+		return pipeline.Registries{}, fmt.Errorf("register appendorder merger: %w", err)
+	}
+	if err := noop.Register(registries.Normalizers); err != nil {
+		return pipeline.Registries{}, fmt.Errorf("register noop normalizer: %w", err)
+	}
+	if err := jsonoutput.Register(registries.Outputs); err != nil {
+		return pipeline.Registries{}, fmt.Errorf("register json output encoder: %w", err)
+	}
+	return registries, nil
+}
+
+func productionCatalog() (pipeline.ModuleCatalog, error) {
+	registries, err := productionRegistries()
+	if err != nil {
+		return pipeline.ModuleCatalog{}, err
+	}
+	return catalogFromRegistries(registries), nil
+}
+
+func effectiveCatalog(opts Options) (pipeline.ModuleCatalog, error) {
+	if !isEmptyCatalog(opts.Catalog) {
+		return opts.Catalog, nil
+	}
+	if !isEmptyRegistries(opts.Registries) {
+		return catalogFromRegistries(opts.Registries), nil
+	}
+	return productionCatalog()
+}
+
+func effectiveRegistries(opts Options) (pipeline.Registries, error) {
+	if !isEmptyRegistries(opts.Registries) {
+		return opts.Registries, nil
+	}
+	if !isEmptyCatalog(opts.Catalog) {
+		return registriesFromCatalog(opts.Catalog), nil
+	}
+	return productionRegistries()
+}
+
+func catalogFromRegistries(registries pipeline.Registries) pipeline.ModuleCatalog {
+	return pipeline.ModuleCatalog{
+		Inputs:      registries.Inputs,
+		Chunkers:    registries.Chunkers,
+		Extractors:  registries.Extractors,
+		Mergers:     registries.Mergers,
+		Normalizers: registries.Normalizers,
+		Validators:  registries.Validators,
+		Outputs:     registries.Outputs,
+	}
+}
+
+func registriesFromCatalog(catalog pipeline.ModuleCatalog) pipeline.Registries {
+	return pipeline.Registries{
+		Inputs:      catalog.Inputs,
+		Chunkers:    catalog.Chunkers,
+		Extractors:  catalog.Extractors,
+		Mergers:     catalog.Mergers,
+		Normalizers: catalog.Normalizers,
+		Validators:  catalog.Validators,
+		Outputs:     catalog.Outputs,
+	}
+}
+
+func isEmptyCatalog(catalog pipeline.ModuleCatalog) bool {
+	return catalog.Inputs == nil &&
+		catalog.Chunkers == nil &&
+		catalog.Extractors == nil &&
+		catalog.Mergers == nil &&
+		catalog.Normalizers == nil &&
+		catalog.Validators == nil &&
+		catalog.Outputs == nil
+}
+
+func isEmptyRegistries(registries pipeline.Registries) bool {
+	return registries.Inputs == nil &&
+		registries.Chunkers == nil &&
+		registries.Extractors == nil &&
+		registries.Mergers == nil &&
+		registries.Normalizers == nil &&
+		registries.Validators == nil &&
+		registries.Outputs == nil
+}
+
+func productionLLMClientFactory(ctx context.Context, cfg config.Config, profileID string) (contracts.StructuredLLMClient, []artifacts.LLMProfileManifest, error) {
+	if err := ctx.Err(); err != nil {
+		return nil, nil, err
+	}
+	trimmedID := strings.TrimSpace(profileID)
+	if trimmedID == "" {
+		trimmedID = pipeline.DefaultLLMProfile
+	}
+
+	profile, ok := cfg.LLMProfile(trimmedID)
+	if !ok {
+		return nil, nil, fmt.Errorf("LLM profile %q is not configured", trimmedID)
+	}
+	clientCfg, err := cfg.OpenAICompatibleClientConfig(trimmedID)
+	if err != nil {
+		return nil, nil, err
+	}
+	client, err := llm.NewOpenAICompatibleClient(clientCfg)
+	if err != nil {
+		return nil, nil, fmt.Errorf("create LLM client for profile %q: %w", trimmedID, err)
+	}
+
+	scheduler, err := llm.NewScheduler(effectiveLLMConcurrency(cfg, profile))
+	if err != nil {
+		return nil, nil, fmt.Errorf("create LLM scheduler for profile %q: %w", trimmedID, err)
+	}
+	provider := strings.TrimSpace(profile.Provider)
+	if provider == "" {
+		provider = "openai-compatible"
+	}
+	metadata := []artifacts.LLMProfileManifest{
+		{
+			ID:       trimmedID,
+			Provider: provider,
+			Model:    strings.TrimSpace(profile.Model),
+		},
+	}
+	return llm.NewScheduledClient(client, scheduler), metadata, nil
+}
+
+func effectiveLLMConcurrency(cfg config.Config, profile config.LLMProfile) int {
+	if profile.MaxConcurrency > 0 {
+		return profile.MaxConcurrency
+	}
+	if cfg.Concurrency.TotalLLM > 0 {
+		return cfg.Concurrency.TotalLLM
+	}
+	return 1
+}

internal/cli/run.go

@@ -1,31 +1,45 @@
 package cli
 
 import (
+	"context"
 	"encoding/json"
 	"flag"
 	"fmt"
 	"io"
 	"os"
+	"path"
+	"path/filepath"
 	"sort"
 	"strings"
+	"time"
 
+	"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/framework/contracts"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
 )
 
 const defaultConfigPath = "/usr/local/etc/notarius/config.yml"
+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 config validate --config path/to/config.yml [--pipeline pipeline-id] [--only lane-a,lane-b]
   notarius pipelines list --config path/to/config.yml [--json]
 `
 
 type Options struct {
-	Catalog   pipeline.ModuleCatalog
-	LookupEnv func(string) (string, bool)
+	Catalog          pipeline.ModuleCatalog
+	Registries       pipeline.Registries
+	LLMClientFactory LLMClientFactory
+	LookupEnv        func(string) (string, bool)
+	Now              func() time.Time
 }
 
+type LLMClientFactory func(ctx context.Context, cfg config.Config, profileID string) (contracts.StructuredLLMClient, []artifacts.LLMProfileManifest, error)
+
 // Run executes the command-line interface and returns a process exit code.
 func Run(args []string, stdout, stderr io.Writer) int {
 	return RunWithOptions(args, stdout, stderr, Options{})
@@ -46,6 +60,8 @@ func RunWithOptions(args []string, stdout, stderr io.Writer, opts Options) int {
 		return runConfig(args[1:], stdout, stderr, opts)
 	case "pipelines":
 		return runPipelines(args[1:], stdout, stderr, opts)
+	case "run":
+		return runPipelineCommand(args[1:], stdout, stderr, opts)
 	default:
 		fmt.Fprintf(stderr, "notarius: unknown command %q\n", args[0])
 		writeUsage(stderr)
@@ -61,9 +77,389 @@ func normalizeOptions(opts Options) Options {
 	if opts.LookupEnv == nil {
 		opts.LookupEnv = os.LookupEnv
 	}
+	if opts.Now == nil {
+		opts.Now = time.Now
+	}
+	if opts.LLMClientFactory == nil {
+		opts.LLMClientFactory = productionLLMClientFactory
+	}
 	return opts
 }
 
+func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) int {
+	fs := flag.NewFlagSet("run", flag.ContinueOnError)
+	fs.SetOutput(io.Discard)
+	configPath := fs.String("config", "", "config file path")
+	inputPath := fs.String("input", "", "source input file path")
+	onlyRaw := fs.String("only", "", "comma-separated artifact lanes")
+	outputDir := fs.String("output-dir", "", "output directory")
+	diagnosticsDir := fs.String("diagnostics-dir", "", "diagnostics directory")
+	llmProfile := fs.String("llm-profile", "", "LLM profile override")
+	if err := fs.Parse(reorderRunArgs(args)); err != nil {
+		fmt.Fprintf(stderr, "notarius: %v\n", err)
+		return 2
+	}
+	if fs.NArg() == 0 {
+		fmt.Fprintln(stderr, "notarius: run requires a pipeline ID")
+		return 2
+	}
+	if fs.NArg() > 1 {
+		fmt.Fprintf(stderr, "notarius: unexpected argument %q\n", fs.Arg(1))
+		return 2
+	}
+	pipelineID := strings.TrimSpace(fs.Arg(0))
+	if pipelineID == "" {
+		fmt.Fprintln(stderr, "notarius: run requires a pipeline ID")
+		return 2
+	}
+	if strings.TrimSpace(*inputPath) == "" {
+		fmt.Fprintln(stderr, "notarius: run requires --input")
+		return 2
+	}
+	only, err := parseOnly(*onlyRaw)
+	if err != nil {
+		fmt.Fprintf(stderr, "notarius: %v\n", err)
+		return 2
+	}
+
+	cfg, loadedConfigPath, err := loadConfig(*configPath, opts)
+	if err != nil {
+		fmt.Fprintf(stderr, "notarius: %v\n", err)
+		return 1
+	}
+	if dir := strings.TrimSpace(*diagnosticsDir); dir != "" {
+		cfg.Diagnostics.WorkDir = dir
+	}
+
+	startedAt := opts.Now().UTC()
+	runDir, err := diagnostics.NewRunDirectory(cfg.Diagnostics.WorkDir, cfg.Diagnostics.Retention)
+	if err != nil {
+		fmt.Fprintf(stderr, "notarius: %v\n", err)
+		return 1
+	}
+	invocation := diagnostics.InvocationMetadata{
+		Operation:    "run",
+		PipelineID:   pipelineID,
+		InputPath:    strings.TrimSpace(*inputPath),
+		ConfigPath:   loadedConfigPath,
+		ConfigSource: configSource(*configPath),
+		OnlyLanes:    append([]string(nil), only...),
+		RunID:        runDir.RunID(),
+		StartedAt:    startedAt,
+	}
+	if err := runDir.WriteInvocationMetadata(invocation); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics invocation metadata: %w", err))
+	}
+
+	catalog, err := effectiveCatalog(opts)
+	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,
+	})
+	if err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
+	}
+	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))
+	}
+	if err := runDir.WriteRedactedEffectiveConfig(effective); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics effective config: %w", err))
+	}
+	if err := runDir.WriteResolvedPipeline(effective.ResolvedPipeline); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics resolved pipeline: %w", err))
+	}
+
+	profileIDs := effectiveLLMProfileIDs(effective.ResolvedPipeline)
+	if len(profileIDs) != 1 {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("pipeline %q uses %d distinct LLM profiles; current runs require exactly one: %s", pipelineID, len(profileIDs), strings.Join(profileIDs, ", ")))
+	}
+
+	rawInput, err := os.ReadFile(strings.TrimSpace(*inputPath))
+	if err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("read input %q: %w", strings.TrimSpace(*inputPath), err))
+	}
+
+	registries, err := effectiveRegistries(opts)
+	if err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
+	}
+
+	ctx := context.Background()
+	llmClient, llmProfiles, err := opts.LLMClientFactory(ctx, effective.Config, profileIDs[0])
+	if err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("create LLM client for profile %q: %w", profileIDs[0], err))
+	}
+
+	output, err := pipeline.New(registries).Run(ctx, pipeline.RunInput{
+		Pipeline:    effective.ResolvedPipeline,
+		Path:        strings.TrimSpace(*inputPath),
+		RawInput:    rawInput,
+		LLMClient:   llmClient,
+		RunID:       runDir.RunID(),
+		StartedAt:   startedAt,
+		LLMProfiles: llmProfiles,
+		Metadata:    runMetadata(*outputDir, *diagnosticsDir),
+	})
+	if err != nil {
+		if output.Manifest.PipelineID != "" {
+			_ = runDir.WriteRunManifest(output.Manifest)
+		}
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("run pipeline %q: %w", pipelineID, err))
+	}
+
+	runOutputDir := filepath.Join(outputRoot(*outputDir), runDir.RunID())
+	if err := writeOutputFiles(runOutputDir, output.OutputFiles); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
+	}
+	if err := runDir.WriteRunManifest(output.Manifest); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics run manifest: %w", err))
+	}
+	if err := runDir.WriteWarnings(output.Warnings); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics warnings: %w", err))
+	}
+	if err := runDir.WriteRunReport(runReport{
+		RunID:            runDir.RunID(),
+		PipelineID:       effective.PipelineID,
+		OutputPath:       runOutputDir,
+		DiagnosticsPath:  runDir.Path(),
+		ApprovedCount:    len(output.Approved),
+		RejectedCount:    len(output.Rejected),
+		WarningCount:     len(output.Warnings),
+		ValidationStatus: output.Manifest.ValidationStatus,
+	}); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics run report: %w", err))
+	}
+	if err := runDir.ApplyRetention(diagnostics.RetentionDecisionInput{
+		RetentionMode: cfg.Diagnostics.Retention,
+		RunSucceeded:  true,
+		HasWarnings:   len(output.Warnings) > 0,
+	}); err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("apply diagnostics retention: %w", err))
+	}
+
+	fmt.Fprintf(stdout, "pipeline %q complete: approved=%d rejected=%d output=%s\n", effective.PipelineID, len(output.Approved), len(output.Rejected), runOutputDir)
+	if len(output.Warnings) > 0 {
+		fmt.Fprintf(stderr, "notarius: run completed with %d warning(s)\n", len(output.Warnings))
+	}
+	return 0
+}
+
+type runReport struct {
+	RunID            string `json:"run_id"`
+	PipelineID       string `json:"pipeline_id"`
+	OutputPath       string `json:"output_path"`
+	DiagnosticsPath  string `json:"diagnostics_path,omitempty"`
+	ApprovedCount    int    `json:"approved_count"`
+	RejectedCount    int    `json:"rejected_count"`
+	WarningCount     int    `json:"warning_count"`
+	ValidationStatus string `json:"validation_status,omitempty"`
+}
+
+func failPipelineCommand(stderr io.Writer, runDir *diagnostics.RunDirectory, retention diagnostics.RetentionMode, err error) int {
+	fmt.Fprintf(stderr, "notarius: %v\n", err)
+	if runDir != nil {
+		if logErr := runDir.WriteErrorLog(err.Error()); logErr != nil {
+			fmt.Fprintf(stderr, "notarius: write diagnostics error log: %v\n", logErr)
+		}
+		if retentionErr := runDir.ApplyRetention(diagnostics.RetentionDecisionInput{
+			RetentionMode: retention,
+			RunSucceeded:  false,
+		}); retentionErr != nil {
+			fmt.Fprintf(stderr, "notarius: apply diagnostics retention: %v\n", retentionErr)
+		}
+	}
+	return 1
+}
+
+func configSource(configPath string) string {
+	if strings.TrimSpace(configPath) != "" {
+		return "flag"
+	}
+	return "discovered"
+}
+
+func outputRoot(outputDir string) string {
+	if dir := strings.TrimSpace(outputDir); dir != "" {
+		return dir
+	}
+	return defaultOutputRoot
+}
+
+func writeOutputFiles(runOutputDir string, files []contracts.OutputFile) error {
+	type outputTarget struct {
+		path string
+		file contracts.OutputFile
+	}
+	targets := make([]outputTarget, 0, len(files))
+	for _, file := range files {
+		targetPath, err := outputFilePath(runOutputDir, file.Name)
+		if err != nil {
+			return err
+		}
+		targets = append(targets, outputTarget{path: targetPath, file: file})
+	}
+
+	if err := os.MkdirAll(runOutputDir, 0o755); err != nil {
+		return fmt.Errorf("create output directory %q: %w", runOutputDir, err)
+	}
+	for _, target := range targets {
+		if err := os.MkdirAll(filepath.Dir(target.path), 0o755); err != nil {
+			return fmt.Errorf("create output directory %q: %w", filepath.Dir(target.path), err)
+		}
+		if err := writeFileAtomic(target.path, target.file.Bytes, 0o644); err != nil {
+			return fmt.Errorf("write output file %q: %w", target.file.Name, err)
+		}
+	}
+	return nil
+}
+
+func outputFilePath(runOutputDir, logicalName string) (string, error) {
+	name := strings.TrimSpace(logicalName)
+	if name == "" {
+		return "", fmt.Errorf("output file name must not be empty")
+	}
+	if strings.Contains(name, `\`) {
+		return "", fmt.Errorf("output file name %q must use slash-separated relative paths", name)
+	}
+	if path.IsAbs(name) || filepath.IsAbs(name) {
+		return "", fmt.Errorf("output file name %q must be relative", name)
+	}
+	if strings.Contains(name, "..") {
+		return "", fmt.Errorf("output file name %q must not contain ..", name)
+	}
+	cleaned := path.Clean(name)
+	if cleaned == "." || cleaned != name {
+		return "", fmt.Errorf("output file name %q must be clean", name)
+	}
+
+	root, err := filepath.Abs(runOutputDir)
+	if err != nil {
+		return "", fmt.Errorf("resolve output directory %q: %w", runOutputDir, err)
+	}
+	target, err := filepath.Abs(filepath.Join(root, filepath.FromSlash(cleaned)))
+	if err != nil {
+		return "", fmt.Errorf("resolve output file %q: %w", name, err)
+	}
+	rel, err := filepath.Rel(root, target)
+	if err != nil {
+		return "", fmt.Errorf("resolve output file %q: %w", name, err)
+	}
+	if rel == "." || strings.HasPrefix(rel, ".."+string(filepath.Separator)) || rel == ".." {
+		return "", fmt.Errorf("output file name %q resolves outside output directory", name)
+	}
+	return target, nil
+}
+
+func writeFileAtomic(path string, data []byte, perm os.FileMode) error {
+	dir := filepath.Dir(path)
+	temp, err := os.CreateTemp(dir, "."+filepath.Base(path)+".tmp-*")
+	if err != nil {
+		return err
+	}
+	tempPath := temp.Name()
+	removeTemp := true
+	defer func() {
+		if removeTemp {
+			_ = os.Remove(tempPath)
+		}
+	}()
+
+	if _, err := temp.Write(data); err != nil {
+		_ = temp.Close()
+		return err
+	}
+	if err := temp.Chmod(perm); err != nil {
+		_ = temp.Close()
+		return err
+	}
+	if err := temp.Close(); err != nil {
+		return err
+	}
+	if err := os.Rename(tempPath, path); err != nil {
+		return err
+	}
+	removeTemp = false
+	return nil
+}
+
+func reorderRunArgs(args []string) []string {
+	var flags []string
+	var positionals []string
+	for i := 0; i < len(args); i++ {
+		arg := args[i]
+		if arg == "--" {
+			positionals = append(positionals, args[i+1:]...)
+			break
+		}
+		if strings.HasPrefix(arg, "-") {
+			flags = append(flags, arg)
+			if runFlagTakesValue(arg) && !strings.Contains(arg, "=") && i+1 < len(args) {
+				i++
+				flags = append(flags, args[i])
+			}
+			continue
+		}
+		positionals = append(positionals, arg)
+	}
+	return append(flags, positionals...)
+}
+
+func runFlagTakesValue(arg string) bool {
+	switch arg {
+	case "--config", "--input", "--only", "--output-dir", "--diagnostics-dir", "--llm-profile":
+		return true
+	default:
+		return false
+	}
+}
+
+func effectiveLLMProfileIDs(resolved pipeline.ResolvedPipeline) []string {
+	seen := make(map[string]struct{})
+	add := func(binding pipeline.ModuleBinding) {
+		id := strings.TrimSpace(binding.LLMProfile)
+		if id != "" {
+			seen[id] = struct{}{}
+		}
+	}
+	add(resolved.Input)
+	add(resolved.Chunk)
+	add(resolved.Output)
+	for _, lane := range resolved.ArtifactLanes {
+		add(lane.Extract)
+		add(lane.Merge)
+		add(lane.Normalize)
+		for _, validator := range lane.Validators {
+			add(validator)
+		}
+	}
+	ids := make([]string, 0, len(seen))
+	for id := range seen {
+		ids = append(ids, id)
+	}
+	sort.Strings(ids)
+	return ids
+}
+
+func runMetadata(outputDir, diagnosticsDir string) map[string]any {
+	metadata := make(map[string]any)
+	if dir := strings.TrimSpace(outputDir); dir != "" {
+		metadata["output_dir"] = dir
+	}
+	if dir := strings.TrimSpace(diagnosticsDir); dir != "" {
+		metadata["diagnostics_dir"] = dir
+	}
+	if len(metadata) == 0 {
+		return nil
+	}
+	return metadata
+}
+
 func runConfig(args []string, stdout, stderr io.Writer, opts Options) int {
 	if len(args) == 0 {
 		fmt.Fprintln(stderr, "notarius: config requires a subcommand")
@@ -111,10 +507,15 @@ func runConfigValidate(args []string, stdout, stderr io.Writer, opts Options) in
 	}
 
 	if strings.TrimSpace(*pipelineID) != "" {
+		catalog, err := effectiveCatalog(opts)
+		if err != nil {
+			fmt.Fprintf(stderr, "notarius: %v\n", err)
+			return 1
+		}
 		if _, err := cfg.Resolve(config.ResolveInput{
 			PipelineID: *pipelineID,
 			Only:       only,
-			Catalog:    opts.Catalog,
+			Catalog:    catalog,
 		}); err != nil {
 			fmt.Fprintf(stderr, "notarius: %v\n", err)
 			return 1

internal/cli/testdata/invalid-seriatim-empty-segments.json

@@ -0,0 +1,6 @@
+{
+  "metadata": {
+    "id": "session-alpha"
+  },
+  "segments": []
+}

internal/core/artifacts/artifacts.go

@@ -34,11 +34,18 @@ type RejectedArtifact struct {
 }
 
 type ArtifactLaneManifest struct {
-	ID         string   `json:"id"`
-	Extractor  string   `json:"extractor"`
-	Merger     string   `json:"merger"`
-	Normalizer string   `json:"normalizer"`
-	Validators []string `json:"validators,omitempty"`
+	ID         string         `json:"id"`
+	Extractor  string         `json:"extractor"`
+	Merger     string         `json:"merger"`
+	Normalizer string         `json:"normalizer"`
+	Validators []string       `json:"validators,omitempty"`
+	Metadata   map[string]any `json:"metadata,omitempty"`
+}
+
+type LLMProfileManifest struct {
+	ID       string `json:"id"`
+	Provider string `json:"provider,omitempty"`
+	Model    string `json:"model,omitempty"`
 }
 
 type RunManifest struct {
@@ -53,6 +60,7 @@ type RunManifest struct {
 	Normalizer       string                 `json:"normalizer,omitempty"`
 	OutputEncoder    string                 `json:"output_encoder,omitempty"`
 	ArtifactLanes    []ArtifactLaneManifest `json:"artifact_lanes,omitempty"`
+	LLMProfiles      []LLMProfileManifest   `json:"llm_profiles,omitempty"`
 	SchemaVersion    string                 `json:"schema_version,omitempty"`
 	ValidationStatus string                 `json:"validation_status,omitempty"`
 	StartedAt        *time.Time             `json:"started_at,omitempty"`

internal/core/artifacts/artifacts_test.go

@@ -127,6 +127,9 @@ func TestRunManifestIncludesPipelineAndArtifactLaneFields(t *testing.T) {
 	manifest := RunManifest{
 		PipelineID:     "pipeline-1",
 		PipelineDigest: "sha256:abc123",
+		LLMProfiles: []LLMProfileManifest{
+			{ID: "default", Provider: "openai-compatible", Model: "model-a"},
+		},
 		ArtifactLanes: []ArtifactLaneManifest{
 			{
 				ID:         "events",
@@ -134,6 +137,9 @@ func TestRunManifestIncludesPipelineAndArtifactLaneFields(t *testing.T) {
 				Merger:     "appendorder",
 				Normalizer: "noop",
 				Validators: []string{"grounded"},
+				Metadata: map[string]any{
+					"extractor": map[string]any{"prompt_id": "test.prompt"},
+				},
 			},
 		},
 	}
@@ -148,7 +154,20 @@ func TestRunManifestIncludesPipelineAndArtifactLaneFields(t *testing.T) {
 		t.Fatalf("json.Unmarshal() error = %v", err)
 	}
 
-	assertHasKeys(t, got, "pipeline_id", "pipeline_digest", "artifact_lanes")
+	assertHasKeys(t, got, "pipeline_id", "pipeline_digest", "artifact_lanes", "llm_profiles")
+
+	profiles, ok := got["llm_profiles"].([]any)
+	if !ok {
+		t.Fatalf("llm_profiles = %#v, want array", got["llm_profiles"])
+	}
+	if len(profiles) != 1 {
+		t.Fatalf("len(llm_profiles) = %d, want 1", len(profiles))
+	}
+	profile, ok := profiles[0].(map[string]any)
+	if !ok {
+		t.Fatalf("llm_profiles[0] = %#v, want object", profiles[0])
+	}
+	assertHasKeys(t, profile, "id", "provider", "model")
 
 	lanes, ok := got["artifact_lanes"].([]any)
 	if !ok {
@@ -161,7 +180,7 @@ func TestRunManifestIncludesPipelineAndArtifactLaneFields(t *testing.T) {
 	if !ok {
 		t.Fatalf("artifact_lanes[0] = %#v, want object", lanes[0])
 	}
-	assertHasKeys(t, lane, "id", "extractor", "merger", "normalizer", "validators")
+	assertHasKeys(t, lane, "id", "extractor", "merger", "normalizer", "validators", "metadata")
 }
 
 func assertHasKeys(t *testing.T, values map[string]any, keys ...string) {

internal/core/config/effective_config.go

@@ -10,9 +10,10 @@ import (
 )
 
 type ResolveInput struct {
-	PipelineID string
-	Only       []string
-	Catalog    pipeline.ModuleCatalog
+	PipelineID         string
+	Only               []string
+	Catalog            pipeline.ModuleCatalog
+	LLMProfileOverride string
 }
 
 type EffectiveConfig struct {
@@ -38,6 +39,12 @@ func (c Config) Resolve(input ResolveInput) (EffectiveConfig, error) {
 	}
 	profile = clonePipelineProfile(profile)
 	profile.ID = pipelineID
+	if override := strings.TrimSpace(input.LLMProfileOverride); override != "" {
+		if !hasLLMProfile(c.LLMProfiles, override) {
+			return EffectiveConfig{}, fmt.Errorf("LLM profile override %q is not configured", override)
+		}
+		applyLLMProfileOverride(&profile, override)
+	}
 
 	resolved, err := pipeline.ResolvePipeline(profile, pipeline.ResolveOptions{Only: input.Only}, input.Catalog)
 	if err != nil {
@@ -52,6 +59,21 @@ func (c Config) Resolve(input ResolveInput) (EffectiveConfig, error) {
 	}, nil
 }
 
+func applyLLMProfileOverride(profile *pipeline.PipelineProfile, profileID string) {
+	profile.Input.LLMProfile = profileID
+	profile.Chunk.LLMProfile = profileID
+	profile.Output.LLMProfile = profileID
+	for laneID, lane := range profile.Artifacts {
+		lane.Extract.LLMProfile = profileID
+		lane.Merge.LLMProfile = profileID
+		lane.Normalize.LLMProfile = profileID
+		for i := range lane.Validators {
+			lane.Validators[i].LLMProfile = profileID
+		}
+		profile.Artifacts[laneID] = lane
+	}
+}
+
 func lookupPipelineProfile(profiles map[string]pipeline.PipelineProfile, pipelineID string) (pipeline.PipelineProfile, bool) {
 	pipelineID = strings.TrimSpace(pipelineID)
 	for rawID, profile := range profiles {

internal/core/config/effective_config_test.go

@@ -118,6 +118,51 @@ func TestResolveDigestChangesWhenEffectiveConfigChanges(t *testing.T) {
 	}
 }
 
+func TestResolveLLMProfileOverrideAppliesBeforeDigest(t *testing.T) {
+	cfg := validConfig()
+	cfg.LLMProfiles["runtime"] = LLMProfile{Provider: "openai-compatible"}
+
+	base, err := cfg.Resolve(ResolveInput{PipelineID: "example", Catalog: fakeCatalog(t)})
+	if err != nil {
+		t.Fatalf("Resolve base: %v", err)
+	}
+	effective, err := cfg.Resolve(ResolveInput{
+		PipelineID:         "example",
+		Catalog:            fakeCatalog(t),
+		LLMProfileOverride: "runtime",
+	})
+	if err != nil {
+		t.Fatalf("Resolve override: %v", err)
+	}
+
+	if base.ResolvedPipeline.Digest == effective.ResolvedPipeline.Digest {
+		t.Fatalf("expected digest to change after LLM profile override")
+	}
+	for _, binding := range resolvedBindings(effective.ResolvedPipeline) {
+		if binding.LLMProfile != "runtime" {
+			t.Fatalf("binding profile = %q, want runtime", binding.LLMProfile)
+		}
+	}
+
+	_, err = cfg.Resolve(ResolveInput{
+		PipelineID:         "example",
+		Catalog:            fakeCatalog(t),
+		LLMProfileOverride: "missing",
+	})
+	if err == nil || !strings.Contains(err.Error(), "LLM profile override") {
+		t.Fatalf("expected override profile error, got %v", err)
+	}
+}
+
+func resolvedBindings(resolved pipeline.ResolvedPipeline) []pipeline.ModuleBinding {
+	bindings := []pipeline.ModuleBinding{resolved.Input, resolved.Chunk, resolved.Output}
+	for _, lane := range resolved.ArtifactLanes {
+		bindings = append(bindings, lane.Extract, lane.Merge, lane.Normalize)
+		bindings = append(bindings, lane.Validators...)
+	}
+	return bindings
+}
+
 func TestOpenAICompatibleClientConfigRejectsIncompleteDefaultProfile(t *testing.T) {
 	cfg := Default()
 

internal/core/diagnostics/run_dir.go

@@ -173,7 +173,7 @@ func (r *RunDirectory) WriteErrorLog(errorMessage string) error {
 	if err != nil {
 		return err
 	}
-	if err := os.WriteFile(path, []byte(errorMessage+"\n"), 0o644); err != nil {
+	if err := writeFileAtomic(path, []byte(errorMessage+"\n"), 0o644); err != nil {
 		return fmt.Errorf("write diagnostics artifact %q: %w", ArtifactErrorLog, err)
 	}
 	return nil
@@ -193,7 +193,7 @@ func (r *RunDirectory) WriteJSONArtifact(name string, payload any) error {
 		return fmt.Errorf("marshal diagnostics artifact %q: %w", name, err)
 	}
 	data = append(data, '\n')
-	if err := os.WriteFile(path, data, 0o644); err != nil {
+	if err := writeFileAtomic(path, data, 0o644); err != nil {
 		return fmt.Errorf("write diagnostics artifact %q: %w", name, err)
 	}
 	return nil
@@ -241,3 +241,39 @@ func (r *RunDirectory) artifactPath(name string) (string, error) {
 	}
 	return artifactPath, nil
 }
+
+func writeFileAtomic(path string, data []byte, perm os.FileMode) error {
+	dir := filepath.Dir(path)
+	if err := os.MkdirAll(dir, 0o755); err != nil {
+		return err
+	}
+
+	temp, err := os.CreateTemp(dir, "."+filepath.Base(path)+".tmp-*")
+	if err != nil {
+		return err
+	}
+	tempPath := temp.Name()
+	removeTemp := true
+	defer func() {
+		if removeTemp {
+			_ = os.Remove(tempPath)
+		}
+	}()
+
+	if _, err := temp.Write(data); err != nil {
+		_ = temp.Close()
+		return err
+	}
+	if err := temp.Chmod(perm); err != nil {
+		_ = temp.Close()
+		return err
+	}
+	if err := temp.Close(); err != nil {
+		return err
+	}
+	if err := os.Rename(tempPath, path); err != nil {
+		return err
+	}
+	removeTemp = false
+	return nil
+}

internal/core/diagnostics/run_dir_test.go

@@ -118,6 +118,24 @@ func TestWriteJSONArtifactWritesIndentedNewlineTerminatedJSON(t *testing.T) {
 	}
 }
 
+func TestWriteJSONArtifactLeavesNoTemporaryFiles(t *testing.T) {
+	runDir := newTestRunDirectory(t)
+
+	if err := runDir.WriteJSONArtifact("artifact.json", map[string]any{"value": "ok"}); err != nil {
+		t.Fatalf("WriteJSONArtifact: %v", err)
+	}
+
+	entries, err := os.ReadDir(runDir.Path())
+	if err != nil {
+		t.Fatalf("read run directory: %v", err)
+	}
+	for _, entry := range entries {
+		if strings.Contains(entry.Name(), ".tmp-") {
+			t.Fatalf("temporary diagnostics file remains after success: %s", entry.Name())
+		}
+	}
+}
+
 func TestWriteInvocationMetadataFillsMissingRunIDAndStartTime(t *testing.T) {
 	runDir := newTestRunDirectory(t)
 

internal/framework/contracts/composition_test.go

@@ -124,10 +124,13 @@ func TestContractsComposeAcrossPackages(t *testing.T) {
 	if err != nil {
 		t.Fatalf("Encode() error = %v, want nil", err)
 	}
-	if output.ContentType != "application/json" {
-		t.Fatalf("ContentType = %q, want application/json", output.ContentType)
+	if len(output.Files) != 1 {
+		t.Fatalf("len(Files) = %d, want 1", len(output.Files))
 	}
-	if len(output.Bytes) == 0 {
+	if output.Files[0].ContentType != "application/json" {
+		t.Fatalf("ContentType = %q, want application/json", output.Files[0].ContentType)
+	}
+	if len(output.Files[0].Bytes) == 0 {
 		t.Fatal("len(Bytes) = 0, want encoded bytes")
 	}
 }
@@ -293,7 +296,12 @@ func (encoder compositionOutputEncoder) Encode(ctx context.Context, req contract
 	}
 
 	return contracts.OutputResult{
-		Bytes:       encoded,
-		ContentType: "application/json",
+		Files: []contracts.OutputFile{
+			{
+				Name:        "artifacts/generic.json",
+				ContentType: "application/json",
+				Bytes:       encoded,
+			},
+		},
 	}, nil
 }

internal/framework/contracts/contracts.go

@@ -182,8 +182,17 @@ type OutputRequest struct {
 	Metadata   map[string]any               `json:"metadata,omitempty"`
 }
 
+type OutputFile struct {
+	Name        string `json:"name"`
+	ContentType string `json:"content_type,omitempty"`
+	Bytes       []byte `json:"-"`
+}
+
 type OutputResult struct {
-	Bytes       []byte    `json:"-"`
+	Files []OutputFile `json:"files,omitempty"`
+	// Bytes is the legacy single-output payload. New encoders should return Files.
+	Bytes []byte `json:"-"`
+	// ContentType is the legacy single-output content type. New encoders should return Files.
 	ContentType string    `json:"content_type,omitempty"`
 	Warnings    []Warning `json:"warnings,omitempty"`
 }
@@ -192,3 +201,7 @@ type OutputEncoder interface {
 	Key() string
 	Encode(ctx context.Context, req OutputRequest) (OutputResult, error)
 }
+
+type ManifestMetadataProvider interface {
+	ManifestMetadata() map[string]any
+}

internal/framework/contracts/contracts_test.go

@@ -230,11 +230,44 @@ func TestFakeMergeNormalizeAndOutputContracts(t *testing.T) {
 	if encoder.Key() != "generic-output" {
 		t.Fatalf("OutputEncoder.Key() = %q, want generic-output", encoder.Key())
 	}
-	if encoded.ContentType != "application/json" {
-		t.Fatalf("ContentType = %q, want application/json", encoded.ContentType)
+	if len(encoded.Files) != 1 {
+		t.Fatalf("len(Files) = %d, want 1", len(encoded.Files))
 	}
-	if string(encoded.Bytes) != `{"run_id":"run-1","approved_count":1}` {
-		t.Fatalf("Bytes = %s, want encoded output", encoded.Bytes)
+	if encoded.Files[0].ContentType != "application/json" {
+		t.Fatalf("ContentType = %q, want application/json", encoded.Files[0].ContentType)
+	}
+	if string(encoded.Files[0].Bytes) != `{"run_id":"run-1","approved_count":1}` {
+		t.Fatalf("Bytes = %s, want encoded output", encoded.Files[0].Bytes)
+	}
+}
+
+func TestOutputFileJSONShapeOmitsBytes(t *testing.T) {
+	file := OutputFile{
+		Name:        "artifacts/events.json",
+		ContentType: "application/json",
+		Bytes:       []byte(`{"ignored":true}`),
+	}
+
+	encoded, err := json.Marshal(file)
+	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 got["name"] != "artifacts/events.json" {
+		t.Fatalf("name = %#v, want logical file name", got["name"])
+	}
+	if got["content_type"] != "application/json" {
+		t.Fatalf("content_type = %#v, want application/json", got["content_type"])
+	}
+	if _, ok := got["Bytes"]; ok {
+		t.Fatalf("encoded output file leaked Bytes: %s", encoded)
+	}
+	if _, ok := got["bytes"]; ok {
+		t.Fatalf("encoded output file leaked bytes: %s", encoded)
 	}
 }
 
@@ -397,7 +430,12 @@ func (encoder fakeOutputEncoder) Key() string {
 
 func (encoder fakeOutputEncoder) Encode(ctx context.Context, req OutputRequest) (OutputResult, error) {
 	return OutputResult{
-		Bytes:       []byte(`{"run_id":"` + req.Manifest.RunID + `","approved_count":1}`),
-		ContentType: "application/json",
+		Files: []OutputFile{
+			{
+				Name:        "artifacts/generic.json",
+				ContentType: "application/json",
+				Bytes:       []byte(`{"run_id":"` + req.Manifest.RunID + `","approved_count":1}`),
+			},
+		},
 	}, nil
 }

internal/framework/llm/scheduled_client.go

@@ -0,0 +1,43 @@
+package llm
+
+import (
+	"context"
+	"fmt"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+)
+
+type scheduledClient struct {
+	client    contracts.StructuredLLMClient
+	scheduler *Scheduler
+}
+
+func NewScheduledClient(client contracts.StructuredLLMClient, scheduler *Scheduler) contracts.StructuredLLMClient {
+	return &scheduledClient{
+		client:    client,
+		scheduler: scheduler,
+	}
+}
+
+func (c *scheduledClient) CompleteStructured(ctx context.Context, req contracts.StructuredCompletionRequest, out any) (contracts.StructuredCompletionResponse, error) {
+	if c == nil {
+		return contracts.StructuredCompletionResponse{}, fmt.Errorf("scheduled LLM client must not be nil")
+	}
+	if c.client == nil {
+		return contracts.StructuredCompletionResponse{}, fmt.Errorf("scheduled LLM client inner client must not be nil")
+	}
+	if c.scheduler == nil {
+		return contracts.StructuredCompletionResponse{}, fmt.Errorf("scheduled LLM client scheduler must not be nil")
+	}
+
+	var response contracts.StructuredCompletionResponse
+	err := c.scheduler.Run(ctx, func(ctx context.Context) error {
+		var callErr error
+		response, callErr = c.client.CompleteStructured(ctx, req, out)
+		return callErr
+	})
+	if err != nil {
+		return contracts.StructuredCompletionResponse{}, err
+	}
+	return response, nil
+}

internal/framework/llm/scheduled_client_test.go

@@ -0,0 +1,115 @@
+package llm
+
+import (
+	"context"
+	"encoding/json"
+	"errors"
+	"sync"
+	"sync/atomic"
+	"testing"
+	"time"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+)
+
+func TestScheduledClientEnforcesSchedulerLimit(t *testing.T) {
+	scheduler, err := NewScheduler(1)
+	if err != nil {
+		t.Fatalf("NewScheduler() error = %v, want nil", err)
+	}
+	inner := &blockingStructuredClient{
+		release: make(chan struct{}),
+	}
+	client := NewScheduledClient(inner, scheduler)
+
+	var wg sync.WaitGroup
+	for i := 0; i < 3; i++ {
+		wg.Add(1)
+		go func() {
+			defer wg.Done()
+			var out map[string]any
+			if _, err := client.CompleteStructured(context.Background(), contracts.StructuredCompletionRequest{}, &out); err != nil {
+				t.Errorf("CompleteStructured() error = %v, want nil", err)
+			}
+		}()
+	}
+
+	waitForAtomicAtLeast(t, &inner.calls, 1)
+	time.Sleep(20 * time.Millisecond)
+	if got := atomic.LoadInt32(&inner.maxInFlight); got > 1 {
+		t.Fatalf("max in-flight calls = %d, want <= 1", got)
+	}
+	close(inner.release)
+	wg.Wait()
+	if got := atomic.LoadInt32(&inner.calls); got != 3 {
+		t.Fatalf("calls = %d, want 3", got)
+	}
+}
+
+func TestScheduledClientPropagatesClientError(t *testing.T) {
+	scheduler, err := NewScheduler(1)
+	if err != nil {
+		t.Fatalf("NewScheduler() error = %v, want nil", err)
+	}
+	expected := errors.New("provider unavailable")
+	client := NewScheduledClient(&errorStructuredClient{err: expected}, scheduler)
+
+	_, err = client.CompleteStructured(context.Background(), contracts.StructuredCompletionRequest{}, &struct{}{})
+	if !errors.Is(err, expected) {
+		t.Fatalf("CompleteStructured() error = %v, want %v", err, expected)
+	}
+}
+
+func TestScheduledClientPropagatesSchedulerError(t *testing.T) {
+	scheduler, err := NewScheduler(1)
+	if err != nil {
+		t.Fatalf("NewScheduler() error = %v, want nil", err)
+	}
+	ctx, cancel := context.WithCancel(context.Background())
+	cancel()
+	client := NewScheduledClient(&errorStructuredClient{}, scheduler)
+
+	_, err = client.CompleteStructured(ctx, contracts.StructuredCompletionRequest{}, &struct{}{})
+	if !errors.Is(err, context.Canceled) {
+		t.Fatalf("CompleteStructured() error = %v, want context canceled", err)
+	}
+}
+
+type blockingStructuredClient struct {
+	release     chan struct{}
+	inFlight    int32
+	maxInFlight int32
+	calls       int32
+}
+
+func (c *blockingStructuredClient) CompleteStructured(ctx context.Context, req contracts.StructuredCompletionRequest, out any) (contracts.StructuredCompletionResponse, error) {
+	atomic.AddInt32(&c.calls, 1)
+	current := atomic.AddInt32(&c.inFlight, 1)
+	for {
+		seen := atomic.LoadInt32(&c.maxInFlight)
+		if current <= seen || atomic.CompareAndSwapInt32(&c.maxInFlight, seen, current) {
+			break
+		}
+	}
+	defer atomic.AddInt32(&c.inFlight, -1)
+
+	select {
+	case <-c.release:
+	case <-ctx.Done():
+		return contracts.StructuredCompletionResponse{}, ctx.Err()
+	}
+	if target, ok := out.(*map[string]any); ok {
+		*target = map[string]any{"ok": true}
+	}
+	return contracts.StructuredCompletionResponse{
+		Content: json.RawMessage(`{"ok":true}`),
+	}, nil
+}
+
+type errorStructuredClient struct {
+	err error
+}
+
+func (c *errorStructuredClient) CompleteStructured(ctx context.Context, req contracts.StructuredCompletionRequest, out any) (contracts.StructuredCompletionResponse, error) {
+	return contracts.StructuredCompletionResponse{}, c.err
+}

internal/framework/llm/schema_registry.go

@@ -6,6 +6,7 @@ import (
 	"encoding/hex"
 	"encoding/json"
 	"fmt"
+	"io/fs"
 	"sort"
 	"strings"
 )
@@ -17,13 +18,21 @@ var schemaAssets embed.FS
 type ResponseSchemaKey string
 
 const (
-	DNDSpellsSchemaKey             ResponseSchemaKey = "dnd_spells"
 	TestArtifactSchemaKey          ResponseSchemaKey = "test_artifact"
 	TestValidatorDecisionSchemaKey ResponseSchemaKey = "test_validator_decision"
 
 	schemaVersionV1 = "v1"
 )
 
+// ResponseSchemaDefinition identifies a caller-owned structured response schema asset.
+type ResponseSchemaDefinition struct {
+	Key       ResponseSchemaKey
+	ID        string
+	Version   string
+	Name      string
+	AssetPath string
+}
+
 // ResponseSchema describes one registered structured response schema.
 type ResponseSchema struct {
 	Key        ResponseSchemaKey `json:"key"`
@@ -35,27 +44,20 @@ type ResponseSchema struct {
 }
 
 var responseSchemaRegistry = map[ResponseSchemaKey]ResponseSchema{
-	DNDSpellsSchemaKey: mustLoadResponseSchema(
-		DNDSpellsSchemaKey,
-		"notarius.dnd.spells",
-		schemaVersionV1,
-		"notarius_dnd_spells_v1",
-		"assets/schemas/dnd_spells.v1.json",
-	),
-	TestArtifactSchemaKey: mustLoadResponseSchema(
-		TestArtifactSchemaKey,
-		"notarius.test_artifact",
-		schemaVersionV1,
-		"notarius_test_artifact_v1",
-		"assets/schemas/test_artifact.v1.json",
-	),
-	TestValidatorDecisionSchemaKey: mustLoadResponseSchema(
-		TestValidatorDecisionSchemaKey,
-		"notarius.test_validator_decision",
-		schemaVersionV1,
-		"notarius_test_validator_decision_v1",
-		"assets/schemas/test_validator_decision.v1.json",
-	),
+	TestArtifactSchemaKey: mustLoadResponseSchema(schemaAssets, ResponseSchemaDefinition{
+		Key:       TestArtifactSchemaKey,
+		ID:        "notarius.test_artifact",
+		Version:   schemaVersionV1,
+		Name:      "notarius_test_artifact_v1",
+		AssetPath: "assets/schemas/test_artifact.v1.json",
+	}),
+	TestValidatorDecisionSchemaKey: mustLoadResponseSchema(schemaAssets, ResponseSchemaDefinition{
+		Key:       TestValidatorDecisionSchemaKey,
+		ID:        "notarius.test_validator_decision",
+		Version:   schemaVersionV1,
+		Name:      "notarius_test_validator_decision_v1",
+		AssetPath: "assets/schemas/test_validator_decision.v1.json",
+	}),
 }
 
 // RegisteredResponseSchemas returns all registered response schemas sorted by key.
@@ -102,40 +104,35 @@ func (s ResponseSchema) DiagnosticsMap() map[string]any {
 	}
 }
 
-func mustLoadResponseSchema(
-	key ResponseSchemaKey,
-	id string,
-	version string,
-	name string,
-	path string,
-) ResponseSchema {
-	key = ResponseSchemaKey(strings.TrimSpace(string(key)))
-	id = strings.TrimSpace(id)
-	version = strings.TrimSpace(version)
-	name = strings.TrimSpace(name)
-	path = strings.TrimSpace(path)
+// LoadResponseSchema loads a structured response schema from a caller-owned filesystem.
+func LoadResponseSchema(fsys fs.FS, def ResponseSchemaDefinition) (ResponseSchema, error) {
+	key := ResponseSchemaKey(strings.TrimSpace(string(def.Key)))
+	id := strings.TrimSpace(def.ID)
+	version := strings.TrimSpace(def.Version)
+	name := strings.TrimSpace(def.Name)
+	path := strings.TrimSpace(def.AssetPath)
 	if key == "" {
-		panic("response schema key must not be empty")
+		return ResponseSchema{}, fmt.Errorf("response schema key must not be empty")
 	}
 	if id == "" {
-		panic("response schema id must not be empty")
+		return ResponseSchema{}, fmt.Errorf("response schema id must not be empty")
 	}
 	if version == "" {
-		panic("response schema version must not be empty")
+		return ResponseSchema{}, fmt.Errorf("response schema version must not be empty")
 	}
 	if name == "" {
-		panic("response schema name must not be empty")
+		return ResponseSchema{}, fmt.Errorf("response schema name must not be empty")
 	}
 	if path == "" {
-		panic("response schema asset path must not be empty")
+		return ResponseSchema{}, fmt.Errorf("response schema asset path must not be empty")
 	}
 
-	rawSchema, err := schemaAssets.ReadFile(path)
+	rawSchema, err := fs.ReadFile(fsys, path)
 	if err != nil {
-		panic(fmt.Sprintf("read response schema %s: %v", path, err))
+		return ResponseSchema{}, fmt.Errorf("read response schema %s: %w", path, err)
 	}
 	if !json.Valid(rawSchema) {
-		panic(fmt.Sprintf("response schema %s is not valid JSON", path))
+		return ResponseSchema{}, fmt.Errorf("response schema %s is not valid JSON", path)
 	}
 
 	hash := sha256.Sum256(rawSchema)
@@ -146,7 +143,15 @@ func mustLoadResponseSchema(
 		Name:       name,
 		JSONSchema: append(json.RawMessage(nil), rawSchema...),
 		SHA256:     "sha256:" + hex.EncodeToString(hash[:]),
+	}, nil
+}
+
+func mustLoadResponseSchema(fsys fs.FS, def ResponseSchemaDefinition) ResponseSchema {
+	schema, err := LoadResponseSchema(fsys, def)
+	if err != nil {
+		panic(err)
 	}
+	return schema
 }
 
 func cloneResponseSchema(in ResponseSchema) ResponseSchema {

internal/framework/llm/schema_registry_test.go

@@ -9,7 +9,6 @@ import (
 
 func TestLookupResponseSchemaSucceedsForRegisteredSchemas(t *testing.T) {
 	tests := []ResponseSchemaKey{
-		DNDSpellsSchemaKey,
 		TestArtifactSchemaKey,
 		TestValidatorDecisionSchemaKey,
 	}
@@ -39,6 +38,12 @@ func TestLookupResponseSchemaUnknownReturnsFalse(t *testing.T) {
 	}
 }
 
+func TestLookupResponseSchemaDNDSpellsIsNotFrameworkRegistered(t *testing.T) {
+	if schema, ok := LookupResponseSchema("dnd_spells"); ok {
+		t.Fatalf("expected D&D spells schema lookup to fail in framework registry, got %+v", schema)
+	}
+}
+
 func TestMustLookupResponseSchemaPanicsForUnknownKey(t *testing.T) {
 	defer func() {
 		if recover() == nil {
@@ -51,8 +56,8 @@ func TestMustLookupResponseSchemaPanicsForUnknownKey(t *testing.T) {
 
 func TestRegisteredResponseSchemasSortedByKey(t *testing.T) {
 	schemas := RegisteredResponseSchemas()
-	if len(schemas) != 3 {
-		t.Fatalf("expected three schemas, got %d", len(schemas))
+	if len(schemas) != 2 {
+		t.Fatalf("expected two schemas, got %d", len(schemas))
 	}
 
 	keys := make([]string, len(schemas))
@@ -64,8 +69,8 @@ func TestRegisteredResponseSchemasSortedByKey(t *testing.T) {
 	if !sort.StringsAreSorted(keys) {
 		t.Fatalf("expected sorted keys, got %v", keys)
 	}
-	if !seen[DNDSpellsSchemaKey] {
-		t.Fatalf("registered schemas = %v, want %q", keys, DNDSpellsSchemaKey)
+	if !seen[TestArtifactSchemaKey] || !seen[TestValidatorDecisionSchemaKey] {
+		t.Fatalf("registered schemas = %v, want test schemas", keys)
 	}
 }
 
@@ -78,7 +83,7 @@ func TestResponseSchemaContentIsValidJSON(t *testing.T) {
 }
 
 func TestResponseSchemaJSONIsMutationSafe(t *testing.T) {
-	for _, key := range []ResponseSchemaKey{DNDSpellsSchemaKey, TestArtifactSchemaKey} {
+	for _, key := range []ResponseSchemaKey{TestArtifactSchemaKey, TestValidatorDecisionSchemaKey} {
 		t.Run(string(key), func(t *testing.T) {
 			first := MustLookupResponseSchema(key)
 			first.JSONSchema[0] = '['

internal/framework/pipeline/default_modules_test.go

@@ -0,0 +1,124 @@
+package pipeline_test
+
+import (
+	"context"
+	"testing"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/config"
+	"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/generic"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/merge/appendorder"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/normalize/noop"
+	jsonoutput "gitea.maximumdirect.net/eric/notarius/internal/modules/output/json"
+)
+
+func TestPipelineConfigResolvesWithProductionDefaultsRegistered(t *testing.T) {
+	cfg := config.Default()
+	cfg.Pipelines = map[string]pipeline.PipelineProfile{
+		"defaults": {
+			Input: pipeline.Binding("input"),
+			Artifacts: map[string]pipeline.ArtifactLaneProfile{
+				"events": {Extract: pipeline.Binding("extract")},
+			},
+		},
+	}
+
+	resolved, err := cfg.Resolve(config.ResolveInput{
+		PipelineID: "defaults",
+		Catalog:    defaultModuleCatalog(t),
+	})
+	if err != nil {
+		t.Fatalf("Resolve() error = %v, want nil", err)
+	}
+
+	pipeline := resolved.ResolvedPipeline
+	if pipeline.Chunk.Module != generic.Key {
+		t.Fatalf("Chunk.Module = %q, want %q", pipeline.Chunk.Module, generic.Key)
+	}
+	if pipeline.Output.Module != jsonoutput.Key {
+		t.Fatalf("Output.Module = %q, want %q", pipeline.Output.Module, jsonoutput.Key)
+	}
+	lane := pipeline.ArtifactLanes[0]
+	if lane.Merge.Module != appendorder.Key {
+		t.Fatalf("Merge.Module = %q, want %q", lane.Merge.Module, appendorder.Key)
+	}
+	if lane.Normalize.Module != noop.Key {
+		t.Fatalf("Normalize.Module = %q, want %q", lane.Normalize.Module, noop.Key)
+	}
+}
+
+func defaultModuleCatalog(t *testing.T) pipeline.ModuleCatalog {
+	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:      "input",
+		Stage:    pipeline.StageInput,
+		Provides: []string{"source"},
+	}, func() (contracts.InputAdapter, error) {
+		return defaultInput{}, nil
+	}); err != nil {
+		t.Fatalf("register input: %v", err)
+	}
+	if err := generic.Register(chunkers); err != nil {
+		t.Fatalf("register generic chunker: %v", err)
+	}
+	if err := extractors.RegisterWithSpec(pipeline.ModuleSpec{
+		Key:      "extract",
+		Stage:    pipeline.StageExtract,
+		Requires: []string{"chunks"},
+		Provides: []string{"records"},
+	}, func() (contracts.Extractor, error) {
+		return defaultExtractor{}, nil
+	}); err != nil {
+		t.Fatalf("register extractor: %v", err)
+	}
+	if err := appendorder.Register(mergers); err != nil {
+		t.Fatalf("register appendorder merger: %v", err)
+	}
+	if err := noop.Register(normalizers); err != nil {
+		t.Fatalf("register noop normalizer: %v", err)
+	}
+	if err := jsonoutput.Register(outputs); err != nil {
+		t.Fatalf("register json output: %v", err)
+	}
+
+	return pipeline.ModuleCatalog{
+		Inputs:      inputs,
+		Chunkers:    chunkers,
+		Extractors:  extractors,
+		Mergers:     mergers,
+		Normalizers: normalizers,
+		Outputs:     outputs,
+	}
+}
+
+type defaultInput struct{}
+
+func (defaultInput) Key() string { return "input" }
+
+func (defaultInput) Parse(ctx context.Context, req contracts.ParseRequest) (*source.SourceDocument, error) {
+	return nil, nil
+}
+
+type defaultExtractor struct{}
+
+func (defaultExtractor) Key() string { return "extract" }
+
+func (defaultExtractor) ArtifactType() string { return "record" }
+
+func (defaultExtractor) SchemaVersion() string { return "v1" }
+
+func (defaultExtractor) Validators() []contracts.Validator { return nil }
+
+func (defaultExtractor) Extract(ctx context.Context, req contracts.ExtractionRequest) (contracts.ExtractionResult, error) {
+	return contracts.ExtractionResult{}, nil
+}

internal/framework/pipeline/generic_stages.go

@@ -1,70 +0,0 @@
-package pipeline
-
-import (
-	"context"
-	"encoding/json"
-
-	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
-	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
-	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
-)
-
-type AppendOrderMerger struct{}
-
-func (m AppendOrderMerger) Key() string {
-	return DefaultMergeModule
-}
-
-func (m AppendOrderMerger) Merge(ctx context.Context, req contracts.MergeRequest) (contracts.MergeResult, error) {
-	var candidates []artifacts.ArtifactCandidate
-	for _, chunkArtifacts := range req.ChunkArtifacts {
-		candidates = append(candidates, copyArtifactCandidates(chunkArtifacts.Candidates)...)
-	}
-	return contracts.MergeResult{Candidates: candidates}, nil
-}
-
-type NoopNormalizer struct{}
-
-func (n NoopNormalizer) Key() string {
-	return DefaultNormalizeModule
-}
-
-func (n NoopNormalizer) Normalize(ctx context.Context, req contracts.NormalizeRequest) (contracts.NormalizeResult, error) {
-	return contracts.NormalizeResult{Candidates: copyArtifactCandidates(req.Candidates)}, nil
-}
-
-func copyArtifactCandidates(candidates []artifacts.ArtifactCandidate) []artifacts.ArtifactCandidate {
-	if len(candidates) == 0 {
-		return nil
-	}
-
-	copied := make([]artifacts.ArtifactCandidate, 0, len(candidates))
-	for _, candidate := range candidates {
-		copied = append(copied, copyArtifactCandidate(candidate))
-	}
-	return copied
-}
-
-func copyArtifactCandidate(candidate artifacts.ArtifactCandidate) artifacts.ArtifactCandidate {
-	return artifacts.ArtifactCandidate{
-		Index:         candidate.Index,
-		ExtractorKey:  candidate.ExtractorKey,
-		ArtifactType:  candidate.ArtifactType,
-		SchemaVersion: candidate.SchemaVersion,
-		Payload:       append(json.RawMessage(nil), candidate.Payload...),
-		SourceRefs:    append([]source.SourceRef(nil), candidate.SourceRefs...),
-		Metadata:      copyArtifactMetadata(candidate.Metadata),
-	}
-}
-
-func copyArtifactMetadata(metadata map[string]any) map[string]any {
-	if len(metadata) == 0 {
-		return nil
-	}
-
-	copied := make(map[string]any, len(metadata))
-	for key, value := range metadata {
-		copied[key] = value
-	}
-	return copied
-}

internal/framework/pipeline/generic_stages_test.go

@@ -1,221 +0,0 @@
-package pipeline
-
-import (
-	"context"
-	"encoding/json"
-	"reflect"
-	"testing"
-
-	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
-	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
-	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
-)
-
-func TestGenericMergeAndNormalizeKeys(t *testing.T) {
-	merger := AppendOrderMerger{}
-	normalizer := NoopNormalizer{}
-
-	if merger.Key() != DefaultMergeModule {
-		t.Fatalf("AppendOrderMerger.Key() = %q, want %q", merger.Key(), DefaultMergeModule)
-	}
-	if normalizer.Key() != DefaultNormalizeModule {
-		t.Fatalf("NoopNormalizer.Key() = %q, want %q", normalizer.Key(), DefaultNormalizeModule)
-	}
-}
-
-func TestAppendOrderMergerConcatenatesByChunkAndCandidateOrder(t *testing.T) {
-	merger := AppendOrderMerger{}
-	chunks := []contracts.ChunkArtifacts{
-		{
-			Chunk: sourceChunk(0),
-			Candidates: []artifacts.ArtifactCandidate{
-				candidate(2, "first-b"),
-				candidate(1, "first-a"),
-			},
-		},
-		{
-			Chunk: sourceChunk(1),
-			Candidates: []artifacts.ArtifactCandidate{
-				candidate(4, "second-b"),
-				candidate(3, "second-a"),
-			},
-		},
-	}
-
-	result, err := merger.Merge(context.Background(), contracts.MergeRequest{ChunkArtifacts: chunks})
-	if err != nil {
-		t.Fatalf("Merge() error = %v, want nil", err)
-	}
-	if len(result.Warnings) != 0 {
-		t.Fatalf("Warnings = %#v, want none", result.Warnings)
-	}
-
-	got := candidateNames(result.Candidates)
-	want := []string{"first-b", "first-a", "second-b", "second-a"}
-	if !reflect.DeepEqual(got, want) {
-		t.Fatalf("candidate order = %#v, want %#v", got, want)
-	}
-}
-
-func TestAppendOrderMergerReturnsMutationSafeCandidates(t *testing.T) {
-	merger := AppendOrderMerger{}
-	input := []contracts.ChunkArtifacts{
-		{
-			Chunk: sourceChunk(0),
-			Candidates: []artifacts.ArtifactCandidate{
-				candidate(1, "original"),
-			},
-		},
-	}
-
-	result, err := merger.Merge(context.Background(), contracts.MergeRequest{ChunkArtifacts: input})
-	if err != nil {
-		t.Fatalf("Merge() error = %v, want nil", err)
-	}
-	if len(result.Candidates) != 1 {
-		t.Fatalf("len(Candidates) = %d, want 1", len(result.Candidates))
-	}
-
-	input[0].Candidates[0].Index = 99
-	input[0].Candidates[0].Payload[0] = '['
-	input[0].Candidates[0].SourceRefs[0].StartUnitID = "changed"
-	input[0].Candidates[0].Metadata["name"] = "changed"
-
-	got := result.Candidates[0]
-	if got.Index != 1 {
-		t.Fatalf("Index = %d, want 1", got.Index)
-	}
-	if string(got.Payload) != `{"name":"original"}` {
-		t.Fatalf("Payload = %s, want original payload", got.Payload)
-	}
-	if got.SourceRefs[0].StartUnitID != "u1" {
-		t.Fatalf("SourceRefs = %#v, want original source ref", got.SourceRefs)
-	}
-	if got.Metadata["name"] != "original" {
-		t.Fatalf("Metadata = %#v, want original metadata", got.Metadata)
-	}
-}
-
-func TestNoopNormalizerPreservesOrderAndValues(t *testing.T) {
-	normalizer := NoopNormalizer{}
-	input := []artifacts.ArtifactCandidate{
-		candidate(3, "third"),
-		candidate(1, "first"),
-		candidate(2, "second"),
-	}
-
-	result, err := normalizer.Normalize(context.Background(), contracts.NormalizeRequest{Candidates: input})
-	if err != nil {
-		t.Fatalf("Normalize() error = %v, want nil", err)
-	}
-	if len(result.Warnings) != 0 {
-		t.Fatalf("Warnings = %#v, want none", result.Warnings)
-	}
-
-	got := candidateNames(result.Candidates)
-	want := []string{"third", "first", "second"}
-	if !reflect.DeepEqual(got, want) {
-		t.Fatalf("candidate order = %#v, want %#v", got, want)
-	}
-
-	if !reflect.DeepEqual(result.Candidates[0].SourceRefs, input[0].SourceRefs) {
-		t.Fatalf("SourceRefs = %#v, want %#v", result.Candidates[0].SourceRefs, input[0].SourceRefs)
-	}
-	if !reflect.DeepEqual(result.Candidates[0].Metadata, input[0].Metadata) {
-		t.Fatalf("Metadata = %#v, want %#v", result.Candidates[0].Metadata, input[0].Metadata)
-	}
-}
-
-func TestNoopNormalizerReturnsMutationSafeCandidates(t *testing.T) {
-	normalizer := NoopNormalizer{}
-	input := []artifacts.ArtifactCandidate{candidate(1, "original")}
-
-	result, err := normalizer.Normalize(context.Background(), contracts.NormalizeRequest{Candidates: input})
-	if err != nil {
-		t.Fatalf("Normalize() error = %v, want nil", err)
-	}
-	if len(result.Candidates) != 1 {
-		t.Fatalf("len(Candidates) = %d, want 1", len(result.Candidates))
-	}
-
-	input[0].Index = 99
-	input[0].Payload[0] = '['
-	input[0].SourceRefs[0].EndUnitID = "changed"
-	input[0].Metadata["name"] = "changed"
-
-	got := result.Candidates[0]
-	if got.Index != 1 {
-		t.Fatalf("Index = %d, want 1", got.Index)
-	}
-	if string(got.Payload) != `{"name":"original"}` {
-		t.Fatalf("Payload = %s, want original payload", got.Payload)
-	}
-	if got.SourceRefs[0].EndUnitID != "u1" {
-		t.Fatalf("SourceRefs = %#v, want original source ref", got.SourceRefs)
-	}
-	if got.Metadata["name"] != "original" {
-		t.Fatalf("Metadata = %#v, want original metadata", got.Metadata)
-	}
-}
-
-func TestGenericMergeAndNormalizeHandleEmptyInput(t *testing.T) {
-	merger := AppendOrderMerger{}
-	normalizer := NoopNormalizer{}
-
-	mergeResult, err := merger.Merge(context.Background(), contracts.MergeRequest{})
-	if err != nil {
-		t.Fatalf("Merge() error = %v, want nil", err)
-	}
-	if len(mergeResult.Candidates) != 0 {
-		t.Fatalf("len(mergeResult.Candidates) = %d, want 0", len(mergeResult.Candidates))
-	}
-	if len(mergeResult.Warnings) != 0 {
-		t.Fatalf("merge warnings = %#v, want none", mergeResult.Warnings)
-	}
-
-	normalizeResult, err := normalizer.Normalize(context.Background(), contracts.NormalizeRequest{})
-	if err != nil {
-		t.Fatalf("Normalize() error = %v, want nil", err)
-	}
-	if len(normalizeResult.Candidates) != 0 {
-		t.Fatalf("len(normalizeResult.Candidates) = %d, want 0", len(normalizeResult.Candidates))
-	}
-	if len(normalizeResult.Warnings) != 0 {
-		t.Fatalf("normalize warnings = %#v, want none", normalizeResult.Warnings)
-	}
-}
-
-func candidate(index int, name string) artifacts.ArtifactCandidate {
-	return artifacts.ArtifactCandidate{
-		Index:         index,
-		ExtractorKey:  "generic-extractor",
-		ArtifactType:  "generic-artifact",
-		SchemaVersion: "v1",
-		Payload:       json.RawMessage(`{"name":"` + name + `"}`),
-		SourceRefs: []source.SourceRef{
-			{SourceID: "source-1", StartUnitID: "u1", EndUnitID: "u1"},
-		},
-		Metadata: map[string]any{
-			"name": name,
-		},
-	}
-}
-
-func candidateNames(candidates []artifacts.ArtifactCandidate) []string {
-	names := make([]string, 0, len(candidates))
-	for _, candidate := range candidates {
-		names = append(names, candidate.Metadata["name"].(string))
-	}
-	return names
-}
-
-func sourceChunk(index int) contracts.SourceChunk {
-	return contracts.SourceChunk{
-		ID:       "chunk",
-		SourceID: "source-1",
-		Index:    index,
-		Units: []source.SourceUnit{
-			{ID: "u1", Kind: "unit", Text: "Source unit."},
-		},
-	}
-}

internal/framework/pipeline/runner.go

@@ -3,6 +3,9 @@ package pipeline
 import (
 	"context"
 	"fmt"
+	"path"
+	"strings"
+	"time"
 
 	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
 	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
@@ -29,21 +32,27 @@ func New(registries Registries) *Runner {
 }
 
 type RunInput struct {
-	Pipeline  ResolvedPipeline
-	SourceID  string
-	Path      string
-	RawInput  []byte
-	LLMClient contracts.StructuredLLMClient
-	Metadata  map[string]any
+	Pipeline    ResolvedPipeline
+	SourceID    string
+	Path        string
+	RawInput    []byte
+	LLMClient   contracts.StructuredLLMClient
+	RunID       string
+	StartedAt   time.Time
+	LLMProfiles []artifacts.LLMProfileManifest
+	Metadata    map[string]any
 }
 
 type RunOutput struct {
-	Manifest      artifacts.RunManifest        `json:"manifest"`
-	Approved      []artifacts.Artifact         `json:"approved,omitempty"`
-	Rejected      []artifacts.RejectedArtifact `json:"rejected,omitempty"`
-	Warnings      []contracts.Warning          `json:"warnings,omitempty"`
-	EncodedOutput []byte                       `json:"-"`
-	ContentType   string                       `json:"content_type,omitempty"`
+	Manifest    artifacts.RunManifest        `json:"manifest"`
+	Approved    []artifacts.Artifact         `json:"approved,omitempty"`
+	Rejected    []artifacts.RejectedArtifact `json:"rejected,omitempty"`
+	Warnings    []contracts.Warning          `json:"warnings,omitempty"`
+	OutputFiles []contracts.OutputFile       `json:"-"`
+	// EncodedOutput is the legacy single-output payload. New callers should use OutputFiles.
+	EncodedOutput []byte `json:"-"`
+	// ContentType is the legacy single-output content type. New callers should use OutputFiles.
+	ContentType string `json:"content_type,omitempty"`
 }
 
 func (r *Runner) Run(ctx context.Context, input RunInput) (RunOutput, error) {
@@ -58,7 +67,7 @@ func (r *Runner) Run(ctx context.Context, input RunInput) (RunOutput, error) {
 		return output, err
 	}
 
-	output.Manifest = manifestFromPipeline(input.Pipeline)
+	output.Manifest = manifestFromPipeline(input)
 
 	adapter, err := r.registries.Inputs.Build(input.Pipeline.Input.Module)
 	if err != nil {
@@ -110,6 +119,7 @@ func (r *Runner) Run(ctx context.Context, input RunInput) (RunOutput, error) {
 	} else {
 		output.Manifest.ValidationStatus = "approved"
 	}
+	output.Manifest.CompletedAt = timePtr(time.Now().UTC())
 
 	encoder, err := r.registries.Outputs.Build(input.Pipeline.Output.Module)
 	if err != nil {
@@ -128,8 +138,15 @@ func (r *Runner) Run(ctx context.Context, input RunInput) (RunOutput, error) {
 	if err != nil {
 		return failOutput(output), fmt.Errorf("encode output with encoder %q: %w", encoder.Key(), err)
 	}
-	output.EncodedOutput = encoded.Bytes
-	output.ContentType = encoded.ContentType
+	files, err := outputFilesFromResult(encoded)
+	if err != nil {
+		return failOutput(output), fmt.Errorf("validate output files from encoder %q: %w", encoder.Key(), err)
+	}
+	output.OutputFiles = files
+	if len(encoded.Files) == 0 {
+		output.EncodedOutput = append([]byte(nil), encoded.Bytes...)
+		output.ContentType = encoded.ContentType
+	}
 
 	return output, nil
 }
@@ -147,6 +164,7 @@ func (r *Runner) runLane(ctx context.Context, input RunInput, doc *source.Source
 	if err != nil {
 		return fmt.Errorf("build normalizer %q for lane %q: %w", lane.Normalize.Module, lane.ID, err)
 	}
+	setLaneManifestMetadata(output, lane.ID, extractor, merger, normalizer)
 
 	var validators []validatorExecution
 	if len(lane.Validators) > 0 {
@@ -315,7 +333,17 @@ func validateRunInput(input RunInput) error {
 	return nil
 }
 
-func manifestFromPipeline(pipeline ResolvedPipeline) artifacts.RunManifest {
+func manifestFromPipeline(input RunInput) artifacts.RunManifest {
+	startedAt := input.StartedAt
+	if startedAt.IsZero() {
+		startedAt = time.Now().UTC()
+	}
+	runID := strings.TrimSpace(input.RunID)
+	if runID == "" {
+		runID = fmt.Sprintf("run-%d", startedAt.UnixNano())
+	}
+
+	pipeline := input.Pipeline
 	manifest := artifacts.RunManifest{
 		PipelineID:     pipeline.ID,
 		PipelineDigest: pipeline.Digest,
@@ -323,6 +351,9 @@ func manifestFromPipeline(pipeline ResolvedPipeline) artifacts.RunManifest {
 		Chunker:        pipeline.Chunk.Module,
 		OutputEncoder:  pipeline.Output.Module,
 		ArtifactLanes:  make([]artifacts.ArtifactLaneManifest, 0, len(pipeline.ArtifactLanes)),
+		RunID:          runID,
+		StartedAt:      timePtr(startedAt),
+		LLMProfiles:    cloneLLMProfiles(input.LLMProfiles),
 	}
 
 	for _, lane := range pipeline.ArtifactLanes {
@@ -343,10 +374,124 @@ func manifestFromPipeline(pipeline ResolvedPipeline) artifacts.RunManifest {
 func failOutput(output RunOutput) RunOutput {
 	if output.Manifest.PipelineID != "" {
 		output.Manifest.ValidationStatus = "failed"
+		output.Manifest.CompletedAt = timePtr(time.Now().UTC())
 	}
 	return output
 }
 
+func setLaneManifestMetadata(output *RunOutput, laneID string, modules ...any) {
+	if output == nil {
+		return
+	}
+	for i := range output.Manifest.ArtifactLanes {
+		if output.Manifest.ArtifactLanes[i].ID != laneID {
+			continue
+		}
+
+		metadata := make(map[string]any)
+		for _, module := range modules {
+			provider, ok := module.(contracts.ManifestMetadataProvider)
+			if !ok {
+				continue
+			}
+			moduleMetadata := cloneMetadata(provider.ManifestMetadata())
+			if len(moduleMetadata) == 0 {
+				continue
+			}
+			key := manifestMetadataKey(module)
+			if key == "" {
+				continue
+			}
+			metadata[key] = moduleMetadata
+		}
+		if len(metadata) > 0 {
+			output.Manifest.ArtifactLanes[i].Metadata = metadata
+		}
+		return
+	}
+}
+
+func manifestMetadataKey(module any) string {
+	switch module.(type) {
+	case contracts.Extractor:
+		return "extractor"
+	case contracts.Merger:
+		return "merger"
+	case contracts.Normalizer:
+		return "normalizer"
+	default:
+		return ""
+	}
+}
+
+func outputFilesFromResult(result contracts.OutputResult) ([]contracts.OutputFile, error) {
+	files := result.Files
+	if len(files) == 0 && len(result.Bytes) > 0 {
+		files = []contracts.OutputFile{
+			{
+				Name:        "output",
+				ContentType: result.ContentType,
+				Bytes:       result.Bytes,
+			},
+		}
+	}
+
+	out := make([]contracts.OutputFile, 0, len(files))
+	for _, file := range files {
+		if err := validateOutputFileName(file.Name); err != nil {
+			return nil, err
+		}
+		out = append(out, contracts.OutputFile{
+			Name:        file.Name,
+			ContentType: file.ContentType,
+			Bytes:       append([]byte(nil), file.Bytes...),
+		})
+	}
+	return out, nil
+}
+
+func validateOutputFileName(name string) error {
+	if strings.TrimSpace(name) == "" {
+		return fmt.Errorf("output file name must not be empty")
+	}
+	if strings.Contains(name, "\\") {
+		return fmt.Errorf("output file name %q must use slash-separated relative paths", name)
+	}
+	if path.IsAbs(name) {
+		return fmt.Errorf("output file name %q must be relative", name)
+	}
+	if strings.Contains(name, "..") {
+		return fmt.Errorf("output file name %q must not contain ..", name)
+	}
+	cleaned := path.Clean(name)
+	if cleaned == "." || cleaned != name {
+		return fmt.Errorf("output file name %q must be clean", name)
+	}
+	return nil
+}
+
+func cloneMetadata(metadata map[string]any) map[string]any {
+	if len(metadata) == 0 {
+		return nil
+	}
+	out := make(map[string]any, len(metadata))
+	for key, value := range metadata {
+		out[key] = value
+	}
+	return out
+}
+
+func cloneLLMProfiles(profiles []artifacts.LLMProfileManifest) []artifacts.LLMProfileManifest {
+	if len(profiles) == 0 {
+		return nil
+	}
+	return append([]artifacts.LLMProfileManifest(nil), profiles...)
+}
+
+func timePtr(t time.Time) *time.Time {
+	return &t
+}
+
 func pipelineUsesConfiguredValidators(pipeline ResolvedPipeline) bool {
 	for _, lane := range pipeline.ArtifactLanes {
 		if len(lane.Validators) > 0 {

internal/framework/pipeline/runner_test.go

@@ -6,6 +6,7 @@ import (
 	"reflect"
 	"strings"
 	"testing"
+	"time"
 
 	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
 	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
@@ -32,6 +33,7 @@ func TestNewAndDataTypes(t *testing.T) {
 		Approved:      []artifacts.Artifact{{ExtractorKey: "extract-alpha"}},
 		Rejected:      []artifacts.RejectedArtifact{{ValidatorName: "validator"}},
 		Warnings:      []contracts.Warning{{ReasonCode: "note", Message: "message"}},
+		OutputFiles:   []contracts.OutputFile{{Name: "artifacts/generic.json", ContentType: "application/json", Bytes: []byte(`{}`)}},
 		EncodedOutput: []byte(`{}`),
 		ContentType:   "application/json",
 	}
@@ -39,7 +41,7 @@ func TestNewAndDataTypes(t *testing.T) {
 	if input.Pipeline.ID != "pipeline-1" || input.SourceID != "source-1" {
 		t.Fatalf("RunInput = %#v, want constructed fields", input)
 	}
-	if output.Manifest.PipelineID != "pipeline-1" || len(output.Approved) != 1 || len(output.Rejected) != 1 || len(output.Warnings) != 1 {
+	if output.Manifest.PipelineID != "pipeline-1" || len(output.Approved) != 1 || len(output.Rejected) != 1 || len(output.Warnings) != 1 || len(output.OutputFiles) != 1 {
 		t.Fatalf("RunOutput = %#v, want constructed fields", output)
 	}
 }
@@ -604,11 +606,18 @@ func TestRunOutputEncoderReceivesManifestAndArtifacts(t *testing.T) {
 		t.Fatalf("Run() error = %v, want nil", err)
 	}
 
-	if output.ContentType != "application/json" {
-		t.Fatalf("ContentType = %q, want application/json", output.ContentType)
+	if len(output.OutputFiles) != 1 {
+		t.Fatalf("len(OutputFiles) = %d, want 1", len(output.OutputFiles))
 	}
-	if string(output.EncodedOutput) != `{"encoded":true}` {
-		t.Fatalf("EncodedOutput = %s, want encoded payload", output.EncodedOutput)
+	file := output.OutputFiles[0]
+	if file.Name != "artifacts/generic.json" {
+		t.Fatalf("OutputFiles[0].Name = %q, want artifacts/generic.json", file.Name)
+	}
+	if file.ContentType != "application/json" {
+		t.Fatalf("ContentType = %q, want application/json", file.ContentType)
+	}
+	if string(file.Bytes) != `{"encoded":true}` {
+		t.Fatalf("OutputFiles[0].Bytes = %s, want encoded payload", file.Bytes)
 	}
 	if len(modules.output.requests) != 1 {
 		t.Fatalf("len(output requests) = %d, want 1", len(modules.output.requests))
@@ -622,6 +631,35 @@ func TestRunOutputEncoderReceivesManifestAndArtifacts(t *testing.T) {
 	}
 }
 
+func TestRunRejectsUnsafeOutputFileNames(t *testing.T) {
+	tests := []struct {
+		name     string
+		fileName string
+	}{
+		{name: "empty", fileName: ""},
+		{name: "absolute", fileName: "/tmp/output.json"},
+		{name: "parent", fileName: "artifacts/../manifest.json"},
+		{name: "backslash", fileName: `artifacts\manifest.json`},
+		{name: "unclean", fileName: "artifacts//manifest.json"},
+	}
+
+	for _, test := range tests {
+		t.Run(test.name, func(t *testing.T) {
+			modules := defaultRunnerModules()
+			modules.output.files = []contracts.OutputFile{
+				{Name: test.fileName, ContentType: "application/json", Bytes: []byte(`{}`)},
+			}
+
+			output, err := New(newRunnerRegistries(t, modules)).Run(context.Background(), RunInput{Pipeline: resolvedPipeline()})
+
+			assertRunError(t, err, "output file name")
+			if output.Manifest.ValidationStatus != "failed" {
+				t.Fatalf("ValidationStatus = %q, want failed", output.Manifest.ValidationStatus)
+			}
+		})
+	}
+}
+
 func TestRunReturnsFailedManifestWhenOutputEncoderFails(t *testing.T) {
 	modules := defaultRunnerModules()
 	modules.output.err = errors.New("encode failed")
@@ -632,6 +670,9 @@ func TestRunReturnsFailedManifestWhenOutputEncoderFails(t *testing.T) {
 	if output.Manifest.ValidationStatus != "failed" {
 		t.Fatalf("ValidationStatus = %q, want failed", output.Manifest.ValidationStatus)
 	}
+	if output.Manifest.CompletedAt == nil {
+		t.Fatal("CompletedAt = nil, want failed run completion timestamp")
+	}
 	if len(output.Approved) != 2 {
 		t.Fatalf("len(Approved) = %d, want partial approved output", len(output.Approved))
 	}
@@ -668,6 +709,76 @@ func TestRunManifestIncludesPipelineAndLaneDetails(t *testing.T) {
 	}
 }
 
+func TestRunManifestIncludesRunTimingAndLLMProfiles(t *testing.T) {
+	startedAt := time.Now().Add(-time.Minute).UTC()
+	profiles := []artifacts.LLMProfileManifest{
+		{ID: "default", Provider: "openai-compatible", Model: "model-a"},
+	}
+
+	output, err := New(newRunnerRegistries(t, nil)).Run(context.Background(), RunInput{
+		Pipeline:    resolvedPipeline(),
+		RunID:       "run-test",
+		StartedAt:   startedAt,
+		LLMProfiles: profiles,
+	})
+	if err != nil {
+		t.Fatalf("Run() error = %v, want nil", err)
+	}
+
+	manifest := output.Manifest
+	if manifest.RunID != "run-test" {
+		t.Fatalf("RunID = %q, want run-test", manifest.RunID)
+	}
+	if manifest.StartedAt == nil || !manifest.StartedAt.Equal(startedAt) {
+		t.Fatalf("StartedAt = %v, want %s", manifest.StartedAt, startedAt)
+	}
+	if manifest.CompletedAt == nil || manifest.CompletedAt.Before(startedAt) {
+		t.Fatalf("CompletedAt = %v, want timestamp after start", manifest.CompletedAt)
+	}
+	if !reflect.DeepEqual(manifest.LLMProfiles, profiles) {
+		t.Fatalf("LLMProfiles = %#v, want %#v", manifest.LLMProfiles, profiles)
+	}
+}
+
+func TestRunManifestGeneratesRunIDAndTimestamps(t *testing.T) {
+	output, err := New(newRunnerRegistries(t, nil)).Run(context.Background(), RunInput{Pipeline: resolvedPipeline()})
+	if err != nil {
+		t.Fatalf("Run() error = %v, want nil", err)
+	}
+
+	if !strings.HasPrefix(output.Manifest.RunID, "run-") {
+		t.Fatalf("RunID = %q, want generated run ID", output.Manifest.RunID)
+	}
+	if output.Manifest.StartedAt == nil {
+		t.Fatal("StartedAt = nil, want generated timestamp")
+	}
+	if output.Manifest.CompletedAt == nil {
+		t.Fatal("CompletedAt = nil, want generated timestamp")
+	}
+}
+
+func TestRunManifestIncludesExtractorMetadata(t *testing.T) {
+	modules := defaultRunnerModules()
+	modules.extractors["extract-alpha"].manifestMetadata = map[string]any{
+		"prompt_id":            "test.prompt",
+		"response_schema_name": "test_schema",
+	}
+
+	output, err := New(newRunnerRegistries(t, modules)).Run(context.Background(), RunInput{Pipeline: resolvedPipeline()})
+	if err != nil {
+		t.Fatalf("Run() error = %v, want nil", err)
+	}
+
+	lane := output.Manifest.ArtifactLanes[0]
+	extractorMetadata, ok := lane.Metadata["extractor"].(map[string]any)
+	if !ok {
+		t.Fatalf("lane metadata = %#v, want extractor metadata", lane.Metadata)
+	}
+	if extractorMetadata["prompt_id"] != "test.prompt" || extractorMetadata["response_schema_name"] != "test_schema" {
+		t.Fatalf("extractor metadata = %#v, want prompt and schema metadata", extractorMetadata)
+	}
+}
+
 func TestRunReturnsPartialOutputWhenLaterLaneFails(t *testing.T) {
 	modules := defaultRunnerModules()
 	modules.extractors["extract-beta"] = &runnerExtractor{key: "extract-beta", artifactType: "artifact", schemaVersion: "v1", err: errors.New("extract failed")}
@@ -783,7 +894,12 @@ func defaultRunnerModules() *runnerModules {
 			"configured":       {name: "configured", decisions: approveAll},
 			"second-validator": {name: "second-validator", decisions: approveAll},
 		},
-		output: &runnerOutputEncoder{key: "output", bytes: []byte(`{"encoded":true}`), contentType: "application/json"},
+		output: &runnerOutputEncoder{
+			key: "output",
+			files: []contracts.OutputFile{
+				{Name: "artifacts/generic.json", ContentType: "application/json", Bytes: []byte(`{"encoded":true}`)},
+			},
+		},
 	}
 }
 
@@ -885,17 +1001,18 @@ func (chunker *runnerChunker) Chunk(ctx context.Context, req contracts.ChunkRequ
 }
 
 type runnerExtractor struct {
-	key            string
-	artifactType   string
-	schemaVersion  string
-	candidates     []artifacts.ArtifactCandidate
-	validators     []contracts.Validator
-	warnings       []contracts.Warning
-	err            error
-	requests       []contracts.ExtractionRequest
-	seenChunkIDs   []string
-	seenLLMClients []contracts.StructuredLLMClient
-	seenMetadata   []map[string]any
+	key              string
+	artifactType     string
+	schemaVersion    string
+	manifestMetadata map[string]any
+	candidates       []artifacts.ArtifactCandidate
+	validators       []contracts.Validator
+	warnings         []contracts.Warning
+	err              error
+	requests         []contracts.ExtractionRequest
+	seenChunkIDs     []string
+	seenLLMClients   []contracts.StructuredLLMClient
+	seenMetadata     []map[string]any
 }
 
 func (extractor *runnerExtractor) Key() string {
@@ -910,6 +1027,10 @@ func (extractor *runnerExtractor) SchemaVersion() string {
 	return extractor.schemaVersion
 }
 
+func (extractor *runnerExtractor) ManifestMetadata() map[string]any {
+	return extractor.manifestMetadata
+}
+
 func (extractor *runnerExtractor) Validators() []contracts.Validator {
 	return extractor.validators
 }
@@ -1020,6 +1141,7 @@ func (validator *runnerValidator) Validate(ctx context.Context, req contracts.Va
 
 type runnerOutputEncoder struct {
 	key         string
+	files       []contracts.OutputFile
 	bytes       []byte
 	contentType string
 	warnings    []contracts.Warning
@@ -1034,6 +1156,7 @@ func (encoder *runnerOutputEncoder) Key() string {
 func (encoder *runnerOutputEncoder) Encode(ctx context.Context, req contracts.OutputRequest) (contracts.OutputResult, error) {
 	encoder.requests = append(encoder.requests, req)
 	return contracts.OutputResult{
+		Files:       encoder.files,
 		Bytes:       encoder.bytes,
 		ContentType: encoder.contentType,
 		Warnings:    encoder.warnings,

internal/framework/pipeline/walking_skeleton_test.go

@@ -135,7 +135,7 @@ func walkingSkeletonCatalog(t *testing.T) ModuleCatalog {
 		Stage:    StageMerge,
 		Requires: []string{"fake_artifacts"},
 	}, func() (contracts.Merger, error) {
-		return AppendOrderMerger{}, nil
+		return walkingSkeletonMerger{}, nil
 	}); err != nil {
 		t.Fatalf("register append-order merger: %v", err)
 	}
@@ -143,7 +143,7 @@ func walkingSkeletonCatalog(t *testing.T) ModuleCatalog {
 		Key:   DefaultNormalizeModule,
 		Stage: StageNormalize,
 	}, func() (contracts.Normalizer, error) {
-		return NoopNormalizer{}, nil
+		return walkingSkeletonNormalizer{}, nil
 	}); err != nil {
 		t.Fatalf("register no-op normalizer: %v", err)
 	}
@@ -309,6 +309,30 @@ func (client *walkingSkeletonLLMClient) CompleteStructured(ctx context.Context,
 	}, nil
 }
 
+type walkingSkeletonMerger struct{}
+
+func (merger walkingSkeletonMerger) Key() string {
+	return DefaultMergeModule
+}
+
+func (merger walkingSkeletonMerger) 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 walkingSkeletonNormalizer struct{}
+
+func (normalizer walkingSkeletonNormalizer) Key() string {
+	return DefaultNormalizeModule
+}
+
+func (normalizer walkingSkeletonNormalizer) Normalize(ctx context.Context, req contracts.NormalizeRequest) (contracts.NormalizeResult, error) {
+	return contracts.NormalizeResult{Candidates: req.Candidates}, nil
+}
+
 type walkingSkeletonOutput struct{}
 
 func (output walkingSkeletonOutput) Key() string {

internal/framework/prompt/registry.go

@@ -5,6 +5,7 @@ import (
 	"embed"
 	"encoding/hex"
 	"fmt"
+	"io/fs"
 	"path"
 	"sort"
 	"strings"
@@ -17,7 +18,6 @@ var embeddedAssets embed.FS
 const (
 	SourceBuiltin       = "builtin"
 	VersionV1           = "v1"
-	DNDSpellsPromptID   = "dnd.spells"
 	TestGenericPromptID = "test.generic"
 )
 
@@ -41,21 +41,31 @@ func (m Metadata) DiagnosticsMap() map[string]any {
 	}
 }
 
-type definition struct {
-	id          string
-	version     string
-	embeddedDir string
-	systemPath  string
-	userPath    string
+// Definition identifies a caller-owned system/user prompt bundle.
+type Definition struct {
+	PromptID     string
+	Version      string
+	EmbeddedPath string
+	SystemPath   string
+	UserPath     string
 }
 
-type compiledPrompt struct {
+// Bundle is a compiled system/user prompt pair.
+type Bundle struct {
 	systemTmpl *template.Template
 	userTmpl   *template.Template
 	metadata   Metadata
 }
 
-var promptRegistry map[string]compiledPrompt
+// Metadata returns metadata for the compiled prompt bundle.
+func (b *Bundle) Metadata() Metadata {
+	if b == nil {
+		return Metadata{}
+	}
+	return b.metadata
+}
+
+var promptRegistry map[string]*Bundle
 var sharedHardening string
 
 func init() {
@@ -65,30 +75,23 @@ func init() {
 		panic(err)
 	}
 
-	defs := []definition{
+	defs := []Definition{
 		{
-			id:          DNDSpellsPromptID,
-			version:     VersionV1,
-			embeddedDir: "assets/dnd/spells",
-			systemPath:  "assets/dnd/spells/system.md",
-			userPath:    "assets/dnd/spells/user.md",
-		},
-		{
-			id:          TestGenericPromptID,
-			version:     VersionV1,
-			embeddedDir: "assets/test/generic",
-			systemPath:  "assets/test/generic/system.md",
-			userPath:    "assets/test/generic/user.md",
+			PromptID:     TestGenericPromptID,
+			Version:      VersionV1,
+			EmbeddedPath: "assets/test/generic",
+			SystemPath:   "assets/test/generic/system.md",
+			UserPath:     "assets/test/generic/user.md",
 		},
 	}
 
-	promptRegistry = make(map[string]compiledPrompt, len(defs))
+	promptRegistry = make(map[string]*Bundle, len(defs))
 	for _, def := range defs {
-		compiled, compileErr := compilePrompt(def)
+		compiled, compileErr := LoadBundle(embeddedAssets, def)
 		if compileErr != nil {
 			panic(compileErr)
 		}
-		promptRegistry[def.id] = compiled
+		promptRegistry[compiled.metadata.PromptID] = compiled
 	}
 }
 
@@ -138,51 +141,68 @@ func readAsset(assetPath string) (string, error) {
 	return string(content), nil
 }
 
-func compilePrompt(def definition) (compiledPrompt, error) {
-	if strings.TrimSpace(def.id) == "" {
-		return compiledPrompt{}, fmt.Errorf("prompt id must not be empty")
+// LoadBundle compiles a system/user prompt bundle from a caller-owned filesystem.
+func LoadBundle(fsys fs.FS, def Definition) (*Bundle, error) {
+	promptID := strings.TrimSpace(def.PromptID)
+	version := strings.TrimSpace(def.Version)
+	embeddedPath := strings.TrimSpace(def.EmbeddedPath)
+	systemPath := strings.TrimSpace(def.SystemPath)
+	userPath := strings.TrimSpace(def.UserPath)
+	if promptID == "" {
+		return nil, fmt.Errorf("prompt id must not be empty")
 	}
-	if strings.TrimSpace(def.version) == "" {
-		return compiledPrompt{}, fmt.Errorf("prompt version must not be empty")
+	if version == "" {
+		return nil, fmt.Errorf("prompt version must not be empty")
 	}
-	if strings.TrimSpace(def.embeddedDir) == "" {
-		return compiledPrompt{}, fmt.Errorf("prompt embedded path must not be empty")
+	if embeddedPath == "" {
+		return nil, fmt.Errorf("prompt embedded path must not be empty")
 	}
 
-	systemSource, err := readAsset(def.systemPath)
+	systemSource, err := readPromptAsset(fsys, systemPath)
 	if err != nil {
-		return compiledPrompt{}, err
+		return nil, err
 	}
-	userSource, err := readAsset(def.userPath)
+	userSource, err := readPromptAsset(fsys, userPath)
 	if err != nil {
-		return compiledPrompt{}, err
+		return nil, err
 	}
 
 	funcs := template.FuncMap{
 		"hardening": func() string { return sharedHardening },
 	}
-	systemTmpl, err := template.New(path.Base(def.systemPath)).Option("missingkey=error").Funcs(funcs).Parse(systemSource)
+	systemTmpl, err := template.New(path.Base(systemPath)).Option("missingkey=error").Funcs(funcs).Parse(systemSource)
 	if err != nil {
-		return compiledPrompt{}, fmt.Errorf("parse embedded system prompt %q: %w", def.systemPath, err)
+		return nil, fmt.Errorf("parse embedded system prompt %q: %w", systemPath, err)
 	}
-	userTmpl, err := template.New(path.Base(def.userPath)).Option("missingkey=error").Funcs(funcs).Parse(userSource)
+	userTmpl, err := template.New(path.Base(userPath)).Option("missingkey=error").Funcs(funcs).Parse(userSource)
 	if err != nil {
-		return compiledPrompt{}, fmt.Errorf("parse embedded user prompt %q: %w", def.userPath, err)
+		return nil, fmt.Errorf("parse embedded user prompt %q: %w", userPath, err)
 	}
 
 	hashInput := systemSource + "\n\n" + userSource
 	hash := sha256.Sum256([]byte(hashInput))
 	metadata := Metadata{
-		PromptID:      strings.TrimSpace(def.id),
-		PromptVersion: strings.TrimSpace(def.version),
+		PromptID:      promptID,
+		PromptVersion: version,
 		PromptSource:  SourceBuiltin,
-		EmbeddedPath:  strings.TrimSpace(def.embeddedDir),
+		EmbeddedPath:  embeddedPath,
 		SHA256:        "sha256:" + hex.EncodeToString(hash[:]),
 	}
 
-	return compiledPrompt{
+	return &Bundle{
 		systemTmpl: systemTmpl,
 		userTmpl:   userTmpl,
 		metadata:   metadata,
 	}, nil
 }
+
+func readPromptAsset(fsys fs.FS, assetPath string) (string, error) {
+	if strings.TrimSpace(assetPath) == "" {
+		return "", fmt.Errorf("prompt asset path must not be empty")
+	}
+	content, err := fs.ReadFile(fsys, assetPath)
+	if err != nil {
+		return "", fmt.Errorf("read embedded prompt asset %q: %w", assetPath, err)
+	}
+	return string(content), nil
+}

internal/framework/prompt/registry_test.go

@@ -11,7 +11,6 @@ func TestLookupMetadataSucceedsForRegisteredPrompts(t *testing.T) {
 		promptID     string
 		embeddedPath string
 	}{
-		{promptID: DNDSpellsPromptID, embeddedPath: "assets/dnd/spells"},
 		{promptID: TestGenericPromptID, embeddedPath: "assets/test/generic"},
 	}
 
@@ -59,8 +58,8 @@ func TestMustLookupMetadataPanicsForUnknownPromptID(t *testing.T) {
 
 func TestRegisteredMetadataSortedByPromptID(t *testing.T) {
 	registered := RegisteredMetadata()
-	if len(registered) != 2 {
-		t.Fatalf("expected two registered prompts, got %d", len(registered))
+	if len(registered) != 1 {
+		t.Fatalf("expected one registered prompt, got %d", len(registered))
 	}
 
 	ids := make([]string, len(registered))
@@ -72,8 +71,8 @@ func TestRegisteredMetadataSortedByPromptID(t *testing.T) {
 	if !sort.StringsAreSorted(ids) {
 		t.Fatalf("expected sorted prompt IDs, got %v", ids)
 	}
-	if !seen[DNDSpellsPromptID] {
-		t.Fatalf("registered prompt IDs = %v, want %q", ids, DNDSpellsPromptID)
+	if !seen[TestGenericPromptID] {
+		t.Fatalf("registered prompt IDs = %v, want %q", ids, TestGenericPromptID)
 	}
 }
 

internal/framework/prompt/render.go

@@ -13,16 +13,23 @@ func RenderUserSystem(promptID string, data any) (system string, user string, me
 	if !ok {
 		return "", "", Metadata{}, fmt.Errorf("unknown prompt id %q", promptID)
 	}
+	return compiled.RenderUserSystem(data)
+}
 
+// RenderUserSystem renders the bundle's system and user prompts.
+func (b *Bundle) RenderUserSystem(data any) (system string, user string, metadata Metadata, err error) {
+	if b == nil {
+		return "", "", Metadata{}, fmt.Errorf("prompt bundle must not be nil")
+	}
 	var systemBuf bytes.Buffer
-	if err := compiled.systemTmpl.Execute(&systemBuf, data); err != nil {
-		return "", "", Metadata{}, fmt.Errorf("render system prompt %q: %w", trimmedID, err)
+	if err := b.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 := compiled.userTmpl.Execute(&userBuf, data); err != nil {
-		return "", "", Metadata{}, fmt.Errorf("render user prompt %q: %w", trimmedID, err)
+	if err := b.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()), compiled.metadata, nil
+	return strings.TrimSpace(systemBuf.String()), strings.TrimSpace(userBuf.String()), b.metadata, nil
 }

internal/framework/prompt/render_test.go

@@ -64,47 +64,3 @@ func TestRenderUserSystemIncludesHardeningText(t *testing.T) {
 		t.Fatalf("expected rendered system prompt to include hardening text: %q", system)
 	}
 }
-
-func TestRenderDNDSpellsPromptIncludesHardeningText(t *testing.T) {
-	system, user, metadata, err := RenderUserSystem(DNDSpellsPromptID, map[string]any{
-		"SourceID":   "session-alpha",
-		"HasChunk":   true,
-		"ChunkID":    "session-alpha:chunk:0",
-		"ChunkIndex": 0,
-		"Units": []map[string]any{
-			{
-				"ID":   "seg-001",
-				"Text": "Aria casts Cure Wounds.",
-				"Metadata": []map[string]string{
-					{"Key": "speaker", "Value": "Alice"},
-				},
-			},
-		},
-	})
-	if err != nil {
-		t.Fatalf("RenderUserSystem: %v", err)
-	}
-
-	hardening := strings.TrimSpace(HardeningText())
-	if hardening == "" {
-		t.Fatalf("expected hardening text")
-	}
-	if !strings.Contains(system, hardening) {
-		t.Fatalf("expected rendered system prompt to include hardening text: %q", system)
-	}
-	for _, want := range []string{"session-alpha", "session-alpha:chunk:0", "seg-001", "Aria casts Cure Wounds.", "speaker: Alice"} {
-		if !strings.Contains(user, want) {
-			t.Fatalf("rendered user prompt = %q, want substring %q", user, want)
-		}
-	}
-	if metadata.PromptID != DNDSpellsPromptID {
-		t.Fatalf("unexpected metadata: %+v", metadata)
-	}
-}
-
-func TestRenderDNDSpellsPromptMissingTemplateDataReturnsError(t *testing.T) {
-	_, _, _, err := RenderUserSystem(DNDSpellsPromptID, map[string]any{})
-	if err == nil || !strings.Contains(err.Error(), "SourceID") {
-		t.Fatalf("expected missing SourceID error, got %v", err)
-	}
-}

internal/modules/chunk/generic/chunker.go

@@ -0,0 +1,241 @@
+package generic
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"math"
+	"strconv"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+const Key = "generic"
+
+const (
+	defaultMaxUnits     = 50
+	defaultOverlapUnits = 0
+)
+
+var _ contracts.Chunker = (*Chunker)(nil)
+
+type Chunker struct{}
+
+func New() *Chunker {
+	return &Chunker{}
+}
+
+func (c *Chunker) Key() string {
+	return Key
+}
+
+func (c *Chunker) Chunk(ctx context.Context, req contracts.ChunkRequest) (contracts.ChunkResult, error) {
+	if c == nil {
+		return contracts.ChunkResult{}, chunkerErrorf("chunker must not be nil")
+	}
+	if ctx == nil {
+		return contracts.ChunkResult{}, chunkerErrorf("context must not be nil")
+	}
+	if err := ctx.Err(); err != nil {
+		return contracts.ChunkResult{}, chunkerErrorf("context error before chunking: %w", err)
+	}
+	if req.Source == nil {
+		return contracts.ChunkResult{}, chunkerErrorf("source must not be nil")
+	}
+	if len(req.Source.Units) == 0 {
+		return contracts.ChunkResult{}, chunkerErrorf("source units must not be empty")
+	}
+	if err := source.ValidateDocument(req.Source); err != nil {
+		return contracts.ChunkResult{}, chunkerErrorf("validate source document: %w", err)
+	}
+
+	opts, err := chunkOptionsFrom(req.Options)
+	if err != nil {
+		return contracts.ChunkResult{}, err
+	}
+
+	step := opts.maxUnits - opts.overlapUnits
+	chunks := make([]contracts.SourceChunk, 0, (len(req.Source.Units)+step-1)/step)
+	for start := 0; start < len(req.Source.Units); start += step {
+		end := start + opts.maxUnits
+		if end > len(req.Source.Units) {
+			end = len(req.Source.Units)
+		}
+		units := cloneUnits(req.Source.Units[start:end])
+		chunks = append(chunks, contracts.SourceChunk{
+			ID:       fmt.Sprintf("chunk-%06d", len(chunks)+1),
+			SourceID: req.Source.ID,
+			Index:    len(chunks),
+			Units:    units,
+			Metadata: map[string]any{
+				"start_unit_id": units[0].ID,
+				"end_unit_id":   units[len(units)-1].ID,
+				"unit_count":    len(units),
+			},
+		})
+		if end == len(req.Source.Units) {
+			break
+		}
+	}
+
+	return contracts.ChunkResult{Chunks: chunks}, nil
+}
+
+func ModuleSpec() pipeline.ModuleSpec {
+	return pipeline.ModuleSpec{
+		Key:      Key,
+		Stage:    pipeline.StageChunk,
+		Provides: []string{"chunks"},
+	}
+}
+
+func Register(registry *pipeline.ChunkerRegistry) error {
+	return registry.RegisterWithSpec(ModuleSpec(), func() (contracts.Chunker, error) {
+		return New(), nil
+	})
+}
+
+type chunkOptions struct {
+	maxUnits     int
+	overlapUnits int
+}
+
+func chunkOptionsFrom(options map[string]any) (chunkOptions, error) {
+	opts := chunkOptions{
+		maxUnits:     defaultMaxUnits,
+		overlapUnits: defaultOverlapUnits,
+	}
+	var err error
+	if value, ok := options["max_units"]; ok {
+		opts.maxUnits, err = positiveIntOption("max_units", value)
+		if err != nil {
+			return chunkOptions{}, err
+		}
+	}
+	if value, ok := options["overlap_units"]; ok {
+		opts.overlapUnits, err = nonNegativeIntOption("overlap_units", value)
+		if err != nil {
+			return chunkOptions{}, err
+		}
+	}
+	if opts.overlapUnits >= opts.maxUnits {
+		return chunkOptions{}, chunkerErrorf("overlap_units must be less than max_units")
+	}
+	return opts, nil
+}
+
+func positiveIntOption(name string, value any) (int, error) {
+	got, err := intOption(name, value)
+	if err != nil {
+		return 0, err
+	}
+	if got <= 0 {
+		return 0, chunkerErrorf("%s must be positive", name)
+	}
+	return got, nil
+}
+
+func nonNegativeIntOption(name string, value any) (int, error) {
+	got, err := intOption(name, value)
+	if err != nil {
+		return 0, err
+	}
+	if got < 0 {
+		return 0, chunkerErrorf("%s must be non-negative", name)
+	}
+	return got, nil
+}
+
+func intOption(name string, value any) (int, error) {
+	switch typed := value.(type) {
+	case int:
+		return typed, nil
+	case int8:
+		return int(typed), nil
+	case int16:
+		return int(typed), nil
+	case int32:
+		return int(typed), nil
+	case int64:
+		if typed > maxInt() || typed < minInt() {
+			return 0, chunkerErrorf("%s is outside supported integer range", name)
+		}
+		return int(typed), nil
+	case uint:
+		if uint64(typed) > uint64(maxInt()) {
+			return 0, chunkerErrorf("%s is outside supported integer range", name)
+		}
+		return int(typed), nil
+	case uint8:
+		return int(typed), nil
+	case uint16:
+		return int(typed), nil
+	case uint32:
+		if uint64(typed) > uint64(maxInt()) {
+			return 0, chunkerErrorf("%s is outside supported integer range", name)
+		}
+		return int(typed), nil
+	case uint64:
+		if typed > uint64(maxInt()) {
+			return 0, chunkerErrorf("%s is outside supported integer range", name)
+		}
+		return int(typed), nil
+	case float64:
+		if typed != math.Trunc(typed) {
+			return 0, chunkerErrorf("%s must be an integer", name)
+		}
+		if typed > float64(maxInt()) || typed < float64(minInt()) {
+			return 0, chunkerErrorf("%s is outside supported integer range", name)
+		}
+		return int(typed), nil
+	case json.Number:
+		parsed, err := typed.Int64()
+		if err != nil {
+			return 0, chunkerErrorf("%s must be an integer", name)
+		}
+		if parsed > maxInt() || parsed < minInt() {
+			return 0, chunkerErrorf("%s is outside supported integer range", name)
+		}
+		return int(parsed), nil
+	default:
+		return 0, chunkerErrorf("%s must be an integer", name)
+	}
+}
+
+func maxInt() int64 {
+	return int64(1<<(strconv.IntSize-1) - 1)
+}
+
+func minInt() int64 {
+	return -maxInt() - 1
+}
+
+func cloneUnits(units []source.SourceUnit) []source.SourceUnit {
+	out := make([]source.SourceUnit, 0, len(units))
+	for _, unit := range units {
+		out = append(out, source.SourceUnit{
+			ID:       unit.ID,
+			Kind:     unit.Kind,
+			Text:     unit.Text,
+			Metadata: cloneMetadata(unit.Metadata),
+		})
+	}
+	return out
+}
+
+func cloneMetadata(metadata map[string]any) map[string]any {
+	if len(metadata) == 0 {
+		return nil
+	}
+	out := make(map[string]any, len(metadata))
+	for key, value := range metadata {
+		out[key] = value
+	}
+	return out
+}
+
+func chunkerErrorf(format string, args ...any) error {
+	return fmt.Errorf("generic chunker: "+format, args...)
+}

internal/modules/chunk/generic/chunker_test.go

@@ -0,0 +1,213 @@
+package generic
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"reflect"
+	"strings"
+	"testing"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+func TestModuleSpecAndRegister(t *testing.T) {
+	want := pipeline.ModuleSpec{
+		Key:      Key,
+		Stage:    pipeline.StageChunk,
+		Provides: []string{"chunks"},
+	}
+	if got := ModuleSpec(); !reflect.DeepEqual(got, want) {
+		t.Fatalf("ModuleSpec() = %#v, want %#v", got, want)
+	}
+
+	registry := pipeline.NewChunkerRegistry()
+	if err := Register(registry); err != nil {
+		t.Fatalf("Register() error = %v, want nil", err)
+	}
+	spec, ok := registry.Spec(Key)
+	if !ok {
+		t.Fatalf("Spec(%q) ok = false, want true", Key)
+	}
+	if !reflect.DeepEqual(spec, want) {
+		t.Fatalf("registered spec = %#v, want %#v", spec, want)
+	}
+	chunker, err := registry.Build(Key)
+	if err != nil {
+		t.Fatalf("Build(%q) error = %v, want nil", Key, err)
+	}
+	if chunker.Key() != Key {
+		t.Fatalf("Key() = %q, want %q", chunker.Key(), Key)
+	}
+}
+
+func TestChunkUsesDefaultsForSingleChunk(t *testing.T) {
+	result, err := New().Chunk(context.Background(), contracts.ChunkRequest{Source: testSource(3), Options: nil})
+	if err != nil {
+		t.Fatalf("Chunk() error = %v, want nil", err)
+	}
+
+	if got := chunkIDs(result.Chunks); !reflect.DeepEqual(got, []string{"chunk-000001"}) {
+		t.Fatalf("chunk IDs = %#v, want one stable ID", got)
+	}
+	chunk := result.Chunks[0]
+	if chunk.Index != 0 || chunk.SourceID != "source-1" {
+		t.Fatalf("chunk = %#v, want source and index fields", chunk)
+	}
+	if got := unitIDs(chunk.Units); !reflect.DeepEqual(got, []string{"u001", "u002", "u003"}) {
+		t.Fatalf("unit IDs = %#v, want all units", got)
+	}
+	if chunk.Metadata["start_unit_id"] != "u001" || chunk.Metadata["end_unit_id"] != "u003" || chunk.Metadata["unit_count"] != 3 {
+		t.Fatalf("metadata = %#v, want chunk bounds", chunk.Metadata)
+	}
+}
+
+func TestChunkExactBoundaries(t *testing.T) {
+	result, err := New().Chunk(context.Background(), contracts.ChunkRequest{
+		Source:  testSource(6),
+		Options: map[string]any{"max_units": 2},
+	})
+	if err != nil {
+		t.Fatalf("Chunk() error = %v, want nil", err)
+	}
+
+	if got := chunkIDs(result.Chunks); !reflect.DeepEqual(got, []string{"chunk-000001", "chunk-000002", "chunk-000003"}) {
+		t.Fatalf("chunk IDs = %#v, want stable IDs", got)
+	}
+	gotUnits := [][]string{unitIDs(result.Chunks[0].Units), unitIDs(result.Chunks[1].Units), unitIDs(result.Chunks[2].Units)}
+	wantUnits := [][]string{{"u001", "u002"}, {"u003", "u004"}, {"u005", "u006"}}
+	if !reflect.DeepEqual(gotUnits, wantUnits) {
+		t.Fatalf("chunk units = %#v, want %#v", gotUnits, wantUnits)
+	}
+}
+
+func TestChunkOverlap(t *testing.T) {
+	result, err := New().Chunk(context.Background(), contracts.ChunkRequest{
+		Source:  testSource(7),
+		Options: map[string]any{"max_units": 3, "overlap_units": 1},
+	})
+	if err != nil {
+		t.Fatalf("Chunk() error = %v, want nil", err)
+	}
+
+	gotUnits := make([][]string, 0, len(result.Chunks))
+	for _, chunk := range result.Chunks {
+		gotUnits = append(gotUnits, unitIDs(chunk.Units))
+	}
+	wantUnits := [][]string{{"u001", "u002", "u003"}, {"u003", "u004", "u005"}, {"u005", "u006", "u007"}}
+	if !reflect.DeepEqual(gotUnits, wantUnits) {
+		t.Fatalf("chunk units = %#v, want %#v", gotUnits, wantUnits)
+	}
+}
+
+func TestChunkRejectsInvalidOptions(t *testing.T) {
+	tests := []struct {
+		name    string
+		options map[string]any
+		want    string
+	}{
+		{name: "max wrong type", options: map[string]any{"max_units": "2"}, want: "max_units"},
+		{name: "max fractional", options: map[string]any{"max_units": 1.5}, want: "integer"},
+		{name: "max zero", options: map[string]any{"max_units": 0}, want: "positive"},
+		{name: "overlap negative", options: map[string]any{"overlap_units": -1}, want: "non-negative"},
+		{name: "overlap too large", options: map[string]any{"max_units": 2, "overlap_units": 2}, want: "less than"},
+		{name: "json number", options: map[string]any{"max_units": json.Number("bad")}, want: "integer"},
+	}
+
+	for _, test := range tests {
+		t.Run(test.name, func(t *testing.T) {
+			_, err := New().Chunk(context.Background(), contracts.ChunkRequest{
+				Source:  testSource(3),
+				Options: test.options,
+			})
+			if err == nil {
+				t.Fatal("Chunk() error = nil, want error")
+			}
+			if !strings.Contains(err.Error(), "generic chunker") || !strings.Contains(err.Error(), test.want) {
+				t.Fatalf("Chunk() error = %q, want module context and %q", err.Error(), test.want)
+			}
+		})
+	}
+}
+
+func TestChunkRejectsEmptySource(t *testing.T) {
+	doc := testSource(1)
+	doc.Units = nil
+
+	_, err := New().Chunk(context.Background(), contracts.ChunkRequest{Source: doc})
+	if err == nil {
+		t.Fatal("Chunk() error = nil, want empty source error")
+	}
+	if !strings.Contains(err.Error(), "generic chunker") || !strings.Contains(err.Error(), "units") {
+		t.Fatalf("Chunk() error = %q, want empty source context", err.Error())
+	}
+}
+
+func TestChunkDefensivelyCopiesUnits(t *testing.T) {
+	doc := testSource(2)
+
+	result, err := New().Chunk(context.Background(), contracts.ChunkRequest{
+		Source:  doc,
+		Options: map[string]any{"max_units": 1},
+	})
+	if err != nil {
+		t.Fatalf("Chunk() error = %v, want nil", err)
+	}
+	if len(result.Chunks) != 2 {
+		t.Fatalf("len(Chunks) = %d, want 2", len(result.Chunks))
+	}
+
+	doc.Units[0].ID = "changed"
+	doc.Units[0].Metadata["speaker"] = "changed"
+
+	if result.Chunks[0].Units[0].ID != "u001" {
+		t.Fatalf("chunk unit ID changed after source mutation: %#v", result.Chunks[0].Units[0])
+	}
+	if result.Chunks[0].Units[0].Metadata["speaker"] != "speaker-001" {
+		t.Fatalf("chunk unit metadata changed after source mutation: %#v", result.Chunks[0].Units[0].Metadata)
+	}
+}
+
+func testSource(count int) *source.SourceDocument {
+	units := make([]source.SourceUnit, 0, count)
+	for i := 1; i <= count; i++ {
+		id := "u" + zeroPad3(i)
+		units = append(units, source.SourceUnit{
+			ID:   id,
+			Kind: "unit",
+			Text: "Text for " + id,
+			Metadata: map[string]any{
+				"speaker": "speaker-" + zeroPad3(i),
+			},
+		})
+	}
+	return &source.SourceDocument{
+		ID:     "source-1",
+		Kind:   "document",
+		Format: "text/plain",
+		Digest: "sha256:source",
+		Units:  units,
+	}
+}
+
+func zeroPad3(value int) string {
+	return fmt.Sprintf("%03d", value)
+}
+
+func chunkIDs(chunks []contracts.SourceChunk) []string {
+	ids := make([]string, 0, len(chunks))
+	for _, chunk := range chunks {
+		ids = append(ids, chunk.ID)
+	}
+	return ids
+}
+
+func unitIDs(units []source.SourceUnit) []string {
+	ids := make([]string, 0, len(units))
+	for _, unit := range units {
+		ids = append(ids, unit.ID)
+	}
+	return ids
+}

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

@@ -0,0 +1,6 @@
+package spells
+
+import "embed"
+
+//go:embed assets/prompts/*.md assets/schemas/*.json
+var embeddedAssets embed.FS

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

@@ -11,6 +11,8 @@ import (
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
 	"gitea.maximumdirect.net/eric/notarius/internal/modules/input/seriatim"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/merge/appendorder"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/normalize/noop"
 )
 
 func TestPipelineConfigLoadsAndResolvesWithDNDSpellsExtractor(t *testing.T) {
@@ -188,7 +190,7 @@ func dndSpellsTestCatalog(t *testing.T, specs dndSpellsCatalogSpecs) pipeline.Mo
 		Stage:    pipeline.StageMerge,
 		Requires: []string{"dnd.spell_casts"},
 	}, func() (contracts.Merger, error) {
-		return pipeline.AppendOrderMerger{}, nil
+		return appendorder.New(), nil
 	}); err != nil {
 		t.Fatalf("register merger: %v", err)
 	}
@@ -196,7 +198,7 @@ func dndSpellsTestCatalog(t *testing.T, specs dndSpellsCatalogSpecs) pipeline.Mo
 		Key:   pipeline.DefaultNormalizeModule,
 		Stage: pipeline.StageNormalize,
 	}, func() (contracts.Normalizer, error) {
-		return pipeline.NoopNormalizer{}, nil
+		return noop.New(), nil
 	}); err != nil {
 		t.Fatalf("register normalizer: %v", err)
 	}

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

@@ -9,7 +9,6 @@ import (
 	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
 	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
-	"gitea.maximumdirect.net/eric/notarius/internal/framework/llm"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
 )
 
@@ -46,6 +45,23 @@ func (e *Extractor) SchemaVersion() string {
 	return SchemaVersion
 }
 
+func (e *Extractor) ManifestMetadata() map[string]any {
+	promptMetadata := spellsPromptBundle.Metadata()
+	metadata := map[string]any{
+		"prompt_id":            PromptID,
+		"prompt_version":       promptMetadata.PromptVersion,
+		"prompt_sha256":        promptMetadata.SHA256,
+		"response_schema_key":  string(ResponseSchemaKey),
+		"response_schema_id":   ResponseSchemaID,
+		"response_schema_name": ResponseSchemaName,
+	}
+	if schema, err := loadResponseSchema(); err == nil {
+		metadata["response_schema_version"] = schema.Version
+		metadata["response_schema_sha256"] = schema.SHA256
+	}
+	return metadata
+}
+
 func (e *Extractor) Validators() []contracts.Validator {
 	return []contracts.Validator{
 		ShapeValidator{},
@@ -80,9 +96,9 @@ func (e *Extractor) Extract(ctx context.Context, req contracts.ExtractionRequest
 	if err != nil {
 		return contracts.ExtractionResult{}, extractorErrorf("render prompt: %w", err)
 	}
-	schema, ok := llm.LookupResponseSchema(llm.DNDSpellsSchemaKey)
-	if !ok {
-		return contracts.ExtractionResult{}, extractorErrorf("lookup response schema %q", llm.DNDSpellsSchemaKey)
+	schema, err := loadResponseSchema()
+	if err != nil {
+		return contracts.ExtractionResult{}, extractorErrorf("load response schema %q: %w", ResponseSchemaKey, err)
 	}
 
 	var response extractionResponse

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

@@ -10,7 +10,6 @@ import (
 
 	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
-	"gitea.maximumdirect.net/eric/notarius/internal/framework/llm"
 )
 
 func TestExtractReturnsSpellCandidateFromStructuredOutput(t *testing.T) {
@@ -42,7 +41,10 @@ func TestExtractReturnsSpellCandidateFromStructuredOutput(t *testing.T) {
 	if req.StageName != Key {
 		t.Fatalf("StageName = %q, want %q", req.StageName, Key)
 	}
-	schema := llm.MustLookupResponseSchema(llm.DNDSpellsSchemaKey)
+	schema, err := loadResponseSchema()
+	if err != nil {
+		t.Fatalf("loadResponseSchema() error = %v, want nil", err)
+	}
 	if req.ResponseSchemaName != schema.Name {
 		t.Fatalf("ResponseSchemaName = %q, want %q", req.ResponseSchemaName, schema.Name)
 	}
@@ -90,6 +92,30 @@ func TestExtractReturnsSpellCandidateFromStructuredOutput(t *testing.T) {
 	}
 }
 
+func TestExtractorManifestMetadataIncludesPromptAndSchemaProvenance(t *testing.T) {
+	metadata := New().ManifestMetadata()
+
+	tests := map[string]string{
+		"prompt_id":               PromptID,
+		"prompt_version":          SchemaVersion,
+		"response_schema_key":     string(ResponseSchemaKey),
+		"response_schema_id":      ResponseSchemaID,
+		"response_schema_name":    ResponseSchemaName,
+		"response_schema_version": SchemaVersion,
+	}
+	for key, want := range tests {
+		if metadata[key] != want {
+			t.Fatalf("metadata[%q] = %#v, want %q", key, metadata[key], want)
+		}
+	}
+	for _, key := range []string{"prompt_sha256", "response_schema_sha256"} {
+		value, ok := metadata[key].(string)
+		if !ok || !strings.HasPrefix(value, "sha256:") {
+			t.Fatalf("metadata[%q] = %#v, want sha256 value", key, metadata[key])
+		}
+	}
+}
+
 func TestExtractReturnsNoCandidatesForEmptyResponse(t *testing.T) {
 	client := &fakeSpellsLLMClient{response: extractionResponse{SpellCasts: []spellCastResponse{}}}
 

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

@@ -28,6 +28,22 @@ type promptMetadata struct {
 	Value string
 }
 
+var spellsPromptBundle = mustLoadPromptBundle()
+
+func mustLoadPromptBundle() *prompt.Bundle {
+	bundle, err := prompt.LoadBundle(embeddedAssets, prompt.Definition{
+		PromptID:     PromptID,
+		Version:      SchemaVersion,
+		EmbeddedPath: "assets/prompts",
+		SystemPath:   "assets/prompts/system.md",
+		UserPath:     "assets/prompts/user.md",
+	})
+	if err != nil {
+		panic(err)
+	}
+	return bundle
+}
+
 func buildPromptData(req contracts.ExtractionRequest) (promptData, error) {
 	if req.Source == nil {
 		return promptData{}, fmt.Errorf("dnd spells prompt: source must not be nil")
@@ -58,7 +74,7 @@ func renderPrompt(req contracts.ExtractionRequest) (system string, user string,
 	if err != nil {
 		return "", "", prompt.Metadata{}, err
 	}
-	system, user, metadata, err = prompt.RenderUserSystem(prompt.DNDSpellsPromptID, data)
+	system, user, metadata, err = spellsPromptBundle.RenderUserSystem(data)
 	if err != nil {
 		return "", "", prompt.Metadata{}, fmt.Errorf("dnd spells prompt: %w", err)
 	}

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

@@ -92,8 +92,14 @@ func TestRenderPromptIncludesSourceContext(t *testing.T) {
 			t.Fatalf("user prompt = %q, want substring %q", user, want)
 		}
 	}
-	if metadata.PromptID != prompt.DNDSpellsPromptID {
-		t.Fatalf("metadata.PromptID = %q, want %q", metadata.PromptID, prompt.DNDSpellsPromptID)
+	if metadata.PromptID != PromptID {
+		t.Fatalf("metadata.PromptID = %q, want %q", metadata.PromptID, PromptID)
+	}
+	if metadata.PromptVersion != SchemaVersion {
+		t.Fatalf("metadata.PromptVersion = %q, want %q", metadata.PromptVersion, SchemaVersion)
+	}
+	if metadata.EmbeddedPath != "assets/prompts" {
+		t.Fatalf("metadata.EmbeddedPath = %q, want assets/prompts", metadata.EmbeddedPath)
 	}
 }
 

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

@@ -93,6 +93,15 @@ func TestRunnerProcessesSeriatimInputWithDNDSpellsExtractor(t *testing.T) {
 	if lane.ID != "spells" || lane.Extractor != Key {
 		t.Fatalf("manifest lane = %#v, want spells lane with dnd/spells extractor", lane)
 	}
+	extractorMetadata, ok := lane.Metadata["extractor"].(map[string]any)
+	if !ok {
+		t.Fatalf("manifest lane metadata = %#v, want extractor metadata", lane.Metadata)
+	}
+	if extractorMetadata["prompt_id"] != PromptID ||
+		extractorMetadata["response_schema_key"] != string(ResponseSchemaKey) ||
+		extractorMetadata["response_schema_name"] != ResponseSchemaName {
+		t.Fatalf("extractor metadata = %#v, want prompt/schema identifiers", extractorMetadata)
+	}
 	if output.ContentType != "application/json" {
 		t.Fatalf("ContentType = %q, want application/json", output.ContentType)
 	}

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

@@ -0,0 +1,20 @@
+package spells
+
+import "gitea.maximumdirect.net/eric/notarius/internal/framework/llm"
+
+const (
+	PromptID           = "dnd.spells"
+	ResponseSchemaKey  = llm.ResponseSchemaKey("dnd_spells")
+	ResponseSchemaID   = "notarius.dnd.spells"
+	ResponseSchemaName = "notarius_dnd_spells_v1"
+)
+
+func loadResponseSchema() (llm.ResponseSchema, error) {
+	return llm.LoadResponseSchema(embeddedAssets, llm.ResponseSchemaDefinition{
+		Key:       ResponseSchemaKey,
+		ID:        ResponseSchemaID,
+		Version:   SchemaVersion,
+		Name:      ResponseSchemaName,
+		AssetPath: "assets/schemas/dnd_spells.v1.json",
+	})
+}

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

@@ -4,23 +4,24 @@ import (
 	"encoding/json"
 	"strings"
 	"testing"
-
-	"gitea.maximumdirect.net/eric/notarius/internal/framework/llm"
 )
 
-func TestLookupResponseSchemaForSpells(t *testing.T) {
-	schema, ok := llm.LookupResponseSchema(llm.DNDSpellsSchemaKey)
-	if !ok {
-		t.Fatalf("LookupResponseSchema(%q) ok = false, want true", llm.DNDSpellsSchemaKey)
+func TestLoadResponseSchemaForSpells(t *testing.T) {
+	schema, err := loadResponseSchema()
+	if err != nil {
+		t.Fatalf("loadResponseSchema() error = %v, want nil", err)
 	}
-	if schema.ID != "notarius.dnd.spells" {
-		t.Fatalf("schema.ID = %q, want notarius.dnd.spells", schema.ID)
+	if schema.Key != ResponseSchemaKey {
+		t.Fatalf("schema.Key = %q, want %q", schema.Key, ResponseSchemaKey)
+	}
+	if schema.ID != ResponseSchemaID {
+		t.Fatalf("schema.ID = %q, want %q", schema.ID, ResponseSchemaID)
 	}
 	if schema.Version != SchemaVersion {
 		t.Fatalf("schema.Version = %q, want %q", schema.Version, SchemaVersion)
 	}
-	if schema.Name != "notarius_dnd_spells_v1" {
-		t.Fatalf("schema.Name = %q, want notarius_dnd_spells_v1", schema.Name)
+	if schema.Name != ResponseSchemaName {
+		t.Fatalf("schema.Name = %q, want %q", schema.Name, ResponseSchemaName)
 	}
 	if !strings.HasPrefix(schema.SHA256, "sha256:") {
 		t.Fatalf("schema.SHA256 = %q, want sha256 prefix", schema.SHA256)
@@ -30,12 +31,34 @@ func TestLookupResponseSchemaForSpells(t *testing.T) {
 	}
 }
 
+func TestResponseSchemaJSONIsMutationSafe(t *testing.T) {
+	first, err := loadResponseSchema()
+	if err != nil {
+		t.Fatalf("loadResponseSchema() error = %v, want nil", err)
+	}
+	first.JSONSchema[0] = '['
+
+	second, err := loadResponseSchema()
+	if err != nil {
+		t.Fatalf("loadResponseSchema() error = %v, want nil", err)
+	}
+	if !json.Valid(second.JSONSchema) {
+		t.Fatalf("schema JSON was mutated: %s", second.JSONSchema)
+	}
+	if len(second.JSONSchema) > 0 && second.JSONSchema[0] == '[' {
+		t.Fatalf("schema JSON did not use defensive copy")
+	}
+}
+
 func TestResponseSchemaDiagnosticsOmitRawSchema(t *testing.T) {
-	schema := llm.MustLookupResponseSchema(llm.DNDSpellsSchemaKey)
+	schema, err := loadResponseSchema()
+	if err != nil {
+		t.Fatalf("loadResponseSchema() error = %v, want nil", err)
+	}
 	diagnostics := schema.DiagnosticsMap()
 
-	if diagnostics["key"] != llm.DNDSpellsSchemaKey {
-		t.Fatalf("diagnostics[key] = %#v, want %q", diagnostics["key"], llm.DNDSpellsSchemaKey)
+	if diagnostics["key"] != ResponseSchemaKey {
+		t.Fatalf("diagnostics[key] = %#v, want %q", diagnostics["key"], ResponseSchemaKey)
 	}
 	for _, key := range []string{"id", "version", "name", "sha256"} {
 		if diagnostics[key] == "" {
@@ -45,4 +68,7 @@ func TestResponseSchemaDiagnosticsOmitRawSchema(t *testing.T) {
 	if _, ok := diagnostics["json_schema"]; ok {
 		t.Fatalf("diagnostics should omit raw schema content: %#v", diagnostics)
 	}
+	if _, ok := diagnostics["JSONSchema"]; ok {
+		t.Fatalf("diagnostics should omit raw schema content: %#v", diagnostics)
+	}
 }

internal/modules/input/seriatim/config_test.go

@@ -10,6 +10,8 @@ import (
 	"gitea.maximumdirect.net/eric/notarius/internal/core/config"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/merge/appendorder"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/normalize/noop"
 )
 
 func TestPipelineConfigLoadsAndResolvesWithSeriatimInput(t *testing.T) {
@@ -179,7 +181,7 @@ func mustRegisterExtractor(t *testing.T, registry *pipeline.ExtractorRegistry, s
 func mustRegisterMerger(t *testing.T, registry *pipeline.MergerRegistry, spec pipeline.ModuleSpec) {
 	t.Helper()
 	if err := registry.RegisterWithSpec(spec, func() (contracts.Merger, error) {
-		return pipeline.AppendOrderMerger{}, nil
+		return appendorder.New(), nil
 	}); err != nil {
 		t.Fatalf("register merger: %v", err)
 	}
@@ -188,7 +190,7 @@ func mustRegisterMerger(t *testing.T, registry *pipeline.MergerRegistry, spec pi
 func mustRegisterNormalizer(t *testing.T, registry *pipeline.NormalizerRegistry, spec pipeline.ModuleSpec) {
 	t.Helper()
 	if err := registry.RegisterWithSpec(spec, func() (contracts.Normalizer, error) {
-		return pipeline.NoopNormalizer{}, nil
+		return noop.New(), nil
 	}); err != nil {
 		t.Fatalf("register normalizer: %v", err)
 	}

internal/modules/input/seriatim/runner_test.go

@@ -12,6 +12,8 @@ import (
 	"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/merge/appendorder"
+	"gitea.maximumdirect.net/eric/notarius/internal/modules/normalize/noop"
 )
 
 func TestRunnerProcessesSeriatimInputWithFakeModules(t *testing.T) {
@@ -121,12 +123,12 @@ func seriatimRunnerRegistries(t *testing.T, extractor contracts.Extractor) pipel
 		t.Fatalf("register extractor: %v", err)
 	}
 	if err := mergers.Register(pipeline.DefaultMergeModule, func() (contracts.Merger, error) {
-		return pipeline.AppendOrderMerger{}, nil
+		return appendorder.New(), nil
 	}); err != nil {
 		t.Fatalf("register merger: %v", err)
 	}
 	if err := normalizers.Register(pipeline.DefaultNormalizeModule, func() (contracts.Normalizer, error) {
-		return pipeline.NoopNormalizer{}, nil
+		return noop.New(), nil
 	}); err != nil {
 		t.Fatalf("register normalizer: %v", err)
 	}

internal/modules/merge/appendorder/merger.go

@@ -0,0 +1,97 @@
+package appendorder
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+const Key = "appendorder"
+
+var _ contracts.Merger = (*Merger)(nil)
+
+type Merger struct{}
+
+func New() *Merger {
+	return &Merger{}
+}
+
+func (m *Merger) Key() string {
+	return Key
+}
+
+func (m *Merger) Merge(ctx context.Context, req contracts.MergeRequest) (contracts.MergeResult, error) {
+	if m == nil {
+		return contracts.MergeResult{}, mergerErrorf("merger must not be nil")
+	}
+	if ctx == nil {
+		return contracts.MergeResult{}, mergerErrorf("context must not be nil")
+	}
+	if err := ctx.Err(); err != nil {
+		return contracts.MergeResult{}, mergerErrorf("context error before merge: %w", err)
+	}
+
+	var candidates []artifacts.ArtifactCandidate
+	for _, chunkArtifacts := range req.ChunkArtifacts {
+		candidates = append(candidates, cloneCandidates(chunkArtifacts.Candidates)...)
+	}
+	return contracts.MergeResult{Candidates: candidates}, nil
+}
+
+func ModuleSpec() pipeline.ModuleSpec {
+	return pipeline.ModuleSpec{
+		Key:      Key,
+		Stage:    pipeline.StageMerge,
+		Provides: []string{"merged"},
+	}
+}
+
+func Register(registry *pipeline.MergerRegistry) error {
+	return registry.RegisterWithSpec(ModuleSpec(), func() (contracts.Merger, error) {
+		return New(), nil
+	})
+}
+
+func cloneCandidates(candidates []artifacts.ArtifactCandidate) []artifacts.ArtifactCandidate {
+	if len(candidates) == 0 {
+		return nil
+	}
+
+	out := make([]artifacts.ArtifactCandidate, 0, len(candidates))
+	for _, candidate := range candidates {
+		out = append(out, cloneCandidate(candidate))
+	}
+	return out
+}
+
+func cloneCandidate(candidate artifacts.ArtifactCandidate) artifacts.ArtifactCandidate {
+	return artifacts.ArtifactCandidate{
+		Index:         candidate.Index,
+		ExtractorKey:  candidate.ExtractorKey,
+		ArtifactType:  candidate.ArtifactType,
+		SchemaVersion: candidate.SchemaVersion,
+		Payload:       append(json.RawMessage(nil), candidate.Payload...),
+		SourceRefs:    append([]source.SourceRef(nil), candidate.SourceRefs...),
+		Metadata:      cloneMetadata(candidate.Metadata),
+	}
+}
+
+func cloneMetadata(metadata map[string]any) map[string]any {
+	if len(metadata) == 0 {
+		return nil
+	}
+	out := make(map[string]any, len(metadata))
+	for key, value := range metadata {
+		out[key] = value
+	}
+	return out
+}
+
+func mergerErrorf(format string, args ...any) error {
+	return fmt.Errorf("appendorder merger: "+format, args...)
+}

internal/modules/merge/appendorder/merger_test.go

@@ -0,0 +1,147 @@
+package appendorder
+
+import (
+	"context"
+	"encoding/json"
+	"reflect"
+	"testing"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+func TestModuleSpecAndRegister(t *testing.T) {
+	want := pipeline.ModuleSpec{
+		Key:      Key,
+		Stage:    pipeline.StageMerge,
+		Provides: []string{"merged"},
+	}
+	if got := ModuleSpec(); !reflect.DeepEqual(got, want) {
+		t.Fatalf("ModuleSpec() = %#v, want %#v", got, want)
+	}
+
+	registry := pipeline.NewMergerRegistry()
+	if err := Register(registry); err != nil {
+		t.Fatalf("Register() error = %v, want nil", err)
+	}
+	spec, ok := registry.Spec(Key)
+	if !ok {
+		t.Fatalf("Spec(%q) ok = false, want true", Key)
+	}
+	if !reflect.DeepEqual(spec, want) {
+		t.Fatalf("registered spec = %#v, want %#v", spec, want)
+	}
+}
+
+func TestMergePreservesChunkAndCandidateOrder(t *testing.T) {
+	result, err := New().Merge(context.Background(), contracts.MergeRequest{
+		ChunkArtifacts: []contracts.ChunkArtifacts{
+			{
+				Chunk:      sourceChunk(0),
+				Candidates: []artifacts.ArtifactCandidate{candidate(2, "first-b"), candidate(1, "first-a")},
+			},
+			{
+				Chunk:      sourceChunk(1),
+				Candidates: []artifacts.ArtifactCandidate{candidate(4, "second-b"), candidate(3, "second-a")},
+			},
+		},
+	})
+	if err != nil {
+		t.Fatalf("Merge() error = %v, want nil", err)
+	}
+
+	got := candidateNames(result.Candidates)
+	want := []string{"first-b", "first-a", "second-b", "second-a"}
+	if !reflect.DeepEqual(got, want) {
+		t.Fatalf("candidate order = %#v, want %#v", got, want)
+	}
+	if len(result.Warnings) != 0 {
+		t.Fatalf("Warnings = %#v, want none", result.Warnings)
+	}
+}
+
+func TestMergeDefensivelyCopiesCandidates(t *testing.T) {
+	input := []contracts.ChunkArtifacts{
+		{
+			Chunk:      sourceChunk(0),
+			Candidates: []artifacts.ArtifactCandidate{candidate(1, "original")},
+		},
+	}
+
+	result, err := New().Merge(context.Background(), contracts.MergeRequest{ChunkArtifacts: input})
+	if err != nil {
+		t.Fatalf("Merge() error = %v, want nil", err)
+	}
+	if len(result.Candidates) != 1 {
+		t.Fatalf("len(Candidates) = %d, want 1", len(result.Candidates))
+	}
+
+	input[0].Candidates[0].Index = 99
+	input[0].Candidates[0].Payload[0] = '['
+	input[0].Candidates[0].SourceRefs[0].StartUnitID = "changed"
+	input[0].Candidates[0].Metadata["name"] = "changed"
+
+	got := result.Candidates[0]
+	if got.Index != 1 {
+		t.Fatalf("Index = %d, want 1", got.Index)
+	}
+	if string(got.Payload) != `{"name":"original"}` {
+		t.Fatalf("Payload = %s, want original payload", got.Payload)
+	}
+	if got.SourceRefs[0].StartUnitID != "u1" {
+		t.Fatalf("SourceRefs = %#v, want original source ref", got.SourceRefs)
+	}
+	if got.Metadata["name"] != "original" {
+		t.Fatalf("Metadata = %#v, want original metadata", got.Metadata)
+	}
+}
+
+func TestMergeHandlesEmptyInput(t *testing.T) {
+	result, err := New().Merge(context.Background(), contracts.MergeRequest{})
+	if err != nil {
+		t.Fatalf("Merge() error = %v, want nil", err)
+	}
+	if len(result.Candidates) != 0 {
+		t.Fatalf("len(Candidates) = %d, want 0", len(result.Candidates))
+	}
+	if len(result.Warnings) != 0 {
+		t.Fatalf("Warnings = %#v, want none", result.Warnings)
+	}
+}
+
+func candidate(index int, name string) artifacts.ArtifactCandidate {
+	return artifacts.ArtifactCandidate{
+		Index:         index,
+		ExtractorKey:  "generic-extractor",
+		ArtifactType:  "generic-artifact",
+		SchemaVersion: "v1",
+		Payload:       json.RawMessage(`{"name":"` + name + `"}`),
+		SourceRefs: []source.SourceRef{
+			{SourceID: "source-1", StartUnitID: "u1", EndUnitID: "u1"},
+		},
+		Metadata: map[string]any{
+			"name": name,
+		},
+	}
+}
+
+func candidateNames(candidates []artifacts.ArtifactCandidate) []string {
+	names := make([]string, 0, len(candidates))
+	for _, candidate := range candidates {
+		names = append(names, candidate.Metadata["name"].(string))
+	}
+	return names
+}
+
+func sourceChunk(index int) contracts.SourceChunk {
+	return contracts.SourceChunk{
+		ID:       "chunk",
+		SourceID: "source-1",
+		Index:    index,
+		Units: []source.SourceUnit{
+			{ID: "u1", Kind: "unit", Text: "Source unit."},
+		},
+	}
+}

internal/modules/normalize/noop/normalizer.go

@@ -0,0 +1,89 @@
+package noop
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+const Key = "noop"
+
+var _ contracts.Normalizer = (*Normalizer)(nil)
+
+type Normalizer struct{}
+
+func New() *Normalizer {
+	return &Normalizer{}
+}
+
+func (n *Normalizer) Key() string {
+	return Key
+}
+
+func (n *Normalizer) Normalize(ctx context.Context, req contracts.NormalizeRequest) (contracts.NormalizeResult, error) {
+	if n == nil {
+		return contracts.NormalizeResult{}, normalizerErrorf("normalizer must not be nil")
+	}
+	if ctx == nil {
+		return contracts.NormalizeResult{}, normalizerErrorf("context must not be nil")
+	}
+	if err := ctx.Err(); err != nil {
+		return contracts.NormalizeResult{}, normalizerErrorf("context error before normalize: %w", err)
+	}
+	return contracts.NormalizeResult{Candidates: cloneCandidates(req.Candidates)}, nil
+}
+
+func ModuleSpec() pipeline.ModuleSpec {
+	return pipeline.ModuleSpec{
+		Key:      Key,
+		Stage:    pipeline.StageNormalize,
+		Requires: []string{"merged"},
+		Provides: []string{"normalized"},
+	}
+}
+
+func Register(registry *pipeline.NormalizerRegistry) error {
+	return registry.RegisterWithSpec(ModuleSpec(), func() (contracts.Normalizer, error) {
+		return New(), nil
+	})
+}
+
+func cloneCandidates(candidates []artifacts.ArtifactCandidate) []artifacts.ArtifactCandidate {
+	if len(candidates) == 0 {
+		return nil
+	}
+
+	out := make([]artifacts.ArtifactCandidate, 0, len(candidates))
+	for _, candidate := range candidates {
+		out = append(out, artifacts.ArtifactCandidate{
+			Index:         candidate.Index,
+			ExtractorKey:  candidate.ExtractorKey,
+			ArtifactType:  candidate.ArtifactType,
+			SchemaVersion: candidate.SchemaVersion,
+			Payload:       append(json.RawMessage(nil), candidate.Payload...),
+			SourceRefs:    append([]source.SourceRef(nil), candidate.SourceRefs...),
+			Metadata:      cloneMetadata(candidate.Metadata),
+		})
+	}
+	return out
+}
+
+func cloneMetadata(metadata map[string]any) map[string]any {
+	if len(metadata) == 0 {
+		return nil
+	}
+	out := make(map[string]any, len(metadata))
+	for key, value := range metadata {
+		out[key] = value
+	}
+	return out
+}
+
+func normalizerErrorf(format string, args ...any) error {
+	return fmt.Errorf("noop normalizer: "+format, args...)
+}

internal/modules/normalize/noop/normalizer_test.go

@@ -0,0 +1,133 @@
+package noop
+
+import (
+	"context"
+	"encoding/json"
+	"reflect"
+	"testing"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+func TestModuleSpecAndRegister(t *testing.T) {
+	want := pipeline.ModuleSpec{
+		Key:      Key,
+		Stage:    pipeline.StageNormalize,
+		Requires: []string{"merged"},
+		Provides: []string{"normalized"},
+	}
+	if got := ModuleSpec(); !reflect.DeepEqual(got, want) {
+		t.Fatalf("ModuleSpec() = %#v, want %#v", got, want)
+	}
+
+	registry := pipeline.NewNormalizerRegistry()
+	if err := Register(registry); err != nil {
+		t.Fatalf("Register() error = %v, want nil", err)
+	}
+	spec, ok := registry.Spec(Key)
+	if !ok {
+		t.Fatalf("Spec(%q) ok = false, want true", Key)
+	}
+	if !reflect.DeepEqual(spec, want) {
+		t.Fatalf("registered spec = %#v, want %#v", spec, want)
+	}
+}
+
+func TestNormalizePassesThroughOrderAndValues(t *testing.T) {
+	input := []artifacts.ArtifactCandidate{
+		candidate(3, "third"),
+		candidate(1, "first"),
+		candidate(2, "second"),
+	}
+
+	result, err := New().Normalize(context.Background(), contracts.NormalizeRequest{Candidates: input})
+	if err != nil {
+		t.Fatalf("Normalize() error = %v, want nil", err)
+	}
+	if len(result.Warnings) != 0 {
+		t.Fatalf("Warnings = %#v, want none", result.Warnings)
+	}
+
+	got := candidateNames(result.Candidates)
+	want := []string{"third", "first", "second"}
+	if !reflect.DeepEqual(got, want) {
+		t.Fatalf("candidate order = %#v, want %#v", got, want)
+	}
+	if !reflect.DeepEqual(result.Candidates[0].SourceRefs, input[0].SourceRefs) {
+		t.Fatalf("SourceRefs = %#v, want %#v", result.Candidates[0].SourceRefs, input[0].SourceRefs)
+	}
+	if !reflect.DeepEqual(result.Candidates[0].Metadata, input[0].Metadata) {
+		t.Fatalf("Metadata = %#v, want %#v", result.Candidates[0].Metadata, input[0].Metadata)
+	}
+}
+
+func TestNormalizeDefensivelyCopiesCandidates(t *testing.T) {
+	input := []artifacts.ArtifactCandidate{candidate(1, "original")}
+
+	result, err := New().Normalize(context.Background(), contracts.NormalizeRequest{Candidates: input})
+	if err != nil {
+		t.Fatalf("Normalize() error = %v, want nil", err)
+	}
+	if len(result.Candidates) != 1 {
+		t.Fatalf("len(Candidates) = %d, want 1", len(result.Candidates))
+	}
+
+	input[0].Index = 99
+	input[0].Payload[0] = '['
+	input[0].SourceRefs[0].EndUnitID = "changed"
+	input[0].Metadata["name"] = "changed"
+
+	got := result.Candidates[0]
+	if got.Index != 1 {
+		t.Fatalf("Index = %d, want 1", got.Index)
+	}
+	if string(got.Payload) != `{"name":"original"}` {
+		t.Fatalf("Payload = %s, want original payload", got.Payload)
+	}
+	if got.SourceRefs[0].EndUnitID != "u1" {
+		t.Fatalf("SourceRefs = %#v, want original source ref", got.SourceRefs)
+	}
+	if got.Metadata["name"] != "original" {
+		t.Fatalf("Metadata = %#v, want original metadata", got.Metadata)
+	}
+}
+
+func TestNormalizeHandlesEmptyInput(t *testing.T) {
+	result, err := New().Normalize(context.Background(), contracts.NormalizeRequest{})
+	if err != nil {
+		t.Fatalf("Normalize() error = %v, want nil", err)
+	}
+	if len(result.Candidates) != 0 {
+		t.Fatalf("len(Candidates) = %d, want 0", len(result.Candidates))
+	}
+	if len(result.Warnings) != 0 {
+		t.Fatalf("Warnings = %#v, want none", result.Warnings)
+	}
+}
+
+func candidate(index int, name string) artifacts.ArtifactCandidate {
+	return artifacts.ArtifactCandidate{
+		Index:         index,
+		ExtractorKey:  "generic-extractor",
+		ArtifactType:  "generic-artifact",
+		SchemaVersion: "v1",
+		Payload:       json.RawMessage(`{"name":"` + name + `"}`),
+		SourceRefs: []source.SourceRef{
+			{SourceID: "source-1", StartUnitID: "u1", EndUnitID: "u1"},
+		},
+		Metadata: map[string]any{
+			"name": name,
+		},
+	}
+}
+
+func candidateNames(candidates []artifacts.ArtifactCandidate) []string {
+	names := make([]string, 0, len(candidates))
+	for _, candidate := range candidates {
+		names = append(names, candidate.Metadata["name"].(string))
+	}
+	return names
+}

internal/modules/output/json/encoder.go

@@ -0,0 +1,253 @@
+package json
+
+import (
+	"context"
+	stdjson "encoding/json"
+	"fmt"
+	"regexp"
+	"sort"
+	"strings"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+const Key = "json"
+
+const contentTypeJSON = "application/json"
+
+var safeArtifactFileChar = regexp.MustCompile(`[^A-Za-z0-9._-]`)
+
+var _ contracts.OutputEncoder = (*Encoder)(nil)
+
+type Encoder struct{}
+
+func New() *Encoder {
+	return &Encoder{}
+}
+
+func (e *Encoder) Key() string {
+	return Key
+}
+
+func (e *Encoder) Encode(ctx context.Context, req contracts.OutputRequest) (contracts.OutputResult, error) {
+	if e == nil {
+		return contracts.OutputResult{}, encoderErrorf("encoder must not be nil")
+	}
+	if ctx == nil {
+		return contracts.OutputResult{}, encoderErrorf("context must not be nil")
+	}
+	if err := ctx.Err(); err != nil {
+		return contracts.OutputResult{}, encoderErrorf("context error before encoding: %w", err)
+	}
+
+	files, err := logicalFiles(req)
+	if err != nil {
+		return contracts.OutputResult{}, err
+	}
+	return contracts.OutputResult{Files: files}, nil
+}
+
+func ModuleSpec() pipeline.ModuleSpec {
+	return pipeline.ModuleSpec{
+		Key:      Key,
+		Stage:    pipeline.StageOutput,
+		Requires: []string{"normalized"},
+		Provides: []string{"encoded"},
+	}
+}
+
+func Register(registry *pipeline.OutputEncoderRegistry) error {
+	return registry.RegisterWithSpec(ModuleSpec(), func() (contracts.OutputEncoder, error) {
+		return New(), nil
+	})
+}
+
+type indexFile struct {
+	ManifestFile  string              `json:"manifest_file"`
+	ArtifactFiles []artifactFileIndex `json:"artifact_files"`
+	RejectedFile  string              `json:"rejected_file"`
+	WarningsFile  string              `json:"warnings_file"`
+}
+
+type artifactFileIndex struct {
+	ArtifactType string `json:"artifact_type"`
+	File         string `json:"file"`
+}
+
+type artifactFile struct {
+	ArtifactType string               `json:"artifact_type"`
+	Artifacts    []artifacts.Artifact `json:"artifacts"`
+}
+
+type rejectedFile struct {
+	Rejected []artifacts.RejectedArtifact `json:"rejected"`
+}
+
+type warningsFile struct {
+	Warnings []contracts.Warning `json:"warnings"`
+}
+
+func logicalFiles(req contracts.OutputRequest) ([]contracts.OutputFile, error) {
+	artifactsByType := make(map[string][]artifacts.Artifact)
+	for _, artifact := range req.Approved {
+		artifactsByType[artifact.ArtifactType] = append(artifactsByType[artifact.ArtifactType], cloneArtifact(artifact))
+	}
+
+	artifactTypes := make([]string, 0, len(artifactsByType))
+	for artifactType := range artifactsByType {
+		artifactTypes = append(artifactTypes, artifactType)
+	}
+	sort.Strings(artifactTypes)
+
+	artifactIndexes := make([]artifactFileIndex, 0, len(artifactTypes))
+	files := make([]contracts.OutputFile, 0, len(artifactTypes)+4)
+	manifestFile, err := jsonFile("manifest.json", req.Manifest)
+	if err != nil {
+		return nil, err
+	}
+	files = append(files, manifestFile)
+
+	usedArtifactFiles := make(map[string]string, len(artifactTypes))
+	for _, artifactType := range artifactTypes {
+		name, err := artifactFileName(artifactType)
+		if err != nil {
+			return nil, err
+		}
+		if existingType, ok := usedArtifactFiles[name]; ok {
+			return nil, encoderErrorf("artifact types %q and %q produce duplicate output file %q", existingType, artifactType, name)
+		}
+		usedArtifactFiles[name] = artifactType
+		artifactIndexes = append(artifactIndexes, artifactFileIndex{
+			ArtifactType: artifactType,
+			File:         name,
+		})
+		file, err := jsonFile(name, artifactFile{
+			ArtifactType: artifactType,
+			Artifacts:    artifactsByType[artifactType],
+		})
+		if err != nil {
+			return nil, err
+		}
+		files = append(files, file)
+	}
+
+	index := indexFile{
+		ManifestFile:  "manifest.json",
+		ArtifactFiles: artifactIndexes,
+		RejectedFile:  "rejected.json",
+		WarningsFile:  "warnings.json",
+	}
+	indexOutput, err := jsonFile("index.json", index)
+	if err != nil {
+		return nil, err
+	}
+	rejectedOutput, err := jsonFile("rejected.json", rejectedFile{Rejected: cloneRejected(req.Rejected)})
+	if err != nil {
+		return nil, err
+	}
+	warningsOutput, err := jsonFile("warnings.json", warningsFile{Warnings: cloneWarnings(req.Warnings)})
+	if err != nil {
+		return nil, err
+	}
+	files = append(files, indexOutput, rejectedOutput, warningsOutput)
+	sort.Slice(files, func(i, j int) bool {
+		return files[i].Name < files[j].Name
+	})
+	return files, nil
+}
+
+func jsonFile(name string, value any) (contracts.OutputFile, error) {
+	data, err := marshalPretty(value)
+	if err != nil {
+		return contracts.OutputFile{}, encoderErrorf("encode %s: %w", name, err)
+	}
+	return contracts.OutputFile{
+		Name:        name,
+		ContentType: contentTypeJSON,
+		Bytes:       data,
+	}, nil
+}
+
+func marshalPretty(value any) ([]byte, error) {
+	data, err := stdjson.MarshalIndent(value, "", "  ")
+	if err != nil {
+		return nil, err
+	}
+	return append(data, '\n'), nil
+}
+
+func artifactFileName(artifactType string) (string, error) {
+	sanitized := safeArtifactFileChar.ReplaceAllString(strings.TrimSpace(artifactType), "_")
+	for strings.Contains(sanitized, "..") {
+		sanitized = strings.ReplaceAll(sanitized, "..", "__")
+	}
+	sanitized = strings.Trim(sanitized, "._")
+	if sanitized == "" {
+		return "", encoderErrorf("artifact type %q cannot produce a safe file name", artifactType)
+	}
+	return "artifacts/" + sanitized + ".json", nil
+}
+
+func cloneArtifact(artifact artifacts.Artifact) artifacts.Artifact {
+	return artifacts.Artifact{
+		ExtractorKey:  artifact.ExtractorKey,
+		ArtifactType:  artifact.ArtifactType,
+		SchemaVersion: artifact.SchemaVersion,
+		Payload:       append(stdjson.RawMessage(nil), artifact.Payload...),
+		SourceRefs:    append([]source.SourceRef(nil), artifact.SourceRefs...),
+		Metadata:      cloneMetadata(artifact.Metadata),
+	}
+}
+
+func cloneRejected(rejected []artifacts.RejectedArtifact) []artifacts.RejectedArtifact {
+	if len(rejected) == 0 {
+		return []artifacts.RejectedArtifact{}
+	}
+	out := make([]artifacts.RejectedArtifact, 0, len(rejected))
+	for _, item := range rejected {
+		out = append(out, artifacts.RejectedArtifact{
+			Candidate:     cloneCandidate(item.Candidate),
+			ValidatorName: item.ValidatorName,
+			ReasonCode:    item.ReasonCode,
+			Message:       item.Message,
+		})
+	}
+	return out
+}
+
+func cloneCandidate(candidate artifacts.ArtifactCandidate) artifacts.ArtifactCandidate {
+	return artifacts.ArtifactCandidate{
+		Index:         candidate.Index,
+		ExtractorKey:  candidate.ExtractorKey,
+		ArtifactType:  candidate.ArtifactType,
+		SchemaVersion: candidate.SchemaVersion,
+		Payload:       append(stdjson.RawMessage(nil), candidate.Payload...),
+		SourceRefs:    append([]source.SourceRef(nil), candidate.SourceRefs...),
+		Metadata:      cloneMetadata(candidate.Metadata),
+	}
+}
+
+func cloneWarnings(warnings []contracts.Warning) []contracts.Warning {
+	if len(warnings) == 0 {
+		return []contracts.Warning{}
+	}
+	return append([]contracts.Warning(nil), warnings...)
+}
+
+func cloneMetadata(metadata map[string]any) map[string]any {
+	if len(metadata) == 0 {
+		return nil
+	}
+	out := make(map[string]any, len(metadata))
+	for key, value := range metadata {
+		out[key] = value
+	}
+	return out
+}
+
+func encoderErrorf(format string, args ...any) error {
+	return fmt.Errorf("json output encoder: "+format, args...)
+}

internal/modules/output/json/encoder_test.go

@@ -0,0 +1,316 @@
+package json
+
+import (
+	"context"
+	stdjson "encoding/json"
+	"reflect"
+	"strings"
+	"testing"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/artifacts"
+	"gitea.maximumdirect.net/eric/notarius/internal/core/source"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+func TestModuleSpecAndRegister(t *testing.T) {
+	want := pipeline.ModuleSpec{
+		Key:      Key,
+		Stage:    pipeline.StageOutput,
+		Requires: []string{"normalized"},
+		Provides: []string{"encoded"},
+	}
+	if got := ModuleSpec(); !reflect.DeepEqual(got, want) {
+		t.Fatalf("ModuleSpec() = %#v, want %#v", got, want)
+	}
+
+	registry := pipeline.NewOutputEncoderRegistry()
+	if err := Register(registry); err != nil {
+		t.Fatalf("Register() error = %v, want nil", err)
+	}
+	spec, ok := registry.Spec(Key)
+	if !ok {
+		t.Fatalf("Spec(%q) ok = false, want true", Key)
+	}
+	if !reflect.DeepEqual(spec, want) {
+		t.Fatalf("registered spec = %#v, want %#v", spec, want)
+	}
+}
+
+func TestEncodeReturnsLogicalFilesGroupedByArtifactType(t *testing.T) {
+	req := contracts.OutputRequest{
+		Manifest: artifacts.RunManifest{RunID: "run-1", PipelineID: "pipeline-1"},
+		Approved: []artifacts.Artifact{
+			artifact("dnd.spell-cast", "first"),
+			artifact("notes/item", "item"),
+			artifact("dnd.spell-cast", "second"),
+		},
+		Rejected: []artifacts.RejectedArtifact{
+			{
+				Candidate:     candidate("bad type", "bad"),
+				ValidatorName: "validator",
+				ReasonCode:    "invalid",
+				Message:       "not accepted",
+			},
+		},
+		Warnings: []contracts.Warning{{ReasonCode: "warning", Message: "check source"}},
+	}
+
+	result, err := New().Encode(context.Background(), req)
+	if err != nil {
+		t.Fatalf("Encode() error = %v, want nil", err)
+	}
+
+	wantNames := []string{
+		"artifacts/dnd.spell-cast.json",
+		"artifacts/notes_item.json",
+		"index.json",
+		"manifest.json",
+		"rejected.json",
+		"warnings.json",
+	}
+	if got := outputFileNames(result.Files); !reflect.DeepEqual(got, wantNames) {
+		t.Fatalf("file names = %#v, want %#v", got, wantNames)
+	}
+	for _, file := range result.Files {
+		if file.ContentType != contentTypeJSON {
+			t.Fatalf("%s ContentType = %q, want %q", file.Name, file.ContentType, contentTypeJSON)
+		}
+		if !strings.HasSuffix(string(file.Bytes), "\n") {
+			t.Fatalf("%s does not end with newline: %q", file.Name, string(file.Bytes))
+		}
+		if !stdjson.Valid(file.Bytes) {
+			t.Fatalf("%s has invalid JSON: %s", file.Name, file.Bytes)
+		}
+	}
+
+	spellFile := decodeObject(t, fileBytes(t, result.Files, "artifacts/dnd.spell-cast.json"))
+	if spellFile["artifact_type"] != "dnd.spell-cast" {
+		t.Fatalf("artifact_type = %#v, want dnd.spell-cast", spellFile["artifact_type"])
+	}
+	spells := spellFile["artifacts"].([]any)
+	if len(spells) != 2 {
+		t.Fatalf("len(spells) = %d, want 2", len(spells))
+	}
+	firstPayload := spells[0].(map[string]any)["payload"].(map[string]any)
+	secondPayload := spells[1].(map[string]any)["payload"].(map[string]any)
+	if firstPayload["name"] != "first" || secondPayload["name"] != "second" {
+		t.Fatalf("spell order payloads = %#v then %#v, want runner order", firstPayload, secondPayload)
+	}
+
+	index := decodeObject(t, fileBytes(t, result.Files, "index.json"))
+	artifactFiles := index["artifact_files"].([]any)
+	if len(artifactFiles) != 2 {
+		t.Fatalf("len(index artifact_files) = %d, want 2", len(artifactFiles))
+	}
+	firstIndex := artifactFiles[0].(map[string]any)
+	secondIndex := artifactFiles[1].(map[string]any)
+	if firstIndex["artifact_type"] != "dnd.spell-cast" || secondIndex["artifact_type"] != "notes/item" {
+		t.Fatalf("artifact_files = %#v, want sorted by artifact type", artifactFiles)
+	}
+}
+
+func TestEncodeIncludesRejectedAndWarningsWhenEmpty(t *testing.T) {
+	result, err := New().Encode(context.Background(), contracts.OutputRequest{
+		Manifest: artifacts.RunManifest{RunID: "run-1"},
+	})
+	if err != nil {
+		t.Fatalf("Encode() error = %v, want nil", err)
+	}
+
+	rejected := decodeObject(t, fileBytes(t, result.Files, "rejected.json"))
+	if got := rejected["rejected"].([]any); len(got) != 0 {
+		t.Fatalf("rejected = %#v, want empty array", got)
+	}
+	warnings := decodeObject(t, fileBytes(t, result.Files, "warnings.json"))
+	if got := warnings["warnings"].([]any); len(got) != 0 {
+		t.Fatalf("warnings = %#v, want empty array", got)
+	}
+}
+
+func TestEncodePrettyPrintsJSON(t *testing.T) {
+	result, err := New().Encode(context.Background(), contracts.OutputRequest{
+		Manifest: artifacts.RunManifest{RunID: "run-1"},
+	})
+	if err != nil {
+		t.Fatalf("Encode() error = %v, want nil", err)
+	}
+
+	manifest := string(fileBytes(t, result.Files, "manifest.json"))
+	if !strings.Contains(manifest, "\n  \"run_id\": \"run-1\"\n") {
+		t.Fatalf("manifest JSON = %q, want two-space indentation", manifest)
+	}
+}
+
+func TestEncodeRejectsArtifactTypeWithoutSafeFileName(t *testing.T) {
+	_, err := New().Encode(context.Background(), contracts.OutputRequest{
+		Approved: []artifacts.Artifact{artifact("///", "unsafe")},
+	})
+	if err == nil {
+		t.Fatal("Encode() error = nil, want unsafe artifact type error")
+	}
+	if !strings.Contains(err.Error(), "json output encoder") || !strings.Contains(err.Error(), "safe file name") {
+		t.Fatalf("Encode() error = %q, want safe file name context", err.Error())
+	}
+}
+
+func TestEncodeSanitizesParentPathSequences(t *testing.T) {
+	result, err := New().Encode(context.Background(), contracts.OutputRequest{
+		Approved: []artifacts.Artifact{artifact("dnd..spell.", "spell")},
+	})
+	if err != nil {
+		t.Fatalf("Encode() error = %v, want nil", err)
+	}
+
+	if got := outputFileNames(result.Files); !containsString(got, "artifacts/dnd__spell.json") {
+		t.Fatalf("file names = %#v, want sanitized artifact filename", got)
+	}
+}
+
+func TestEncodeRejectsSanitizedFilenameCollisions(t *testing.T) {
+	_, err := New().Encode(context.Background(), contracts.OutputRequest{
+		Approved: []artifacts.Artifact{
+			artifact("a/b", "slash"),
+			artifact("a?b", "question"),
+		},
+	})
+	if err == nil {
+		t.Fatal("Encode() error = nil, want duplicate file error")
+	}
+	if !strings.Contains(err.Error(), "duplicate output file") {
+		t.Fatalf("Encode() error = %q, want duplicate file context", err.Error())
+	}
+}
+
+func TestEncodeDoesNotMutateInputs(t *testing.T) {
+	req := contracts.OutputRequest{
+		Manifest: artifacts.RunManifest{RunID: "run-1"},
+		Approved: []artifacts.Artifact{
+			artifact("dnd.spell", "original"),
+		},
+		Rejected: []artifacts.RejectedArtifact{
+			{
+				Candidate:     candidate("bad", "rejected"),
+				ValidatorName: "validator",
+				ReasonCode:    "invalid",
+				Message:       "not accepted",
+			},
+		},
+		Warnings: []contracts.Warning{{ReasonCode: "warning", Message: "message"}},
+	}
+	before := mustMarshal(t, req)
+
+	result, err := New().Encode(context.Background(), req)
+	if err != nil {
+		t.Fatalf("Encode() error = %v, want nil", err)
+	}
+	after := mustMarshal(t, req)
+	if before != after {
+		t.Fatalf("request mutated:\nbefore: %s\nafter:  %s", before, after)
+	}
+
+	req.Approved[0].Payload[0] = '['
+	req.Approved[0].SourceRefs[0].StartUnitID = "changed"
+	req.Approved[0].Metadata["name"] = "changed"
+	req.Rejected[0].Candidate.Payload[0] = '['
+	req.Warnings[0].Message = "changed"
+
+	if !stdjson.Valid(fileBytes(t, result.Files, "artifacts/dnd.spell.json")) {
+		t.Fatal("artifact output changed after request mutation")
+	}
+	warnings := decodeObject(t, fileBytes(t, result.Files, "warnings.json"))
+	gotWarnings := warnings["warnings"].([]any)
+	if gotWarnings[0].(map[string]any)["message"] != "message" {
+		t.Fatalf("warnings output changed after request mutation: %#v", gotWarnings)
+	}
+}
+
+func TestArtifactFilesDoNotContainWarnings(t *testing.T) {
+	result, err := New().Encode(context.Background(), contracts.OutputRequest{
+		Approved: []artifacts.Artifact{artifact("dnd.spell", "spell")},
+		Warnings: []contracts.Warning{
+			{ReasonCode: "pipeline-warning", Message: "warning"},
+		},
+	})
+	if err != nil {
+		t.Fatalf("Encode() error = %v, want nil", err)
+	}
+
+	artifactFile := decodeObject(t, fileBytes(t, result.Files, "artifacts/dnd.spell.json"))
+	if _, ok := artifactFile["warnings"]; ok {
+		t.Fatalf("artifact file contains warnings: %#v", artifactFile)
+	}
+}
+
+func artifact(artifactType, name string) artifacts.Artifact {
+	return artifacts.Artifact{
+		ExtractorKey:  "extractor",
+		ArtifactType:  artifactType,
+		SchemaVersion: "v1",
+		Payload:       stdjson.RawMessage(`{"name":"` + name + `"}`),
+		SourceRefs: []source.SourceRef{
+			{SourceID: "source-1", StartUnitID: "u1", EndUnitID: "u1"},
+		},
+		Metadata: map[string]any{"name": name},
+	}
+}
+
+func candidate(artifactType, name string) artifacts.ArtifactCandidate {
+	return artifacts.ArtifactCandidate{
+		Index:         1,
+		ExtractorKey:  "extractor",
+		ArtifactType:  artifactType,
+		SchemaVersion: "v1",
+		Payload:       stdjson.RawMessage(`{"name":"` + name + `"}`),
+		SourceRefs: []source.SourceRef{
+			{SourceID: "source-1", StartUnitID: "u1", EndUnitID: "u1"},
+		},
+		Metadata: map[string]any{"name": name},
+	}
+}
+
+func outputFileNames(files []contracts.OutputFile) []string {
+	names := make([]string, 0, len(files))
+	for _, file := range files {
+		names = append(names, file.Name)
+	}
+	return names
+}
+
+func containsString(values []string, want string) bool {
+	for _, value := range values {
+		if value == want {
+			return true
+		}
+	}
+	return false
+}
+
+func fileBytes(t *testing.T, files []contracts.OutputFile, name string) []byte {
+	t.Helper()
+	for _, file := range files {
+		if file.Name == name {
+			return file.Bytes
+		}
+	}
+	t.Fatalf("file %q not found in %#v", name, outputFileNames(files))
+	return nil
+}
+
+func decodeObject(t *testing.T, data []byte) map[string]any {
+	t.Helper()
+	var got map[string]any
+	if err := stdjson.Unmarshal(data, &got); err != nil {
+		t.Fatalf("Unmarshal() error = %v, want nil\n%s", err, data)
+	}
+	return got
+}
+
+func mustMarshal(t *testing.T, value any) string {
+	t.Helper()
+	data, err := stdjson.Marshal(value)
+	if err != nil {
+		t.Fatalf("Marshal() error = %v, want nil", err)
+	}
+	return string(data)
+}