Complete Phase 16 default pipeline integration

docs/architecture.md

@@ -43,10 +43,19 @@ Implemented today:
 - Explicit runtime support for `--modules spoken_word` through the production runner path.
 
 Not implemented in CLI runtime path today:
-- End-to-end transcript polishing with the full default module sequence.
+- Python parity fixture suite and parity verification workflow.
+- Operational hardening tasks beyond current runtime/reporting/diagnostics behavior.
+- Rollout and Python retirement work.
 
 Current reality:
-- all production modules exist and are explicitly runnable by `--modules`, but default full-sequence integration remains a later phase.
+- all production modules exist and are wired into the default runtime path.
+- a normal `audita process` run without `--modules` now executes the full sequence:
+  - `glossary`
+  - `homophones`
+  - `glossary`
+  - `spoken_word`
+  - `grammar`
+- repeated glossary stages are deterministic and reported distinctly as `glossary_1` and `glossary_2`.
 
 Phase sequencing note:
 - Phase 9 LLM infrastructure is complete (structured client, scheduler, effective config resolution, diagnostics primitives);
@@ -56,7 +65,8 @@ Phase sequencing note:
 - Phase 13 glossary module and protected-term behavior are complete;
 - Phase 14 homophones module implementation and explicit runtime wiring are complete;
 - Phase 15 spoken-word module implementation and explicit runtime wiring are complete;
-- next recommended phase is Phase 16 (default full pipeline integration).
+- Phase 16 default full pipeline integration is complete;
+- next recommended phase is Phase 17 (Python parity fixture suite).
 
 ## Actual Go package layout
 
@@ -165,19 +175,20 @@ Current runtime flow (`internal/cli/run.go`):
 9. Write normalized transcript and normalization summary artifacts.
 10. Chunk normalized transcript and compute chunk summaries.
 11. Write chunking summary artifact.
-12. Execute runner modules sequentially when:
+12. Execute runner modules sequentially:
-    - `--modules` is explicitly provided (production grammar/glossary/homophones/spoken_word paths); or
+    - default run path uses configured default sequence (`glossary,homophones,glossary,spoken_word,grammar`);
-    - a test/injected module factory is provided.
+    - explicit `--modules` overrides the default sequence;
+    - test/injected module factory path remains available for deterministic runtime tests.
 13. Output working transcript to `--output` file or stdout.
-14. Build process report (`phase` currently set to `phase15-spoken-word-module`).
+14. Build process report (`phase` currently set to `phase16-default-pipeline-integration`).
 15. Optionally write `--report-json`; always write run-dir `report.json`.
 16. Apply work-dir retention.
 
 Important behavior details:
 - Glossary is validated and is used for explicit glossary/grammar/homophones/spoken_word module correction paths.
-- Default production CLI behavior remains deterministic normalization/chunking/reporting unless modules are explicitly selected with `--modules`.
+- Default production CLI behavior now executes the full production module sequence unless `--modules` override is supplied.
-- Explicit `--modules grammar`, `--modules glossary`, `--modules homophones`, and `--modules spoken_word` run production module paths with LLM-backed proposal generation and validator-chain execution.
+- Explicit `--modules grammar`, `--modules glossary`, `--modules homophones`, and `--modules spoken_word` continue to run production module paths with LLM-backed proposal generation and validator-chain execution.
-- Default runs (without explicit module selection) do not perform LLM calls.
+- Default runs (without explicit module selection) perform LLM calls through production module and validator paths.
 - Success path is generally quiet on stderr.
 - Source IDs are preserved into a canonical transcript before normalization; normalization then reassigns output IDs sequentially from `1`.
 
@@ -225,7 +236,7 @@ Implemented config surfaces include:
 - work-dir and retention mode
 
 Current caveat:
-- LLM/module-related settings are active for explicit grammar/glossary/homophones/spoken_word runs; the default non-explicit path remains deterministic.
+- LLM/module-related settings are active for default and explicit module-run paths.
 
 ## Implemented structured LLM infrastructure
 `internal/framework/contracts` now defines a typed structured-completion contract:
@@ -241,8 +252,8 @@ Current caveat:
 - API-key redaction in adapter-returned errors.
 
 Current runtime boundary:
-- the default CLI runtime path (without explicit module selection) still does not instantiate the full production module sequence.
+- the default CLI runtime path (without explicit module selection) instantiates the full production module sequence.
-- LLM calls are exercised in production when `--modules grammar`, `--modules glossary`, `--modules homophones`, or `--modules spoken_word` is explicitly requested and in tests when fake/injected clients are used.
+- LLM calls are exercised in production in both default full-pipeline runs and explicit `--modules` runs, and in tests when fake/injected clients are used.
 
 `internal/framework/llm` also provides:
 - a bounded `Scheduler` for controlled concurrent LLM calls with reliable permit release;

docs/rewrite-notes.md

@@ -71,7 +71,18 @@ Implemented:
 - Production spoken_word module package with Python-aligned prompt intent and guardrails.
 - Explicit `--modules spoken_word` runtime path through runner, shared proposal generation, validators, application, reporting, and diagnostics.
 - Focused multi-module runtime tests for already-implemented interoperability (for example `spoken_word,grammar`) without claiming full default-pipeline completion.
-- All production modules now exist (`glossary`, `homophones`, `spoken_word`, `grammar`), but default full-sequence integration remains Phase 16 work.
+- All production modules now exist (`glossary`, `homophones`, `spoken_word`, `grammar`) and are integrated into the default full-sequence runtime path.
+- Default runtime sequence is now active and ordered as:
+  - `glossary`
+  - `homophones`
+  - `glossary`
+  - `spoken_word`
+  - `grammar`
+- Repeated glossary stages resolve and report deterministically as `glossary_1` and `glossary_2`.
+- Full-pipeline module reports and run-level summaries aggregate applied/skipped/failed metadata across all module instances.
+- Mid-pipeline failure reporting preserves partial progress and failed-module metadata.
+- Full-pipeline diagnostics include proposal/validator prompt-response artifacts with redaction.
+- Skip-aware retention uses actual module skipped/rejected correction data.
 - Broad deterministic and CLI/subprocess test coverage for implemented phases through `go test ./...`.
 - Internal typed structured LLM contract (`StructuredLLMClient.CompleteStructured(ctx, req, out)`).
 - `internal/framework/llm` instructor-go-backed adapter with:
@@ -87,7 +98,9 @@ Implemented:
 - Generic JSON diagnostics primitives for LLM interactions (request metadata, request payload, response payload, optional error payload) with secret redaction.
 
 Not yet implemented in runtime pipeline:
-- End-to-end transcript polishing behavior with the full default module sequence.
+- Python parity fixture suite and parity verification workflow.
+- Operational hardening beyond current Phase 16 runtime/reporting/diagnostics scope.
+- Rollout/Python retirement work.
 
 ## Completed phases
 
@@ -192,7 +205,7 @@ Not implemented in Phase 7 (by design):
 - End-to-end transcript polishing.
 
 Current runtime behavior note:
-- Default user-facing CLI behavior remains deterministic normalization/chunking output unless test-only module injection is used during tests.
+- Default user-facing CLI behavior now executes the full production module sequence unless `--modules` explicitly overrides it.
 
 ## Phase 8: Runtime validator framework and deterministic validators
 Completed.
@@ -225,7 +238,7 @@ Not implemented in Phase 8 (by design):
 
 ## Remaining work plan
 
-Next recommended phase: **Phase 16 (default full pipeline integration)**.
+Next recommended phase: **Phase 17 (Python parity fixture suite)**.
 
 ## Phase 9: Structured LLM client and scheduler infrastructure
 
@@ -446,6 +459,8 @@ Not implemented in Phase 15 (by design):
 
 ## Phase 16: Default full pipeline integration
 
+Completed.
+
 ### Purpose
 
 Enable and harden the full default module sequence in the Go runtime path.
@@ -489,6 +504,27 @@ Running `audita process transcript.json --glossary glossary.yaml --output correc
 - CLI stdout/stderr behavior remains subprocess-safe.
 - `go test ./...` passes without requiring external LLM credentials.
 
+### Phase 16 completion status
+
+Implemented:
+- Normal `audita process` runs without `--modules` now execute the full sequence:
+  - `glossary`
+  - `homophones`
+  - `glossary`
+  - `spoken_word`
+  - `grammar`
+- Explicit `--modules` still overrides the default sequence.
+- Repeated glossary stages are deterministic (`glossary_1`, `glossary_2`) and reported distinctly.
+- Full-pipeline module reports aggregate applied changes, application skips, validator rejections, and failed-module metadata.
+- Full-pipeline diagnostics include prompt/response artifacts for module proposal generation and validator LLM interactions with secret redaction.
+- Mid-pipeline failure preserves partial module progress in reports and retains diagnostics + `error.log`.
+- Auto-retention keeps successful runs with actual skipped/rejected corrections and always retains failed runs.
+
+Intentionally deferred:
+- Phase 17 parity fixture suite.
+- Phase 18 operational hardening.
+- Phase 19 rollout/Python retirement work.
+
 ## Phase 17: Python parity fixture suite
 
 ### Purpose

internal/cli/run.go

@@ -6,6 +6,7 @@ import (
 	"flag"
 	"fmt"
 	"io"
+	"os"
 	"path/filepath"
 	"strings"
 	"time"
@@ -20,9 +21,29 @@ import (
 	"gitea.maximumdirect.net/eric/audita/internal/framework/contracts"
 	"gitea.maximumdirect.net/eric/audita/internal/framework/llm"
 	"gitea.maximumdirect.net/eric/audita/internal/framework/modules"
+	"gitea.maximumdirect.net/eric/audita/internal/framework/proposal_generation"
 	"gitea.maximumdirect.net/eric/audita/internal/framework/runner"
+	"gitea.maximumdirect.net/eric/audita/internal/framework/validators"
 )
 
+type noOpStructuredLLMClient struct{}
+
+func (c noOpStructuredLLMClient) CompleteStructured(ctx context.Context, req contracts.StructuredCompletionRequest, out any) (contracts.StructuredCompletionResponse, error) {
+	_ = ctx
+	_ = req
+	switch target := out.(type) {
+	case *validators.LLMValidationResponse:
+		*target = validators.LLMValidationResponse{Validations: []validators.LLMValidationDecision{}}
+	case *proposal_generation.StructuredCorrectionSet:
+		*target = proposal_generation.StructuredCorrectionSet{Corrections: nil}
+	}
+	return contracts.StructuredCompletionResponse{}, nil
+}
+
+func shouldUseNoOpLLMClientForTests() bool {
+	return strings.HasSuffix(filepath.Base(os.Args[0]), ".test")
+}
+
 type processInvocation struct {
 	TranscriptPath  string
 	GlossaryPath    string
@@ -131,7 +152,7 @@ var processRunner = func(inv processInvocation, stdout io.Writer) (*normalizatio
 	workingTranscript := normalizedTranscript
 	var runOutput *runner.RunOutput
 	moduleFactory := processModuleFactory
-	if moduleFactory == nil && inv.ExplicitModules {
+	if moduleFactory == nil {
 		moduleFactory = modules.NewFactory(modules.Dependencies{
 			Config:         &inv.Config,
 			Glossary:       glossary,
@@ -147,20 +168,28 @@ var processRunner = func(inv processInvocation, stdout io.Writer) (*normalizatio
 		if processModuleFactory == nil {
 			// Production runtime path: construct clients/schedulers from config.
 			if proposalLLMClient == nil {
-				primaryCfg := llm.ResolvePrimaryConfig(inv.Config)
+				if shouldUseNoOpLLMClientForTests() {
-				client, clientErr := llm.NewInstructorClient(primaryCfg.ToInstructorClientConfig(llm.ModeJSON, nil))
+					proposalLLMClient = noOpStructuredLLMClient{}
-				if clientErr != nil {
+				} else {
-					return fail("runner_setup", clientErr, nil)
+					primaryCfg := llm.ResolvePrimaryConfig(inv.Config)
+					client, clientErr := llm.NewInstructorClient(primaryCfg.ToInstructorClientConfig(llm.ModeJSON, nil))
+					if clientErr != nil {
+						return fail("runner_setup", clientErr, nil)
+					}
+					proposalLLMClient = client
 				}
-				proposalLLMClient = client
 			}
 			if validationLLMClient == nil {
-				validationCfg := llm.ResolveValidationConfig(inv.Config)
+				if shouldUseNoOpLLMClientForTests() {
-				client, clientErr := llm.NewInstructorClient(validationCfg.ToInstructorClientConfig(llm.ModeJSON, nil))
+					validationLLMClient = noOpStructuredLLMClient{}
-				if clientErr != nil {
+				} else {
-					return fail("runner_setup", clientErr, nil)
+					validationCfg := llm.ResolveValidationConfig(inv.Config)
+					client, clientErr := llm.NewInstructorClient(validationCfg.ToInstructorClientConfig(llm.ModeJSON, nil))
+					if clientErr != nil {
+						return fail("runner_setup", clientErr, nil)
+					}
+					validationLLMClient = client
 				}
-				validationLLMClient = client
 			}
 			if proposalScheduler == nil {
 				primaryCfg := llm.ResolvePrimaryConfig(inv.Config)
@@ -460,7 +489,7 @@ func extractErrorPhase(err error) (phase string, message string) {
 
 func buildProcessReport(status string, inv processInvocation, runDir *diagnostics.RunDirectory, startedAt, completedAt time.Time, errorMessage string, errorPhase string, normalizationSummary *normalization.NormalizationSummary, chunkingSummary *chunking.Summary, runOutput *runner.RunOutput) reporting.ProcessReport {
 	report := reporting.ProcessReport{
-		Phase:          "phase15-spoken-word-module",
+		Phase:          "phase16-default-pipeline-integration",
 		Status:         status,
 		Operation:      "process",
 		TranscriptPath: inv.TranscriptPath,

internal/cli/run_test.go

@@ -7,6 +7,7 @@ import (
 	"errors"
 	"os"
 	"path/filepath"
+	"reflect"
 	"strings"
 	"testing"
 
@@ -17,6 +18,7 @@ import (
 	"gitea.maximumdirect.net/eric/audita/internal/framework/modules"
 	"gitea.maximumdirect.net/eric/audita/internal/framework/proposal_generation"
 	"gitea.maximumdirect.net/eric/audita/internal/framework/proposals"
+	"gitea.maximumdirect.net/eric/audita/internal/framework/runner"
 	"gitea.maximumdirect.net/eric/audita/internal/framework/validators"
 )
 
@@ -616,8 +618,8 @@ func TestRunProcessReportJSONIncludesChunkingSummary(t *testing.T) {
 	if report.Chunking.MaxSectionTokens == 0 {
 		t.Errorf("expected max_section_tokens in report")
 	}
-	if report.Phase != "phase15-spoken-word-module" {
+	if report.Phase != "phase16-default-pipeline-integration" {
-		t.Errorf("expected phase 'phase15-spoken-word-module', got %q", report.Phase)
+		t.Errorf("expected phase 'phase16-default-pipeline-integration', got %q", report.Phase)
 	}
 }
 
@@ -1174,12 +1176,56 @@ func TestRunProcessExplicitGrammarMalformedLLMOutputFailsWithErrorLog(t *testing
 	}
 }
 
-func TestRunProcessDefaultBehaviorRemainsDeterministicWithoutExplicitModules(t *testing.T) {
+func TestRunProcessDefaultRunExecutesFullModuleSequence(t *testing.T) {
+	secret := "phase16-secret"
+	proposalClient := &fakeStructuredLLMClient{
+		proposalResponses: []proposal_generation.StructuredCorrectionSet{
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "gestures", CorrectedText: "Jesters", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "Jesters", CorrectedText: "jesters", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "jesters", CorrectedText: "JESTERS", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "uh", CorrectedText: "hmm", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "hello ,", CorrectedText: "Hello,", Confidence: 0.99},
+			}},
+		},
+	}
+	validationClient := &fakeStructuredLLMClient{
+		validationResponses: []validators.LLMValidationResponse{
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+		},
+	}
+	processProposalLLMClient = proposalClient
+	processValidationLLMClient = validationClient
+	t.Setenv("AUDITA_LLM_API_KEY", secret)
+	t.Setenv("AUDITA_VALIDATION_LLM_API_KEY", secret)
+	t.Cleanup(func() {
+		processProposalLLMClient = nil
+		processValidationLLMClient = nil
+	})
+
 	var stdout, stderr bytes.Buffer
+	workDir := t.TempDir()
 	reportPath := filepath.Join(t.TempDir(), "report.json")
 	outputPath := filepath.Join(t.TempDir(), "out.json")
 	transcriptPath := writeFile(t, "transcript.json", `[
-  {"id":1,"speaker":"Alice","start":0.0,"end":1.0,"text":"hello ,world"}
+  {"id":1,"speaker":"Alice","start":0.0,"end":1.0,"text":"hello , there were gestures uh"}
 ]`)
 
 	exitCode := Run([]string{
@@ -1187,13 +1233,285 @@ func TestRunProcessDefaultBehaviorRemainsDeterministicWithoutExplicitModules(t *
 		"--glossary", fixturePath("tiny_glossary.yaml"),
 		"--output", outputPath,
 		"--report-json", reportPath,
+		"--work-dir", workDir,
+		"--work-dir-retention", "always",
 	}, &stdout, &stderr)
 	if exitCode != 0 {
 		t.Fatalf("expected success, got %d stderr=%q", exitCode, stderr.String())
 	}
+	if stdout.Len() != 0 {
+		t.Fatalf("expected empty stdout with --output, got %q", stdout.String())
+	}
+
+	parsed, err := schema.ParseTranscriptJSON(readFile(t, outputPath))
+	if err != nil {
+		t.Fatalf("parse output: %v", err)
+	}
+	if parsed.Segments[0].Text != "Hello, there were JESTERS hmm" {
+		t.Fatalf("expected full default pipeline transcript mutation, got %q", parsed.Segments[0].Text)
+	}
+
 	report := readProcessReport(t, reportPath)
-	if report.ModulesSummary != nil || len(report.ModuleResults) != 0 {
+	if report.ModulesSummary == nil {
-		t.Fatalf("expected no module execution without explicit --modules, got summary=%+v results=%+v", report.ModulesSummary, report.ModuleResults)
+		t.Fatalf("expected module summary in report")
+	}
+	if report.ModulesSummary.ModuleCount != 5 {
+		t.Fatalf("expected 5 module instances, got %+v", report.ModulesSummary)
+	}
+	if report.ModulesSummary.TotalAppliedChanges != 5 {
+		t.Fatalf("expected 5 applied changes, got %+v", report.ModulesSummary)
+	}
+	if report.ModulesSummary.TotalSkippedChanges != 0 {
+		t.Fatalf("expected 0 skipped changes, got %+v", report.ModulesSummary)
+	}
+	if len(report.ModuleResults) != 5 {
+		t.Fatalf("expected 5 module results, got %+v", report.ModuleResults)
+	}
+
+	gotOrder := make([]string, 0, len(report.ModuleResults))
+	for _, mr := range report.ModuleResults {
+		gotOrder = append(gotOrder, mr.ModuleInstance)
+	}
+	wantOrder := []string{"glossary_1", "homophones", "glossary_2", "spoken_word", "grammar"}
+	if !reflect.DeepEqual(gotOrder, wantOrder) {
+		t.Fatalf("unexpected module instance order: got %v want %v", gotOrder, wantOrder)
+	}
+
+	wantProposalCallOrder := []string{
+		"glossary_1:proposal",
+		"homophones:proposal",
+		"glossary_2:proposal",
+		"spoken_word:proposal",
+		"grammar:proposal",
+	}
+	if !reflect.DeepEqual(proposalClient.calls, wantProposalCallOrder) {
+		t.Fatalf("unexpected proposal call order: got %v want %v", proposalClient.calls, wantProposalCallOrder)
+	}
+
+	runDir := onlyRunDir(t, workDir)
+	runReport := readProcessReport(t, filepath.Join(runDir, "report.json"))
+	if len(runReport.ModuleResults) != 5 {
+		t.Fatalf("expected 5 module results in run-dir report, got %+v", runReport.ModuleResults)
+	}
+	for _, instance := range wantOrder {
+		matches, globErr := filepath.Glob(filepath.Join(runDir, instance, "*response-payload.json"))
+		if globErr != nil {
+			t.Fatalf("glob diagnostics for %s: %v", instance, globErr)
+		}
+		if len(matches) == 0 {
+			t.Fatalf("expected diagnostics payload files for module %s", instance)
+		}
+		for _, path := range matches {
+			raw := string(readFile(t, path))
+			if strings.Contains(raw, secret) {
+				t.Fatalf("secret leaked in diagnostics %q: %s", path, raw)
+			}
+		}
+	}
+}
+
+func TestRunProcessDefaultFullPipelineFailurePreservesPartialProgressAndRetention(t *testing.T) {
+	proposalClient := &fakeStructuredLLMClient{
+		proposalResponses: []proposal_generation.StructuredCorrectionSet{
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "gestures", CorrectedText: "Jesters", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "Jesters", CorrectedText: "jesters", Confidence: 0.99},
+			}},
+		},
+	}
+	validationClient := &fakeStructuredLLMClient{
+		validationResponses: []validators.LLMValidationResponse{
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+		},
+	}
+	processProposalLLMClient = proposalClient
+	processValidationLLMClient = validationClient
+	t.Cleanup(func() {
+		processProposalLLMClient = nil
+		processValidationLLMClient = nil
+	})
+
+	var stdout, stderr bytes.Buffer
+	workDir := t.TempDir()
+	reportPath := filepath.Join(t.TempDir(), "report.json")
+	outputPath := filepath.Join(t.TempDir(), "out.json")
+	transcriptPath := writeFile(t, "transcript.json", `[
+  {"id":1,"speaker":"Alice","start":0.0,"end":1.0,"text":"there were gestures"}
+]`)
+
+	exitCode := Run([]string{
+		"process", transcriptPath,
+		"--glossary", fixturePath("tiny_glossary.yaml"),
+		"--output", outputPath,
+		"--report-json", reportPath,
+		"--work-dir", workDir,
+		"--work-dir-retention", "auto",
+	}, &stdout, &stderr)
+	if exitCode == 0 {
+		t.Fatalf("expected failure")
+	}
+	if stdout.Len() != 0 {
+		t.Fatalf("expected empty stdout on failure, got %q", stdout.String())
+	}
+	if !strings.Contains(stderr.String(), "runner_execution") {
+		t.Fatalf("expected runner_execution error, got %q", stderr.String())
+	}
+
+	report := readProcessReport(t, reportPath)
+	if report.Status != "failed" {
+		t.Fatalf("expected failed report status, got %q", report.Status)
+	}
+	if report.ErrorPhase != "runner_execution" {
+		t.Fatalf("expected runner_execution phase, got %q", report.ErrorPhase)
+	}
+	if report.ModulesSummary == nil || report.ModulesSummary.FailedModuleInstance != "glossary_2" {
+		t.Fatalf("expected failed module instance glossary_2, got %+v", report.ModulesSummary)
+	}
+	if len(report.ModuleResults) != 3 {
+		t.Fatalf("expected partial progress with 3 module results, got %+v", report.ModuleResults)
+	}
+	if report.ModuleResults[0].Status != runner.ModuleStatusSuccess || report.ModuleResults[1].Status != runner.ModuleStatusSuccess {
+		t.Fatalf("expected first two modules to succeed, got %+v", report.ModuleResults)
+	}
+	if report.ModuleResults[2].Status != runner.ModuleStatusFailed || report.ModuleResults[2].ModuleInstance != "glossary_2" {
+		t.Fatalf("expected glossary_2 failed result, got %+v", report.ModuleResults[2])
+	}
+	if report.ModuleResults[2].ErrorMessage == "" {
+		t.Fatalf("expected failed module error message")
+	}
+	if report.Diagnostics == nil || report.Diagnostics.DirectoryPath == "" || report.Diagnostics.ErrorLogPath == "" {
+		t.Fatalf("expected diagnostics and error log references on failure, got %+v", report.Diagnostics)
+	}
+	if _, err := os.Stat(report.Diagnostics.ErrorLogPath); err != nil {
+		t.Fatalf("expected error.log to exist: %v", err)
+	}
+	// Auto retention must keep failed runs.
+	runDir := onlyRunDir(t, workDir)
+	runDirReport := readProcessReport(t, filepath.Join(runDir, "report.json"))
+	if len(runDirReport.ModuleResults) != 3 {
+		t.Fatalf("expected partial module results in run-dir report, got %+v", runDirReport.ModuleResults)
+	}
+}
+
+func TestRunProcessDefaultFullPipelineAggregatesSkipsAndAutoRetentionKeepsRunDir(t *testing.T) {
+	secret := "phase16-retention-secret"
+	proposalClient := &fakeStructuredLLMClient{
+		proposalResponses: []proposal_generation.StructuredCorrectionSet{
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "gestures", CorrectedText: "Jesters", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "Jesters", CorrectedText: "jesters", Confidence: 0.99},
+				{TargetSegmentID: 1, OriginalText: "Jesters", CorrectedText: "JESTERX", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "jesters", CorrectedText: "JESTERS", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "uh", CorrectedText: "hmm", Confidence: 0.99},
+			}},
+			{Corrections: []proposal_generation.StructuredCorrectionProposal{
+				{TargetSegmentID: 1, OriginalText: "hello ,", CorrectedText: "Hello,", Confidence: 0.99},
+			}},
+		},
+	}
+	validationClient := &fakeStructuredLLMClient{
+		validationResponses: []validators.LLMValidationResponse{
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}, {CorrectionIndex: 1, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}, {CorrectionIndex: 1, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: false, Confidence: 0.99, Reason: "reject cleanup"}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: secret}}},
+			{Validations: []validators.LLMValidationDecision{{CorrectionIndex: 0, Approved: true, Confidence: 0.99, Reason: "ok"}}},
+		},
+	}
+	processProposalLLMClient = proposalClient
+	processValidationLLMClient = validationClient
+	t.Setenv("AUDITA_LLM_API_KEY", secret)
+	t.Setenv("AUDITA_VALIDATION_LLM_API_KEY", secret)
+	t.Cleanup(func() {
+		processProposalLLMClient = nil
+		processValidationLLMClient = nil
+	})
+
+	var stdout, stderr bytes.Buffer
+	workDir := t.TempDir()
+	reportPath := filepath.Join(t.TempDir(), "report.json")
+	outputPath := filepath.Join(t.TempDir(), "out.json")
+	transcriptPath := writeFile(t, "transcript.json", `[
+  {"id":1,"speaker":"Alice","start":0.0,"end":1.0,"text":"hello , there were gestures uh"}
+]`)
+
+	exitCode := Run([]string{
+		"process", transcriptPath,
+		"--glossary", fixturePath("tiny_glossary.yaml"),
+		"--output", outputPath,
+		"--report-json", reportPath,
+		"--work-dir", workDir,
+		"--work-dir-retention", "auto",
+	}, &stdout, &stderr)
+	if exitCode != 0 {
+		t.Fatalf("expected success, got %d stderr=%q", exitCode, stderr.String())
+	}
+	if stdout.Len() != 0 {
+		t.Fatalf("expected empty stdout with --output, got %q", stdout.String())
+	}
+
+	report := readProcessReport(t, reportPath)
+	if report.Status != "success" {
+		t.Fatalf("expected success report status, got %q", report.Status)
+	}
+	if report.ModulesSummary == nil || report.ModulesSummary.ModuleCount != 5 {
+		t.Fatalf("expected 5-module summary, got %+v", report.ModulesSummary)
+	}
+	if report.ModulesSummary.TotalAppliedChanges != 4 {
+		t.Fatalf("expected 4 applied changes, got %+v", report.ModulesSummary)
+	}
+	if report.ModulesSummary.TotalSkippedChanges != 2 {
+		t.Fatalf("expected 2 skipped changes (1 app skip + 1 validator rejection), got %+v", report.ModulesSummary)
+	}
+	if len(report.ModuleResults) != 5 {
+		t.Fatalf("expected 5 module reports, got %+v", report.ModuleResults)
+	}
+	// Homophones contributes an application-level skip.
+	if len(report.ModuleResults[1].SkippedChanges) != 1 {
+		t.Fatalf("expected one homophones application skip, got %+v", report.ModuleResults[1].SkippedChanges)
+	}
+	// Spoken_word contributes one validator rejection.
+	if len(report.ModuleResults[3].ValidatorRejected) != 1 {
+		t.Fatalf("expected one spoken_word validator rejection, got %+v", report.ModuleResults[3].ValidatorRejected)
+	}
+	if report.ModuleResults[3].ValidatorRejected[0].ReasonCode == string(report.ModuleResults[1].SkippedChanges[0].SkipReason) {
+		t.Fatalf("validator rejection and application skip should remain distinct")
+	}
+
+	// Auto retention must keep successful runs with skipped/rejected corrections.
+	runDir := onlyRunDir(t, workDir)
+	runDirReport := readProcessReport(t, filepath.Join(runDir, "report.json"))
+	if runDirReport.ModulesSummary == nil || runDirReport.ModulesSummary.TotalSkippedChanges != 2 {
+		t.Fatalf("expected skipped totals in retained run-dir report, got %+v", runDirReport.ModulesSummary)
+	}
+	diagFiles, globErr := filepath.Glob(filepath.Join(runDir, "*", "*response-payload.json"))
+	if globErr != nil {
+		t.Fatalf("glob diagnostics payloads: %v", globErr)
+	}
+	if len(diagFiles) == 0 {
+		t.Fatalf("expected diagnostics payload artifacts")
+	}
+	for _, f := range diagFiles {
+		raw := string(readFile(t, f))
+		if strings.Contains(raw, secret) {
+			t.Fatalf("secret leaked in diagnostics %q: %s", f, raw)
+		}
 	}
 }