Add workspace configuration support

internal/cli/run.go

@@ -156,10 +156,16 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 	}
 
 	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
+	runID := fmt.Sprintf("run-%d", startedAt.UnixNano())
+	var runDir *diagnostics.RunDirectory
+	if cfg.DiagnosticsEnabled() {
+		var err error
+		runDir, err = diagnostics.NewRunDirectory(cfg.Diagnostics.WorkDir, cfg.Diagnostics.Retention)
+		if err != nil {
+			fmt.Fprintf(stderr, "notarius: %v\n", err)
+			return 1
+		}
+		runID = runDir.RunID()
 	}
 	invocation := diagnostics.InvocationMetadata{
 		Operation:    "run",
@@ -168,10 +174,10 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 		ConfigPath:   loadedConfigPath,
 		ConfigSource: configSource(*configPath),
 		OnlyLanes:    append([]string(nil), only...),
-		RunID:        runDir.RunID(),
+		RunID:        runID,
 		StartedAt:    startedAt,
 	}
-	if err := runDir.WriteInvocationMetadata(invocation); err != nil {
+	if err := writeDiagnostics(runDir, func() error { return runDir.WriteInvocationMetadata(invocation) }); err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics invocation metadata: %w", err))
 	}
 
@@ -211,16 +217,18 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 	}
 	effective.ResolvedPipeline = materialized
 	invocation.PipelineDigest = effective.ResolvedPipeline.Digest
-	if err := runDir.WriteInvocationMetadata(invocation); err != nil {
+	if err := writeDiagnostics(runDir, func() error { return 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 {
+	if err := writeDiagnostics(runDir, func() error { return 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 {
+	if err := writeDiagnostics(runDir, func() error { return runDir.WriteResolvedPipeline(effective.ResolvedPipeline) }); err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics resolved pipeline: %w", err))
 	}
-	if err := runDir.WriteResolvedReferences(pipeline.ReferenceProvenance(effective.ResolvedPipeline)); err != nil {
+	if err := writeDiagnostics(runDir, func() error {
+		return runDir.WriteResolvedReferences(pipeline.ReferenceProvenance(effective.ResolvedPipeline))
+	}); err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("write diagnostics resolved references: %w", err))
 	}
 
@@ -250,45 +258,49 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 		RawInput:    rawInput,
 		LLMClient:   llmClient,
 		SessionID:   strings.TrimSpace(sessionID.value),
-		RunID:       runDir.RunID(),
+		RunID:       runID,
 		StartedAt:   startedAt,
 		LLMProfiles: llmProfiles,
 		Metadata:    runMetadata(*outputDir, *diagnosticsDir),
 		Warnings:    referenceWarnings,
 	})
 	if err != nil {
-		if output.Manifest.PipelineID != "" {
+		if output.Manifest.PipelineID != "" && runDir != nil {
 			_ = 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 := runDir.WriteRunManifest(output.Manifest); err != nil {
+	runOutputDir := filepath.Join(outputRoot(*outputDir), runID)
+	if err := writeDiagnostics(runDir, func() error { return 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 {
+	if err := writeDiagnostics(runDir, func() error { return 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(),
-		OutputCount:      len(output.NormalizeOutputs),
-		RejectedCount:    len(output.Rejected),
-		WarningCount:     len(output.Warnings),
-		ValidationStatus: output.Manifest.ValidationStatus,
+	if err := writeDiagnostics(runDir, func() error {
+		return runDir.WriteRunReport(runReport{
+			RunID:            runDir.RunID(),
+			PipelineID:       effective.PipelineID,
+			OutputPath:       runOutputDir,
+			DiagnosticsPath:  runDir.Path(),
+			OutputCount:      len(output.NormalizeOutputs),
+			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 := writeOutputFiles(runOutputDir, output.OutputFiles); err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
 	}
-	if err := runDir.ApplyRetention(diagnostics.RetentionDecisionInput{
-		RetentionMode: cfg.Diagnostics.Retention,
-		RunSucceeded:  true,
-		HasWarnings:   len(output.Warnings) > 0,
+	if err := writeDiagnostics(runDir, func() error {
+		return 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))
 	}
@@ -327,6 +339,13 @@ func failPipelineCommand(stderr io.Writer, runDir *diagnostics.RunDirectory, ret
 	return 1
 }
 
+func writeDiagnostics(runDir *diagnostics.RunDirectory, write func() error) error {
+	if runDir == nil {
+		return nil
+	}
+	return write()
+}
+
 func configSource(configPath string) string {
 	if strings.TrimSpace(configPath) != "" {
 		return "flag"

internal/cli/run_test.go

@@ -2148,6 +2148,29 @@ func TestRunPipelineWritesDiagnosticsArtifactsOnSuccess(t *testing.T) {
 	}
 }
 
+func TestRunPipelineSkipsDiagnosticsWhenWorkspaceDiagnosticsDisabled(t *testing.T) {
+	workspaceDir := filepath.Join(t.TempDir(), "workspace")
+	outputDir := t.TempDir()
+	configPath := writeTestConfig(t, mvpConfigYAMLWithWorkspaceDiagnosticsDisabled("dnd-session", workspaceDir))
+	inputPath := writeSeriatimInput(t)
+	var stdout bytes.Buffer
+	var stderr bytes.Buffer
+
+	code := RunWithOptions([]string{"run", "dnd-session", "--config", configPath, "--input", inputPath, "--output-dir", outputDir}, &stdout, &stderr, Options{
+		LLMClientFactory: fakeLLMFactory(newFakeRunLLMClient(false), nil),
+	})
+
+	if code != 0 {
+		t.Fatalf("RunWithOptions() code = %d, stderr=%q", code, stderr.String())
+	}
+	if _, err := os.Stat(filepath.Join(workspaceDir, "diagnostics")); !os.IsNotExist(err) {
+		t.Fatalf("workspace diagnostics dir stat err = %v, want not exist", err)
+	}
+	if entries := childDirs(t, outputDir); len(entries) != 1 {
+		t.Fatalf("output run dirs = %v, want one run dir", entries)
+	}
+}
+
 func TestRunPipelineWritesErrorLogAfterDiagnosticsCreation(t *testing.T) {
 	diagnosticsDir := t.TempDir()
 	configPath := writeTestConfig(t, mvpConfigYAMLWithDiagnostics("dnd-session", diagnosticsDir, "always"))
@@ -2732,6 +2755,21 @@ pipelines:
 `
 }
 
+func mvpConfigYAMLWithWorkspaceDiagnosticsDisabled(pipelineID, workspaceDir string) string {
+	return `version: 2
+workspace:
+  directory: ` + workspaceDir + `
+  diagnostics:
+    enabled: false
+pipelines:
+  ` + pipelineID + `:
+    input: seriatim
+    artifacts:
+      spells:
+        extract: dnd/spells
+`
+}
+
 func writeSeriatimInput(t *testing.T) string {
 	t.Helper()
 	return writeFile(t, "source.json", `{

internal/core/config/config.go

@@ -1,6 +1,9 @@
 package config
 
 import (
+	"path/filepath"
+	"strings"
+
 	"gitea.maximumdirect.net/eric/notarius/internal/core/diagnostics"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
 )
@@ -12,6 +15,7 @@ type Config struct {
 	Pipelines   map[string]pipeline.PipelineProfile `json:"pipelines"`
 	Concurrency ConcurrencyConfig                   `json:"concurrency"`
 	Diagnostics DiagnosticsConfig                   `json:"diagnostics"`
+	Workspace   WorkspaceConfig                     `json:"workspace"`
 }
 
 type ScriptoriumConfig struct {
@@ -28,6 +32,28 @@ type DiagnosticsConfig struct {
 	Retention diagnostics.RetentionMode `json:"retention"`
 }
 
+type WorkspaceConfig struct {
+	Directory   string                     `json:"directory,omitempty"`
+	Diagnostics WorkspaceDiagnosticsConfig `json:"diagnostics"`
+	Resume      WorkspaceResumeConfig      `json:"resume"`
+	Debug       WorkspaceDebugConfig       `json:"debug"`
+}
+
+type WorkspaceDiagnosticsConfig struct {
+	Enabled      bool                      `json:"enabled"`
+	Retention    diagnostics.RetentionMode `json:"retention,omitempty"`
+	enabledSet   bool
+	retentionSet bool
+}
+
+type WorkspaceResumeConfig struct {
+	Enabled bool `json:"enabled"`
+}
+
+type WorkspaceDebugConfig struct {
+	Enabled bool `json:"enabled"`
+}
+
 func Default() Config {
 	return Config{
 		Pipelines: map[string]pipeline.PipelineProfile{},
@@ -38,9 +64,41 @@ func Default() Config {
 			WorkDir:   "/tmp/notarius",
 			Retention: diagnostics.RetentionAuto,
 		},
+		Workspace: WorkspaceConfig{
+			Diagnostics: WorkspaceDiagnosticsConfig{
+				Enabled: true,
+			},
+		},
 	}
 }
 
+func (c *Config) RecomputeEffectiveDiagnostics() {
+	if c == nil {
+		return
+	}
+	if dir := c.workspaceDirectory(); dir != "" {
+		c.Diagnostics.WorkDir = filepath.Join(dir, "diagnostics")
+	}
+	if c.Workspace.Diagnostics.retentionSet {
+		c.Diagnostics.Retention = c.Workspace.Diagnostics.Retention
+	}
+}
+
+func (c Config) DiagnosticsEnabled() bool {
+	if !c.Workspace.Diagnostics.enabledSet {
+		return true
+	}
+	return c.Workspace.Diagnostics.Enabled
+}
+
+func (c Config) workspaceDirectory() string {
+	dir := strings.TrimSpace(c.Workspace.Directory)
+	if dir == "" {
+		return ""
+	}
+	return filepath.Clean(dir)
+}
+
 func cloneConfig(in Config) Config {
 	out := in
 	out.Pipelines = make(map[string]pipeline.PipelineProfile, len(in.Pipelines))

internal/core/config/config_test.go

@@ -24,6 +24,21 @@ func TestDefaultValues(t *testing.T) {
 	if cfg.Diagnostics.Retention != diagnostics.RetentionAuto {
 		t.Fatalf("unexpected diagnostics retention: %q", cfg.Diagnostics.Retention)
 	}
+	if cfg.Workspace.Directory != "" {
+		t.Fatalf("unexpected workspace directory: %q", cfg.Workspace.Directory)
+	}
+	if !cfg.Workspace.Diagnostics.Enabled || !cfg.DiagnosticsEnabled() {
+		t.Fatalf("expected workspace diagnostics enabled by default: %+v", cfg.Workspace.Diagnostics)
+	}
+	if cfg.Workspace.Diagnostics.Retention != "" {
+		t.Fatalf("unexpected workspace diagnostics retention: %q", cfg.Workspace.Diagnostics.Retention)
+	}
+	if cfg.Workspace.Resume.Enabled {
+		t.Fatalf("workspace resume should be disabled by default")
+	}
+	if cfg.Workspace.Debug.Enabled {
+		t.Fatalf("workspace debug should be disabled by default")
+	}
 }
 
 func TestApplyFileConfigMergesWithDefaults(t *testing.T) {

internal/core/config/env.go

@@ -42,6 +42,36 @@ func (c *Config) applyEnvOverridesWithLookup(lookup func(string) (string, bool))
 	if raw, ok := lookup("NOTARIUS_DIAGNOSTICS_RETENTION"); ok {
 		c.Diagnostics.Retention = diagnostics.RetentionMode(strings.TrimSpace(raw))
 	}
+	if raw, ok := lookup("NOTARIUS_WORKSPACE_DIR"); ok {
+		c.Workspace.Directory = strings.TrimSpace(raw)
+	}
+	if raw, ok := lookup("NOTARIUS_WORKSPACE_DIAGNOSTICS_ENABLED"); ok {
+		value, err := parseBoolEnv("NOTARIUS_WORKSPACE_DIAGNOSTICS_ENABLED", raw)
+		if err != nil {
+			return err
+		}
+		c.Workspace.Diagnostics.Enabled = value
+		c.Workspace.Diagnostics.enabledSet = true
+	}
+	if raw, ok := lookup("NOTARIUS_WORKSPACE_DIAGNOSTICS_RETENTION"); ok {
+		c.Workspace.Diagnostics.Retention = diagnostics.RetentionMode(strings.TrimSpace(raw))
+		c.Workspace.Diagnostics.retentionSet = true
+	}
+	if raw, ok := lookup("NOTARIUS_WORKSPACE_RESUME_ENABLED"); ok {
+		value, err := parseBoolEnv("NOTARIUS_WORKSPACE_RESUME_ENABLED", raw)
+		if err != nil {
+			return err
+		}
+		c.Workspace.Resume.Enabled = value
+	}
+	if raw, ok := lookup("NOTARIUS_WORKSPACE_DEBUG_ENABLED"); ok {
+		value, err := parseBoolEnv("NOTARIUS_WORKSPACE_DEBUG_ENABLED", raw)
+		if err != nil {
+			return err
+		}
+		c.Workspace.Debug.Enabled = value
+	}
+	c.RecomputeEffectiveDiagnostics()
 	return nil
 }
 
@@ -52,3 +82,11 @@ func parseIntEnv(name string, raw string) (int, error) {
 	}
 	return value, nil
 }
+
+func parseBoolEnv(name string, raw string) (bool, error) {
+	value, err := strconv.ParseBool(strings.TrimSpace(raw))
+	if err != nil {
+		return false, fmt.Errorf("%s: must be a boolean", name)
+	}
+	return value, nil
+}

internal/core/config/env_test.go

@@ -13,10 +13,15 @@ func TestApplyEnvOverridesOperationalValues(t *testing.T) {
 	cfg.Pipelines["example"] = pipeline.PipelineProfile{ID: "example", Input: pipeline.Binding("before")}
 
 	err := cfg.applyEnvOverridesWithLookup(mapLookup(map[string]string{
-		"NOTARIUS_TOTAL_LLM_CONCURRENCY": "3",
-		"NOTARIUS_WORK_DIR":              "/tmp/notarius-env",
-		"NOTARIUS_DIAGNOSTICS_RETENTION": "never",
-		"NOTARIUS_PIPELINE_INPUT":        "after",
+		"NOTARIUS_TOTAL_LLM_CONCURRENCY":           "3",
+		"NOTARIUS_WORK_DIR":                        "/tmp/notarius-env",
+		"NOTARIUS_DIAGNOSTICS_RETENTION":           "never",
+		"NOTARIUS_WORKSPACE_DIR":                   "/var/lib/notarius-env",
+		"NOTARIUS_WORKSPACE_DIAGNOSTICS_ENABLED":   "false",
+		"NOTARIUS_WORKSPACE_DIAGNOSTICS_RETENTION": "always",
+		"NOTARIUS_WORKSPACE_RESUME_ENABLED":        "true",
+		"NOTARIUS_WORKSPACE_DEBUG_ENABLED":         "true",
+		"NOTARIUS_PIPELINE_INPUT":                  "after",
 	}))
 	if err != nil {
 		t.Fatalf("ApplyEnvOverrides: %v", err)
@@ -28,9 +33,21 @@ func TestApplyEnvOverridesOperationalValues(t *testing.T) {
 	if cfg.Concurrency.TotalLLM != 3 {
 		t.Fatalf("unexpected total concurrency: %d", cfg.Concurrency.TotalLLM)
 	}
-	if cfg.Diagnostics.WorkDir != "/tmp/notarius-env" || cfg.Diagnostics.Retention != diagnostics.RetentionNever {
+	if cfg.Workspace.Directory != "/var/lib/notarius-env" {
+		t.Fatalf("unexpected workspace directory: %q", cfg.Workspace.Directory)
+	}
+	if cfg.DiagnosticsEnabled() {
+		t.Fatalf("expected workspace diagnostics disabled")
+	}
+	if cfg.Diagnostics.WorkDir != "/var/lib/notarius-env/diagnostics" || cfg.Diagnostics.Retention != diagnostics.RetentionAlways {
 		t.Fatalf("unexpected diagnostics config: %+v", cfg.Diagnostics)
 	}
+	if !cfg.Workspace.Resume.Enabled {
+		t.Fatalf("expected workspace resume enabled")
+	}
+	if !cfg.Workspace.Debug.Enabled {
+		t.Fatalf("expected workspace debug enabled")
+	}
 	if cfg.Pipelines["example"].Input.Module != "before" {
 		t.Fatalf("environment overrides must not change pipeline wiring: %+v", cfg.Pipelines["example"])
 	}
@@ -46,6 +63,41 @@ func TestApplyEnvOverridesRejectsInvalidIntegers(t *testing.T) {
 	}
 }
 
+func TestApplyEnvOverridesRejectsInvalidBooleans(t *testing.T) {
+	for _, name := range []string{
+		"NOTARIUS_WORKSPACE_DIAGNOSTICS_ENABLED",
+		"NOTARIUS_WORKSPACE_RESUME_ENABLED",
+		"NOTARIUS_WORKSPACE_DEBUG_ENABLED",
+	} {
+		t.Run(name, func(t *testing.T) {
+			cfg := Default()
+			err := cfg.applyEnvOverridesWithLookup(mapLookup(map[string]string{name: "maybe"}))
+			if err == nil || !strings.Contains(err.Error(), name) {
+				t.Fatalf("expected named boolean error, got %v", err)
+			}
+		})
+	}
+}
+
+func TestApplyEnvOverridesLegacyDiagnosticsRemainCompatibleWithoutWorkspace(t *testing.T) {
+	cfg := Default()
+
+	err := cfg.applyEnvOverridesWithLookup(mapLookup(map[string]string{
+		"NOTARIUS_WORK_DIR":              "/tmp/notarius-env",
+		"NOTARIUS_DIAGNOSTICS_RETENTION": "never",
+	}))
+	if err != nil {
+		t.Fatalf("ApplyEnvOverrides: %v", err)
+	}
+
+	if cfg.Diagnostics.WorkDir != "/tmp/notarius-env" {
+		t.Fatalf("diagnostics work dir = %q, want legacy env", cfg.Diagnostics.WorkDir)
+	}
+	if cfg.Diagnostics.Retention != diagnostics.RetentionNever {
+		t.Fatalf("diagnostics retention = %q, want legacy env", cfg.Diagnostics.Retention)
+	}
+}
+
 func TestLoadFromEnvUsesDefaultConfig(t *testing.T) {
 	t.Setenv("NOTARIUS_TOTAL_LLM_CONCURRENCY", "2")
 

internal/core/config/file_config.go

@@ -18,6 +18,7 @@ type FileConfig struct {
 	Pipelines   map[string]FilePipelineProfile `yaml:"pipelines,omitempty"`
 	Concurrency *FileConcurrencyConfig         `yaml:"concurrency,omitempty"`
 	Diagnostics *FileDiagnosticsConfig         `yaml:"diagnostics,omitempty"`
+	Workspace   *FileWorkspaceConfig           `yaml:"workspace,omitempty"`
 }
 
 type FileScriptoriumConfig struct {
@@ -50,6 +51,22 @@ type FileDiagnosticsConfig struct {
 	Retention *string `yaml:"retention,omitempty"`
 }
 
+type FileWorkspaceConfig struct {
+	Directory   *string                         `yaml:"directory,omitempty"`
+	Diagnostics *FileWorkspaceDiagnosticsConfig `yaml:"diagnostics,omitempty"`
+	Resume      *FileWorkspaceEnabledConfig     `yaml:"resume,omitempty"`
+	Debug       *FileWorkspaceEnabledConfig     `yaml:"debug,omitempty"`
+}
+
+type FileWorkspaceDiagnosticsConfig struct {
+	Enabled   *bool   `yaml:"enabled,omitempty"`
+	Retention *string `yaml:"retention,omitempty"`
+}
+
+type FileWorkspaceEnabledConfig struct {
+	Enabled *bool `yaml:"enabled,omitempty"`
+}
+
 type fileModuleBinding struct {
 	Module     string
 	LLMProfile string
@@ -307,6 +324,28 @@ func (c *Config) applyFileConfigWithLookup(fileCfg FileConfig, lookup func(strin
 			c.Diagnostics.Retention = diagnostics.RetentionMode(strings.TrimSpace(*fileCfg.Diagnostics.Retention))
 		}
 	}
+	if fileCfg.Workspace != nil {
+		if fileCfg.Workspace.Directory != nil {
+			c.Workspace.Directory = strings.TrimSpace(*fileCfg.Workspace.Directory)
+		}
+		if fileCfg.Workspace.Diagnostics != nil {
+			if fileCfg.Workspace.Diagnostics.Enabled != nil {
+				c.Workspace.Diagnostics.Enabled = *fileCfg.Workspace.Diagnostics.Enabled
+				c.Workspace.Diagnostics.enabledSet = true
+			}
+			if fileCfg.Workspace.Diagnostics.Retention != nil {
+				c.Workspace.Diagnostics.Retention = diagnostics.RetentionMode(strings.TrimSpace(*fileCfg.Workspace.Diagnostics.Retention))
+				c.Workspace.Diagnostics.retentionSet = true
+			}
+		}
+		if fileCfg.Workspace.Resume != nil && fileCfg.Workspace.Resume.Enabled != nil {
+			c.Workspace.Resume.Enabled = *fileCfg.Workspace.Resume.Enabled
+		}
+		if fileCfg.Workspace.Debug != nil && fileCfg.Workspace.Debug.Enabled != nil {
+			c.Workspace.Debug.Enabled = *fileCfg.Workspace.Debug.Enabled
+		}
+	}
+	c.RecomputeEffectiveDiagnostics()
 
 	return nil
 }

internal/core/config/file_config_test.go

@@ -554,6 +554,95 @@ diagnostics:
 	}
 }
 
+func TestApplyFileConfigWorkspaceSection(t *testing.T) {
+	cfg := parseAndApplyConfig(t, `
+version: 2
+workspace:
+  directory: /var/lib/notarius
+  diagnostics:
+    enabled: false
+    retention: never
+  resume:
+    enabled: true
+  debug:
+    enabled: true
+diagnostics:
+  work_dir: /tmp/legacy
+  retention: always
+`)
+
+	if cfg.Workspace.Directory != "/var/lib/notarius" {
+		t.Fatalf("workspace directory = %q, want /var/lib/notarius", cfg.Workspace.Directory)
+	}
+	if cfg.DiagnosticsEnabled() {
+		t.Fatalf("expected diagnostics disabled")
+	}
+	if cfg.Diagnostics.WorkDir != "/var/lib/notarius/diagnostics" {
+		t.Fatalf("effective diagnostics work dir = %q, want workspace diagnostics root", cfg.Diagnostics.WorkDir)
+	}
+	if cfg.Diagnostics.Retention != diagnostics.RetentionNever {
+		t.Fatalf("effective diagnostics retention = %q, want workspace override", cfg.Diagnostics.Retention)
+	}
+	if !cfg.Workspace.Resume.Enabled {
+		t.Fatalf("expected resume enabled")
+	}
+	if !cfg.Workspace.Debug.Enabled {
+		t.Fatalf("expected debug enabled")
+	}
+}
+
+func TestApplyFileConfigLegacyDiagnosticsRemainCompatible(t *testing.T) {
+	cfg := parseAndApplyConfig(t, `
+version: 2
+diagnostics:
+  work_dir: /tmp/legacy
+  retention: always
+`)
+
+	if cfg.Workspace.Directory != "" {
+		t.Fatalf("workspace directory = %q, want unset", cfg.Workspace.Directory)
+	}
+	if !cfg.DiagnosticsEnabled() {
+		t.Fatalf("expected diagnostics enabled")
+	}
+	if cfg.Diagnostics.WorkDir != "/tmp/legacy" {
+		t.Fatalf("effective diagnostics work dir = %q, want legacy", cfg.Diagnostics.WorkDir)
+	}
+	if cfg.Diagnostics.Retention != diagnostics.RetentionAlways {
+		t.Fatalf("effective diagnostics retention = %q, want legacy", cfg.Diagnostics.Retention)
+	}
+}
+
+func TestApplyFileConfigWorkspaceRetentionOverridesLegacyRetentionOnlyWhenSet(t *testing.T) {
+	t.Run("legacy retained", func(t *testing.T) {
+		cfg := parseAndApplyConfig(t, `
+version: 2
+workspace:
+  directory: /var/lib/notarius
+diagnostics:
+  retention: never
+`)
+		if cfg.Diagnostics.Retention != diagnostics.RetentionNever {
+			t.Fatalf("effective diagnostics retention = %q, want legacy", cfg.Diagnostics.Retention)
+		}
+	})
+
+	t.Run("workspace overrides", func(t *testing.T) {
+		cfg := parseAndApplyConfig(t, `
+version: 2
+workspace:
+  directory: /var/lib/notarius
+  diagnostics:
+    retention: always
+diagnostics:
+  retention: never
+`)
+		if cfg.Diagnostics.Retention != diagnostics.RetentionAlways {
+			t.Fatalf("effective diagnostics retention = %q, want workspace", cfg.Diagnostics.Retention)
+		}
+	})
+}
+
 func parseAndApplyConfig(t *testing.T, raw string) Config {
 	t.Helper()
 	fileCfg, err := ParseFileConfigYAML([]byte(raw))

internal/core/config/redaction_test.go

@@ -10,6 +10,8 @@ import (
 func TestRedactedConfigCopiesScriptoriumConfig(t *testing.T) {
 	cfg := Default()
 	cfg.Scriptorium.ProfileDir = "./profiles"
+	cfg.Workspace.Directory = "/var/lib/notarius"
+	cfg.Workspace.Resume.Enabled = true
 
 	redacted := cfg.Redacted()
 
@@ -20,6 +22,13 @@ func TestRedactedConfigCopiesScriptoriumConfig(t *testing.T) {
 	if cfg.Scriptorium.ProfileDir != "./profiles" {
 		t.Fatalf("redaction mutated original config")
 	}
+	if redacted.Workspace.Directory != "/var/lib/notarius" || !redacted.Workspace.Resume.Enabled {
+		t.Fatalf("expected workspace config preserved, got %+v", redacted.Workspace)
+	}
+	redacted.Workspace.Directory = "/changed"
+	if cfg.Workspace.Directory != "/var/lib/notarius" {
+		t.Fatalf("redaction mutated original workspace config")
+	}
 }
 
 func TestConfigRedactedDiagnosticsPayloadCopiesConfig(t *testing.T) {

internal/core/config/validation.go

@@ -12,6 +12,9 @@ func (c Config) Validate() error {
 	if err := validateScriptorium(c.Scriptorium); err != nil {
 		return err
 	}
+	if err := validateWorkspace(c.Workspace); err != nil {
+		return err
+	}
 	if err := validateDiagnostics(c.Diagnostics); err != nil {
 		return err
 	}
@@ -28,6 +31,17 @@ func validateScriptorium(cfg ScriptoriumConfig) error {
 	return nil
 }
 
+func validateWorkspace(cfg WorkspaceConfig) error {
+	if cfg.Diagnostics.retentionSet {
+		switch cfg.Diagnostics.Retention {
+		case "", diagnostics.RetentionAuto, diagnostics.RetentionAlways, diagnostics.RetentionNever:
+		default:
+			return fmt.Errorf("workspace diagnostics retention %q is not supported", cfg.Diagnostics.Retention)
+		}
+	}
+	return nil
+}
+
 func validateDiagnostics(cfg DiagnosticsConfig) error {
 	if strings.TrimSpace(cfg.WorkDir) == "" {
 		return fmt.Errorf("diagnostics work dir must not be empty")

internal/core/config/validation_test.go

@@ -99,6 +99,17 @@ func TestValidateRejectsInvalidDiagnosticsRetention(t *testing.T) {
 	}
 }
 
+func TestValidateRejectsInvalidWorkspaceDiagnosticsRetention(t *testing.T) {
+	cfg := validConfig()
+	cfg.Workspace.Diagnostics.Retention = diagnostics.RetentionMode("sometimes")
+	cfg.Workspace.Diagnostics.retentionSet = true
+
+	err := cfg.Validate()
+	if err == nil || !strings.Contains(err.Error(), "workspace diagnostics retention") {
+		t.Fatalf("expected workspace retention error, got %v", err)
+	}
+}
+
 func TestValidateRejectsInvalidReferenceMaps(t *testing.T) {
 	tests := []struct {
 		name   string