diff --git a/docs/roadmap/implementation.md b/docs/roadmap/implementation.md
index 91b6ce0..d3703e5 100644
--- a/docs/roadmap/implementation.md
+++ b/docs/roadmap/implementation.md
@@ -617,7 +617,7 @@ runs are not yet wired to persistent plan storage.
 
 ## Stage 5: Wire persistent policy into the CLI
 
-**Status:** Not started
+**Status:** Complete
 
 ### Objective
 
diff --git a/internal/cli/chunk_cache_test.go b/internal/cli/chunk_cache_test.go
new file mode 100644
index 0000000..2547d27
--- /dev/null
+++ b/internal/cli/chunk_cache_test.go
@@ -0,0 +1,480 @@
+package cli
+
+import (
+	"bytes"
+	"errors"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"gitea.maximumdirect.net/eric/notarius/internal/core/diagnostics"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
+)
+
+type recordingChunkPlanStore struct {
+	record   pipeline.ChunkPlanRecord
+	decision pipeline.ChunkPlanDecision
+	loadErr  error
+	saveErr  error
+	loads    int
+	saves    int
+}
+
+func (s *recordingChunkPlanStore) Load(string) (pipeline.ChunkPlanRecord, pipeline.ChunkPlanDecision, error) {
+	s.loads++
+	return s.record, s.decision, s.loadErr
+}
+
+func (s *recordingChunkPlanStore) Save(record pipeline.ChunkPlanRecord) error {
+	s.saves++
+	s.record = record
+	return s.saveErr
+}
+
+type recordingChunkPlanFactory struct {
+	roots []string
+	store *recordingChunkPlanStore
+	err   error
+}
+
+func (f *recordingChunkPlanFactory) build(root string) (pipeline.ChunkPlanStore, error) {
+	f.roots = append(f.roots, root)
+	if f.err != nil {
+		return nil, f.err
+	}
+	if f.store == nil {
+		f.store = &recordingChunkPlanStore{decision: pipeline.ChunkPlanDecision{Status: pipeline.ChunkPlanMissing}}
+	}
+	return f.store, nil
+}
+
+func TestRunChunkCachePrecedence(t *testing.T) {
+	tests := []struct {
+		name      string
+		fileMode  string
+		envMode   string
+		flagMode  string
+		wantMode  pipeline.ChunkCacheMode
+		wantBuild bool
+	}{
+		{name: "file refresh", fileMode: "refresh", wantMode: pipeline.ChunkCacheRefresh, wantBuild: true},
+		{name: "environment over file", fileMode: "bypass", envMode: "refresh", wantMode: pipeline.ChunkCacheRefresh, wantBuild: true},
+		{name: "flag over environment", fileMode: "refresh", envMode: "auto", flagMode: "bypass", wantMode: pipeline.ChunkCacheBypass},
+		{name: "explicit auto", fileMode: "bypass", envMode: "refresh", flagMode: "auto", wantMode: pipeline.ChunkCacheAuto, wantBuild: true},
+	}
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			root := filepath.Join(t.TempDir(), "plans")
+			configPath := writeTestConfig(t, cacheTestConfig(tc.fileMode, root, ""))
+			inputPath := writeFile(t, "input.txt", "input")
+			values := map[string]string{}
+			if tc.envMode != "" {
+				values["NOTARIUS_WORKSPACE_CHUNK_CACHE_MODE"] = tc.envMode
+			}
+			factory := &recordingChunkPlanFactory{}
+			args := []string{"run", "example", "--config", configPath, "--input", inputPath, "--output-dir", t.TempDir()}
+			if tc.flagMode != "" {
+				args = append(args, "--chunk_cache", tc.flagMode)
+			}
+			code, stderr := runCacheCommand(t, args, cacheTestOptions(t, values, factory))
+			if code != 0 {
+				t.Fatalf("code = %d stderr = %q", code, stderr)
+			}
+			if got := len(factory.roots) > 0; got != tc.wantBuild {
+				t.Fatalf("store built = %t roots = %#v, want %t", got, factory.roots, tc.wantBuild)
+			}
+			if !tc.wantBuild {
+				return
+			}
+			if tc.wantMode == pipeline.ChunkCacheAuto && (factory.store.loads != 1 || factory.store.saves != 1) {
+				t.Fatalf("auto calls = load %d save %d", factory.store.loads, factory.store.saves)
+			}
+			if tc.wantMode == pipeline.ChunkCacheRefresh && (factory.store.loads != 0 || factory.store.saves != 1) {
+				t.Fatalf("refresh calls = load %d save %d", factory.store.loads, factory.store.saves)
+			}
+		})
+	}
+}
+
+func TestRunChunkCacheInvalidValuesHaveEstablishedExitCodes(t *testing.T) {
+	validConfig := writeTestConfig(t, cacheTestConfig("bypass", "", ""))
+	invalidFile := writeTestConfig(t, cacheTestConfig("sometimes", "", ""))
+	inputPath := writeFile(t, "input.txt", "input")
+	tests := []struct {
+		name   string
+		config string
+		env    map[string]string
+		flag   string
+		want   int
+	}{
+		{name: "flag", config: validConfig, flag: "sometimes", want: 2},
+		{name: "environment", config: validConfig, env: map[string]string{"NOTARIUS_WORKSPACE_CHUNK_CACHE_MODE": "sometimes"}, want: 1},
+		{name: "file", config: invalidFile, want: 1},
+		{name: "flag does not mask invalid file", config: invalidFile, flag: "bypass", want: 1},
+		{name: "flag does not mask invalid environment", config: validConfig, env: map[string]string{"NOTARIUS_WORKSPACE_CHUNK_CACHE_MODE": "sometimes"}, flag: "bypass", want: 1},
+	}
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			args := []string{"run", "example", "--config", tc.config, "--input", inputPath, "--output-dir", t.TempDir()}
+			if tc.flag != "" {
+				args = append(args, "--chunk_cache", tc.flag)
+			}
+			code, _ := runCacheCommand(t, args, cacheTestOptions(t, tc.env, &recordingChunkPlanFactory{}))
+			if code != tc.want {
+				t.Fatalf("code = %d, want %d", code, tc.want)
+			}
+		})
+	}
+}
+
+func TestRunChunkPlanRootResolution(t *testing.T) {
+	t.Run("explicit file root", func(t *testing.T) {
+		factory := &recordingChunkPlanFactory{}
+		resolverCalls := 0
+		opts := cacheTestOptions(t, nil, factory)
+		opts.UserCacheDir = func() (string, error) { resolverCalls++; return "", errors.New("must not be called") }
+		configPath := writeTestConfig(t, cacheTestConfig("auto", "/var/cache/notarius/chunk-plans", ""))
+		code, stderr := runCacheCommand(t, cacheRunArgs(t, configPath), opts)
+		if code != 0 || stderr != "" || resolverCalls != 0 || len(factory.roots) != 1 || factory.roots[0] != "/var/cache/notarius/chunk-plans" {
+			t.Fatalf("code=%d stderr=%q resolver=%d roots=%#v", code, stderr, resolverCalls, factory.roots)
+		}
+	})
+
+	t.Run("environment root", func(t *testing.T) {
+		factory := &recordingChunkPlanFactory{}
+		environmentRoot := filepath.Join(t.TempDir(), "environment-plans")
+		configPath := writeTestConfig(t, cacheTestConfig("auto", filepath.Join(t.TempDir(), "file-plans"), ""))
+		code, stderr := runCacheCommand(t, cacheRunArgs(t, configPath), cacheTestOptions(t, map[string]string{"NOTARIUS_WORKSPACE_CHUNK_CACHE_DIR": environmentRoot}, factory))
+		if code != 0 || stderr != "" || len(factory.roots) != 1 || factory.roots[0] != environmentRoot {
+			t.Fatalf("code=%d stderr=%q roots=%#v", code, stderr, factory.roots)
+		}
+	})
+
+	t.Run("per-user default", func(t *testing.T) {
+		factory := &recordingChunkPlanFactory{}
+		cacheDir := filepath.Join(t.TempDir(), "user-cache")
+		opts := cacheTestOptions(t, nil, factory)
+		opts.UserCacheDir = func() (string, error) { return cacheDir, nil }
+		configPath := writeTestConfig(t, cacheTestConfig("auto", "", ""))
+		code, stderr := runCacheCommand(t, cacheRunArgs(t, configPath), opts)
+		want := filepath.Join(cacheDir, "notarius", "chunk-plans")
+		if code != 0 || stderr != "" || len(factory.roots) != 1 || factory.roots[0] != want {
+			t.Fatalf("code=%d stderr=%q roots=%#v want=%q", code, stderr, factory.roots, want)
+		}
+	})
+}
+
+func TestRunBypassSkipsRootAndStore(t *testing.T) {
+	factory := &recordingChunkPlanFactory{err: errors.New("must not build")}
+	resolverCalls := 0
+	opts := cacheTestOptions(t, nil, factory)
+	opts.UserCacheDir = func() (string, error) { resolverCalls++; return "", errors.New("must not resolve") }
+	configPath := writeTestConfig(t, cacheTestConfig("bypass", "", ""))
+	code, stderr := runCacheCommand(t, cacheRunArgs(t, configPath), opts)
+	if code != 0 || stderr != "" || resolverCalls != 0 || len(factory.roots) != 0 {
+		t.Fatalf("code=%d stderr=%q resolver=%d roots=%#v", code, stderr, resolverCalls, factory.roots)
+	}
+}
+
+func TestRunChunkPlanSetupFailures(t *testing.T) {
+	for _, mode := range []string{"auto", "refresh"} {
+		t.Run(mode+" resolver", func(t *testing.T) {
+			factory := &recordingChunkPlanFactory{}
+			opts := cacheTestOptions(t, nil, factory)
+			opts.UserCacheDir = func() (string, error) { return "", errors.New("cache unavailable") }
+			configPath := writeTestConfig(t, cacheTestConfig(mode, "", ""))
+			code, stderr := runCacheCommand(t, cacheRunArgs(t, configPath), opts)
+			if code != 1 || !strings.Contains(stderr, "cache unavailable") || len(factory.roots) != 0 {
+				t.Fatalf("code=%d stderr=%q roots=%#v", code, stderr, factory.roots)
+			}
+		})
+	}
+
+	t.Run("store", func(t *testing.T) {
+		factory := &recordingChunkPlanFactory{err: errors.New("unwritable store")}
+		configPath := writeTestConfig(t, cacheTestConfig("auto", t.TempDir(), ""))
+		code, stderr := runCacheCommand(t, cacheRunArgs(t, configPath), cacheTestOptions(t, nil, factory))
+		if code != 1 || !strings.Contains(stderr, "unwritable store") {
+			t.Fatalf("code=%d stderr=%q", code, stderr)
+		}
+	})
+
+	t.Run("unwritable filesystem store", func(t *testing.T) {
+		root := writeFile(t, "not-a-directory", "occupied")
+		configPath := writeTestConfig(t, `version: 2
+workspace:
+  chunk_cache:
+    mode: auto
+    directory: `+root+`
+pipelines:
+  dnd-session:
+    input: seriatim
+    artifacts:
+      spells:
+        extract: dnd/spells
+`)
+		code, stderr := runCacheCommand(t, []string{"run", "dnd-session", "--config", configPath, "--input", writeSeriatimInput(t), "--output-dir", t.TempDir()}, Options{LLMClientFactory: fakeLLMFactory(newFakeRunLLMClient(false), nil), LookupEnv: mapLookup(nil)})
+		if code != 1 || (!strings.Contains(stderr, "load chunk plan") && !strings.Contains(stderr, "save chunk plan")) {
+			t.Fatalf("code=%d stderr=%q", code, stderr)
+		}
+	})
+}
+
+func TestConfigCommandsDoNotResolveOrCreateChunkPlanState(t *testing.T) {
+	configPath := writeTestConfig(t, cacheTestConfig("auto", "", ""))
+	for _, args := range [][]string{
+		{"config", "validate", "--config", configPath},
+		{"pipelines", "list", "--config", configPath},
+	} {
+		factory := &recordingChunkPlanFactory{err: errors.New("must not build")}
+		resolverCalls := 0
+		opts := cacheTestOptions(t, nil, factory)
+		opts.UserCacheDir = func() (string, error) { resolverCalls++; return "", errors.New("must not resolve") }
+		code, stderr := runCacheCommand(t, args, opts)
+		if code != 0 || stderr != "" || resolverCalls != 0 || len(factory.roots) != 0 {
+			t.Fatalf("args=%v code=%d stderr=%q resolver=%d roots=%#v", args, code, stderr, resolverCalls, factory.roots)
+		}
+	}
+}
+
+func TestRunRecordsExplicitChunkCacheOverrideAndEffectiveMode(t *testing.T) {
+	diagnosticsDir := t.TempDir()
+	configPath := writeTestConfig(t, cacheTestConfig("bypass", "", diagnosticsDir))
+	factory := &recordingChunkPlanFactory{}
+	args := append(cacheRunArgs(t, configPath), "--chunk_cache", "refresh")
+	code, stderr := runCacheCommand(t, args, cacheTestOptions(t, nil, factory))
+	if code != 0 || stderr != "" {
+		t.Fatalf("code=%d stderr=%q", code, stderr)
+	}
+	runDir := onlyChildDir(t, diagnosticsDir)
+	invocation := string(readFile(t, filepath.Join(runDir, diagnostics.ArtifactInvocationMetadata)))
+	effective := string(readFile(t, filepath.Join(runDir, diagnostics.ArtifactEffectiveConfig)))
+	if !strings.Contains(invocation, `"chunk_cache_override": "refresh"`) || !strings.Contains(effective, `"mode": "refresh"`) {
+		t.Fatalf("invocation=%s effective=%s", invocation, effective)
+	}
+}
+
+func TestDefaultAutoReusesPlanAcrossIndependentInvocations(t *testing.T) {
+	cacheBase := filepath.Join(t.TempDir(), "cache")
+	workspaceDir := filepath.Join(t.TempDir(), "workspace")
+	configPath := writeTestConfig(t, `version: 2
+workspace:
+  directory: `+workspaceDir+`
+  debug:
+    enabled: true
+pipelines:
+  dnd-session:
+    input: seriatim
+    chunk: dnd/scenes
+    artifacts:
+      spells:
+        extract: dnd/spells
+`)
+	inputPath := writeFile(t, "source.json", `{
+  "metadata": {"id": "session-alpha"},
+  "segments": [
+    {"id": 1, "start": 0, "end": 1, "speaker": "Aria", "text": "Aria casts Cure Wounds."},
+    {"id": 2, "start": 1, "end": 2, "speaker": "Borin", "text": "Borin recovers."}
+  ]
+}`)
+	client := newFakeRunLLMClient(false)
+	opts := Options{
+		LLMClientFactory: fakeLLMFactory(client, nil),
+		LookupEnv:        mapLookup(nil),
+		UserCacheDir:     func() (string, error) { return cacheBase, nil },
+	}
+	for i := 0; i < 2; i++ {
+		code, stderr := runCacheCommand(t, []string{"run", "dnd-session", "--config", configPath, "--input", inputPath, "--output-dir", t.TempDir()}, opts)
+		if code != 0 {
+			t.Fatalf("run %d code=%d stderr=%q", i+1, code, stderr)
+		}
+	}
+	if client.calls != 3 {
+		t.Fatalf("LLM calls = %d, want chunk+extract then extract-only reuse", client.calls)
+	}
+	planRoot := filepath.Join(cacheBase, "notarius", "chunk-plans")
+	entries, err := os.ReadDir(planRoot)
+	if err != nil || len(entries) != 1 {
+		t.Fatalf("plan root entries = %v error=%v", entries, err)
+	}
+	if _, err := os.Stat(filepath.Join(planRoot, entries[0].Name(), "plan.json")); err != nil {
+		t.Fatalf("plan file: %v", err)
+	}
+	debugRuns := childDirs(t, filepath.Join(workspaceDir, "debug"))
+	if len(debugRuns) != 2 {
+		t.Fatalf("debug runs = %#v", debugRuns)
+	}
+	attemptCounts := 0
+	for _, runDir := range debugRuns {
+		if _, err := os.Stat(filepath.Join(runDir, "chunk", "attempt-01.json")); err == nil {
+			attemptCounts++
+		} else if !os.IsNotExist(err) {
+			t.Fatal(err)
+		}
+	}
+	if attemptCounts != 1 {
+		t.Fatalf("chunk attempt files across runs = %d, want only generating run", attemptCounts)
+	}
+}
+
+func TestChunkPlanReuseDependsOnlyOnSourceDigest(t *testing.T) {
+	cacheRoot := filepath.Join(t.TempDir(), "plans")
+	inputPath := writeSeriatimInput(t)
+	referencePath := writeFile(t, "players.txt", "Alyx")
+	profilePath := writeScriptoriumProfileFile(t, "chunk-profile", "http://127.0.0.1:8080/v1", "test-model")
+	seedConfig := writeTestConfig(t, `version: 2
+workspace:
+  chunk_cache:
+    mode: auto
+    directory: `+cacheRoot+`
+pipelines:
+  seed:
+    input: seriatim
+    chunk:
+      module: generic
+      options:
+        max_units: 1
+        overlap_units: 0
+    artifacts:
+      spells:
+        extract: dnd/spells
+`)
+	changedConfig := writeTestConfig(t, `version: 2
+scriptorium:
+  profile_file: `+profilePath+`
+workspace:
+  chunk_cache:
+    mode: auto
+    directory: `+cacheRoot+`
+pipelines:
+  changed:
+    input: seriatim
+    chunk:
+      module: dnd/scenes
+      llm_profile: chunk-profile
+      references:
+        players: `+referencePath+`
+      validators:
+        - generic/always_accept
+    artifacts:
+      spells:
+        extract: dnd/spells
+`)
+	client := newFakeRunLLMClient(false)
+	opts := Options{LLMClientFactory: fakeLLMFactory(client, nil), LookupEnv: mapLookup(nil)}
+	for _, run := range []struct {
+		pipeline string
+		config   string
+	}{{pipeline: "seed", config: seedConfig}, {pipeline: "changed", config: changedConfig}} {
+		code, stderr := runCacheCommand(t, []string{"run", run.pipeline, "--config", run.config, "--input", inputPath, "--output-dir", t.TempDir()}, opts)
+		if code != 0 {
+			t.Fatalf("pipeline %q code=%d stderr=%q", run.pipeline, code, stderr)
+		}
+	}
+	if client.calls != 2 {
+		t.Fatalf("LLM calls = %d, want one extractor call per run and no changed chunker call", client.calls)
+	}
+}
+
+func TestResumeAndChunkCacheModesRemainIndependent(t *testing.T) {
+	for _, mode := range []pipeline.ChunkCacheMode{pipeline.ChunkCacheAuto, pipeline.ChunkCacheBypass, pipeline.ChunkCacheRefresh} {
+		t.Run(string(mode), func(t *testing.T) {
+			workspaceDir := filepath.Join(t.TempDir(), "workspace")
+			cacheRoot := filepath.Join(t.TempDir(), "plans")
+			configPath := writeTestConfig(t, cacheTestConfigWithWorkspace(string(mode), cacheRoot, workspaceDir))
+			factory := &recordingChunkPlanFactory{}
+			args := append(cacheRunArgs(t, configPath), "--resume")
+			code, stderr := runCacheCommand(t, args, cacheTestOptions(t, nil, factory))
+			if code != 0 || stderr != "" {
+				t.Fatalf("code=%d stderr=%q", code, stderr)
+			}
+			if mode == pipeline.ChunkCacheBypass {
+				if len(factory.roots) != 0 {
+					t.Fatalf("bypass roots = %#v", factory.roots)
+				}
+			} else if len(factory.roots) != 1 || factory.roots[0] != cacheRoot {
+				t.Fatalf("roots = %#v, want %q", factory.roots, cacheRoot)
+			}
+			if entries := childDirs(t, filepath.Join(workspaceDir, "checkpoints")); len(entries) != 1 {
+				t.Fatalf("checkpoint roots = %#v", entries)
+			}
+			if strings.HasPrefix(cacheRoot, workspaceDir+string(filepath.Separator)) || strings.HasPrefix(workspaceDir, cacheRoot+string(filepath.Separator)) {
+				t.Fatalf("cache root %q and workspace root %q overlap", cacheRoot, workspaceDir)
+			}
+		})
+	}
+}
+
+func TestWorkspaceDirectoryDoesNotSelectChunkPlanRoot(t *testing.T) {
+	cacheBase := filepath.Join(t.TempDir(), "user-cache")
+	factory := &recordingChunkPlanFactory{}
+	for _, workspaceDir := range []string{filepath.Join(t.TempDir(), "workspace-one"), filepath.Join(t.TempDir(), "workspace-two")} {
+		configPath := writeTestConfig(t, cacheTestConfigWithWorkspace("auto", "", workspaceDir))
+		opts := cacheTestOptions(t, nil, factory)
+		opts.UserCacheDir = func() (string, error) { return cacheBase, nil }
+		code, stderr := runCacheCommand(t, cacheRunArgs(t, configPath), opts)
+		if code != 0 || stderr != "" {
+			t.Fatalf("workspace=%q code=%d stderr=%q", workspaceDir, code, stderr)
+		}
+	}
+	want := filepath.Join(cacheBase, "notarius", "chunk-plans")
+	if len(factory.roots) != 2 || factory.roots[0] != want || factory.roots[1] != want {
+		t.Fatalf("roots = %#v, want %q twice", factory.roots, want)
+	}
+}
+
+func cacheTestOptions(t *testing.T, env map[string]string, factory *recordingChunkPlanFactory) Options {
+	t.Helper()
+	registries := fakeExecutionRegistries(t)
+	return Options{
+		Catalog:               catalogFromRegistries(registries),
+		Registries:            registries,
+		LLMClientFactory:      fakeLLMFactory(nil, nil),
+		LookupEnv:             mapLookup(env),
+		UserCacheDir:          func() (string, error) { return filepath.Join(t.TempDir(), "cache"), nil },
+		ChunkPlanStoreFactory: factory.build,
+	}
+}
+
+func cacheRunArgs(t *testing.T, configPath string) []string {
+	t.Helper()
+	return []string{"run", "example", "--config", configPath, "--input", writeFile(t, "input.txt", "input"), "--output-dir", t.TempDir()}
+}
+
+func runCacheCommand(t *testing.T, args []string, opts Options) (int, string) {
+	t.Helper()
+	var stdout bytes.Buffer
+	var stderr bytes.Buffer
+	code := RunWithOptions(args, &stdout, &stderr, opts)
+	return code, stderr.String()
+}
+
+func cacheTestConfig(mode, directory, diagnosticsDir string) string {
+	var b strings.Builder
+	b.WriteString("version: 2\n")
+	if mode != "" || directory != "" {
+		b.WriteString("workspace:\n  chunk_cache:\n")
+		if mode != "" {
+			b.WriteString("    mode: " + mode + "\n")
+		}
+		if directory != "" {
+			b.WriteString("    directory: " + directory + "\n")
+		}
+	}
+	if diagnosticsDir != "" {
+		b.WriteString("diagnostics:\n  work_dir: " + diagnosticsDir + "\n  retention: always\n")
+	}
+	b.WriteString("pipelines:\n  example:\n    input: fake/input\n    artifacts:\n      spells:\n        extract: fake/extract\n")
+	return b.String()
+}
+
+func cacheTestConfigWithWorkspace(mode, cacheRoot, workspaceDir string) string {
+	var b strings.Builder
+	b.WriteString("version: 2\nworkspace:\n  directory: " + workspaceDir + "\n  resume:\n    enabled: true\n  chunk_cache:\n    mode: " + mode + "\n")
+	if cacheRoot != "" {
+		b.WriteString("    directory: " + cacheRoot + "\n")
+	}
+	b.WriteString("pipelines:\n  example:\n    input: fake/input\n    artifacts:\n      spells:\n        extract: fake/extract\n")
+	return b.String()
+}
diff --git a/internal/cli/run.go b/internal/cli/run.go
index 19cab56..9bd8aeb 100644
--- a/internal/cli/run.go
+++ b/internal/cli/run.go
@@ -20,6 +20,7 @@ import (
 	"gitea.maximumdirect.net/eric/notarius/internal/core/diagnostics"
 	"gitea.maximumdirect.net/eric/notarius/internal/core/workspace"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/checkpoint"
+	"gitea.maximumdirect.net/eric/notarius/internal/framework/chunkplan"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/contracts"
 	frameworkdebug "gitea.maximumdirect.net/eric/notarius/internal/framework/debug"
 	"gitea.maximumdirect.net/eric/notarius/internal/framework/pipeline"
@@ -30,17 +31,19 @@ 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] [--resume] [--session-id id] [--reference selector=path] [--without-reference selector]
+  notarius run <pipeline-id> --input path/to/source.json [--config path/to/config.yml] [--only lane-a,lane-b] [--chunk_cache auto|bypass|refresh] [--resume] [--session-id id] [--reference selector=path] [--without-reference selector]
   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
-	Registries       pipeline.Registries
-	LLMClientFactory LLMClientFactory
-	LookupEnv        func(string) (string, bool)
-	Now              func() time.Time
+	Catalog               pipeline.ModuleCatalog
+	Registries            pipeline.Registries
+	LLMClientFactory      LLMClientFactory
+	LookupEnv             func(string) (string, bool)
+	Now                   func() time.Time
+	UserCacheDir          func() (string, error)
+	ChunkPlanStoreFactory pipeline.ChunkPlanStoreFactory
 }
 
 type LLMClientFactory func(ctx context.Context, cfg config.Config, profileID string) (contracts.StructuredLLMClient, []artifacts.LLMProfileManifest, error)
@@ -90,6 +93,12 @@ func normalizeOptions(opts Options) (Options, error) {
 	if opts.Now == nil {
 		opts.Now = time.Now
 	}
+	if opts.UserCacheDir == nil {
+		opts.UserCacheDir = os.UserCacheDir
+	}
+	if opts.ChunkPlanStoreFactory == nil {
+		opts.ChunkPlanStoreFactory = chunkplan.NewFilesystemStore
+	}
 	if isEmptyCatalog(opts.Catalog) && isEmptyRegistries(opts.Registries) {
 		components, err := newProductionComponents()
 		if err != nil {
@@ -117,10 +126,12 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 	diagnosticsDir := fs.String("diagnostics-dir", "", "diagnostics directory")
 	llmProfile := fs.String("llm-profile", "", "LLM profile override")
 	resume := fs.Bool("resume", false, "reuse valid workspace checkpoints")
+	chunkCache := chunkCacheFlag{}
 	sessionID := sessionIDFlag{}
 	referenceFlags := stringListFlag{}
 	withoutReferenceFlags := stringListFlag{}
 	fs.Var(&sessionID, "session-id", "prompt session identifier")
+	fs.Var(&chunkCache, "chunk_cache", "chunk plan cache mode: auto, bypass, or refresh")
 	fs.Var(&referenceFlags, "reference", "reference binding, as slot=path, chunk.slot=path, merge.slot=path, lane.slot=path, lane.extract.slot=path, lane.merge.slot=path, or lane.normalize.slot=path")
 	fs.Var(&withoutReferenceFlags, "without-reference", "unbind a reference, using the same selector forms as --reference")
 	if err := validateRunFlagValues(args); err != nil {
@@ -173,6 +184,9 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 		fmt.Fprintf(stderr, "notarius: %v\n", err)
 		return 1
 	}
+	if chunkCache.set {
+		cfg.Workspace.ChunkCache.Mode = chunkCache.value
+	}
 	workspaceSettings := workspace.FromConfig(cfg)
 	if dir := strings.TrimSpace(*diagnosticsDir); dir != "" {
 		workspaceSettings.DiagnosticsRoot = dir
@@ -191,15 +205,16 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 		runID = runDir.RunID()
 	}
 	invocation := diagnostics.InvocationMetadata{
-		Operation:    "run",
-		PipelineID:   pipelineID,
-		InputPath:    strings.TrimSpace(*inputPath),
-		ConfigPath:   loadedConfigPath,
-		ConfigSource: configSource(*configPath),
-		OnlyLanes:    append([]string(nil), only...),
-		Resume:       *resume,
-		RunID:        runID,
-		StartedAt:    startedAt,
+		Operation:          "run",
+		PipelineID:         pipelineID,
+		InputPath:          strings.TrimSpace(*inputPath),
+		ConfigPath:         loadedConfigPath,
+		ConfigSource:       configSource(*configPath),
+		OnlyLanes:          append([]string(nil), only...),
+		ChunkCacheOverride: chunkCache.explicitValue(),
+		Resume:             *resume,
+		RunID:              runID,
+		StartedAt:          startedAt,
 	}
 	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))
@@ -287,6 +302,10 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 	if err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, fmt.Errorf("read input %q: %w", strings.TrimSpace(*inputPath), err))
 	}
+	chunkPlans, err := chunkPlanStoreForRun(effective.Config.Workspace.ChunkCache, opts)
+	if err != nil {
+		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
+	}
 	checkpointRecorder, checkpointLoader, err := checkpointHandlersForRun(workspaceSettings, effective.ResolvedPipeline, rawInput, only, llmProfiles, strings.TrimSpace(*llmProfile), strings.TrimSpace(sessionID.value), *resume)
 	if err != nil {
 		return failPipelineCommand(stderr, runDir, cfg.Diagnostics.Retention, err)
@@ -302,6 +321,8 @@ func runPipelineCommand(args []string, stdout, stderr io.Writer, opts Options) i
 		LLMProfiles:    llmProfiles,
 		Metadata:       runMetadata(*outputDir, *diagnosticsDir),
 		Warnings:       referenceWarnings,
+		ChunkCacheMode: effective.Config.Workspace.ChunkCache.Mode,
+		ChunkPlans:     chunkPlans,
 		Checkpoints:    checkpointRecorder,
 		Checkpoint:     checkpointLoader,
 		Debug:          debugRecorder,
@@ -598,13 +619,64 @@ func reorderRunArgs(args []string) []string {
 
 func runFlagTakesValue(arg string) bool {
 	switch arg {
-	case "--config", "--input", "--only", "--output-dir", "--diagnostics-dir", "--llm-profile", "--session-id", "--reference", "--without-reference":
+	case "--config", "--input", "--only", "--output-dir", "--diagnostics-dir", "--llm-profile", "--session-id", "--chunk_cache", "--reference", "--without-reference":
 		return true
 	default:
 		return false
 	}
 }
 
+type chunkCacheFlag struct {
+	value pipeline.ChunkCacheMode
+	set   bool
+}
+
+func (f *chunkCacheFlag) String() string {
+	if f == nil {
+		return ""
+	}
+	return string(f.value)
+}
+
+func (f *chunkCacheFlag) Set(raw string) error {
+	mode, err := pipeline.ParseChunkCacheMode(raw)
+	if err != nil {
+		return err
+	}
+	f.value = mode
+	f.set = true
+	return nil
+}
+
+func (f chunkCacheFlag) explicitValue() string {
+	if !f.set {
+		return ""
+	}
+	return string(f.value)
+}
+
+func chunkPlanStoreForRun(cfg config.WorkspaceChunkCacheConfig, opts Options) (pipeline.ChunkPlanStore, error) {
+	if cfg.Mode == pipeline.ChunkCacheBypass {
+		return nil, nil
+	}
+	root := strings.TrimSpace(cfg.Directory)
+	if root == "" {
+		var err error
+		root, err = workspace.DefaultChunkPlanRoot(opts.UserCacheDir)
+		if err != nil {
+			return nil, fmt.Errorf("resolve chunk plan root: %w", err)
+		}
+	}
+	store, err := opts.ChunkPlanStoreFactory(root)
+	if err != nil {
+		return nil, fmt.Errorf("create chunk plan store at %q: %w", root, err)
+	}
+	if store == nil {
+		return nil, fmt.Errorf("create chunk plan store at %q: factory returned nil", root)
+	}
+	return store, nil
+}
+
 func validateRunFlagValues(args []string) error {
 	for i, arg := range args {
 		if arg != "--session-id" {
diff --git a/internal/cli/test_main_test.go b/internal/cli/test_main_test.go
new file mode 100644
index 0000000..7768d03
--- /dev/null
+++ b/internal/cli/test_main_test.go
@@ -0,0 +1,21 @@
+package cli
+
+import (
+	"os"
+	"testing"
+)
+
+func TestMain(m *testing.M) {
+	const name = "NOTARIUS_WORKSPACE_CHUNK_CACHE_MODE"
+	previous, existed := os.LookupEnv(name)
+	if err := os.Setenv(name, "bypass"); err != nil {
+		panic(err)
+	}
+	code := m.Run()
+	if existed {
+		_ = os.Setenv(name, previous)
+	} else {
+		_ = os.Unsetenv(name)
+	}
+	os.Exit(code)
+}
diff --git a/internal/core/diagnostics/run_dir.go b/internal/core/diagnostics/run_dir.go
index e7fcc69..86474eb 100644
--- a/internal/core/diagnostics/run_dir.go
+++ b/internal/core/diagnostics/run_dir.go
@@ -48,16 +48,17 @@ type RedactedEffectiveConfigPayload interface {
 
 // InvocationMetadata captures non-secret invocation details for diagnostics.
 type InvocationMetadata struct {
-	Operation      string    `json:"operation"`
-	PipelineID     string    `json:"pipeline_id,omitempty"`
-	PipelineDigest string    `json:"pipeline_digest,omitempty"`
-	Resume         bool      `json:"resume,omitempty"`
-	InputPath      string    `json:"input_path,omitempty"`
-	ConfigPath     string    `json:"config_path,omitempty"`
-	ConfigSource   string    `json:"config_source,omitempty"`
-	OnlyLanes      []string  `json:"only_lanes,omitempty"`
-	RunID          string    `json:"run_id"`
-	StartedAt      time.Time `json:"started_at"`
+	Operation          string    `json:"operation"`
+	PipelineID         string    `json:"pipeline_id,omitempty"`
+	PipelineDigest     string    `json:"pipeline_digest,omitempty"`
+	Resume             bool      `json:"resume,omitempty"`
+	InputPath          string    `json:"input_path,omitempty"`
+	ConfigPath         string    `json:"config_path,omitempty"`
+	ConfigSource       string    `json:"config_source,omitempty"`
+	OnlyLanes          []string  `json:"only_lanes,omitempty"`
+	ChunkCacheOverride string    `json:"chunk_cache_override,omitempty"`
+	RunID              string    `json:"run_id"`
+	StartedAt          time.Time `json:"started_at"`
 }
 
 func ShouldRetainRunDirectory(input RetentionDecisionInput) bool {