diff --git a/.github/workflows/review-desktop-ci.yml b/.github/workflows/review-desktop-ci.yml
index 80d85b45b..aeb4426bf 100644
--- a/.github/workflows/review-desktop-ci.yml
+++ b/.github/workflows/review-desktop-ci.yml
@@ -161,7 +161,6 @@ jobs:
 
       - name: Bundled diffr integration
         run: |
-          pnpm --filter @dev.fast/whiteboard ensure:diffr --required
           pnpm --filter @dev.fast/whiteboard exec vitest run --config vitest.integration.config.ts
 
       - name: Upload browser test diagnostics
diff --git a/.gitignore b/.gitignore
index 4eefcb39c..c54fa9203 100644
--- a/.gitignore
+++ b/.gitignore
@@ -91,4 +91,3 @@ artifacts/devbox/
 scripts/acceptance/evidence/
 
 packages/review/tutorial/pins.json
-packages/review/bin/
diff --git a/apps/review-desktop/code-oss/build/darwin/sign.ts b/apps/review-desktop/code-oss/build/darwin/sign.ts
index 23aee9992..742895bc1 100644
--- a/apps/review-desktop/code-oss/build/darwin/sign.ts
+++ b/apps/review-desktop/code-oss/build/darwin/sign.ts
@@ -19,7 +19,7 @@ function getElectronVersion(): string {
 }
 
 function getEntitlementsForFile(filePath: string): string {
-	if (filePath.endsWith('/Contents/Resources/app/review-runtime/bin/diffr')) {
+	if (/\/Contents\/Resources\/app\/review-runtime\/node_modules\/@dev\.fast\/diffr-darwin-(arm64|x64)\/diffr$/.test(filePath)) {
 		return path.join(entitlementsDir, 'diffr.plist');
 	}
 	if (filePath.includes(' Helper (GPU).app')) {
diff --git a/apps/review-desktop/code-oss/src/vs/review/common/reviewStructuralDiff.test.ts b/apps/review-desktop/code-oss/src/vs/review/common/reviewStructuralDiff.test.ts
index 0af2fd2a5..e83efa78e 100644
--- a/apps/review-desktop/code-oss/src/vs/review/common/reviewStructuralDiff.test.ts
+++ b/apps/review-desktop/code-oss/src/vs/review/common/reviewStructuralDiff.test.ts
@@ -30,10 +30,10 @@ function leaf(id: number, start: number, end: number, extra: Partial<StructuralL
 }
 function fold(id: number, children: StructuralRegion[], tags: string[] = ["context:body"]): StructuralFold {
 	const first = children[0], last = children[children.length - 1];
-	return { id, fold_state_id: id, kind: "fold", start: first.start, end: last.end, tags, children };
+	return { id, fold_state_id: id, kind: "fold", indent: first.start, start: first.start, end: last.end, tags, children };
 }
 function text(lines: string[], regions: StructuralRegion[]) {
-	return { text: lines.join("\n") + "\n", regions };
+	return { text: lines.join("\n") + "\n", root: {kind: "fold" as const, id: 1000, fold_state_id: 1000, start: {line: 0, column: 0}, end: {line: lines.length, column: 0}, indent: {line: 0, column: 0}, children: regions} };
 }
 const stats = { textual: { added: 0, removed: 0 }, visible: { added: 0, removed: 0 } };
 
diff --git a/apps/review-desktop/code-oss/src/vs/review/common/reviewStructuralDiff.ts b/apps/review-desktop/code-oss/src/vs/review/common/reviewStructuralDiff.ts
index 10a628287..766454d5a 100644
--- a/apps/review-desktop/code-oss/src/vs/review/common/reviewStructuralDiff.ts
+++ b/apps/review-desktop/code-oss/src/vs/review/common/reviewStructuralDiff.ts
@@ -79,7 +79,7 @@ export function structuralContextScopes(diff: StructuralTextDiff) {
 			}
 			region.children.forEach(visit);
 		};
-		source?.regions?.forEach(visit);
+		if (source) visit(source.root);
 		return result;
 	};
 	return { original: scopes(diff.lhs), modified: scopes(diff.rhs) };
@@ -120,7 +120,7 @@ export function structuralHighlights(diff: StructuralTextDiff) {
 			for (let line = start; line < end; line++) changedLines.push(line + 1);
 		}
 		const spans = [];
-		for (const leaf of structuralLeaves(source.regions)) {
+		for (const leaf of structuralLeaves([source.root])) {
 			for (const span of leaf.changed ?? []) {
 				spans.push({
 					startLineNumber: span.line + 1,
@@ -270,8 +270,8 @@ export function structuralContextGaps(
 		for (let index = first; index <= last; index++) if (rows[index][other] !== null) count++;
 		return { start: before + 2, count };
 	};
-	const lhs = knownRegions(diff.lhs?.regions, state);
-	const rhs = knownRegions(diff.rhs?.regions, state);
+	const lhs = knownRegions(diff.lhs ? [diff.lhs.root] : undefined, state);
+	const rhs = knownRegions(diff.rhs ? [diff.rhs.root] : undefined, state);
 	// Leaves pair by alignment; folds pair by fold state, the only identity they share across sides.
 	const usedRhs = new Set<StructuralRegion>();
 	const pairs = (left: StructuralRegion, right: StructuralRegion) => {
diff --git a/apps/review-desktop/code-oss/src/vs/review/contrib/extensions/reviewCuratedExtensions.contribution.ts b/apps/review-desktop/code-oss/src/vs/review/contrib/extensions/reviewCuratedExtensions.contribution.ts
index eae3f8686..2368f2768 100644
--- a/apps/review-desktop/code-oss/src/vs/review/contrib/extensions/reviewCuratedExtensions.contribution.ts
+++ b/apps/review-desktop/code-oss/src/vs/review/contrib/extensions/reviewCuratedExtensions.contribution.ts
@@ -30,9 +30,6 @@ import { IProgressService, ProgressLocation } from '../../../platform/progress/c
 import { IQuickInputService, type IQuickPickItem } from '../../../platform/quickinput/common/quickInput.js';
 import { Registry } from '../../../platform/registry/common/platform.js';
 import { IStorageService, StorageScope, StorageTarget } from '../../../platform/storage/common/storage.js';
-import { IReviewDesktopConnectionService } from '../../services/reviewDesktopConnectionService.js';
-import { IEditorService } from '../../../workbench/services/editor/common/editorService.js';
-import { ReviewCanvasEditorPane } from '../../browser/parts/canvas/reviewCanvasPart.js';
 import { LifecyclePhase } from '../../../workbench/services/lifecycle/common/lifecycle.js';
 import {
 	Extensions as WorkbenchExtensions,
@@ -740,22 +737,3 @@ Registry.as<IWorkbenchContributionsRegistry>(WorkbenchExtensions.Workbench).regi
 	OptionalExtensionPinUpgrades,
 	LifecyclePhase.Eventually
 );
-
-class InstallExtraDiffLanguagesAction extends Action2 {
-	constructor() {
-		super({ id: 'review.installExtraDiffLanguages', title: localize2('review.diff.installLanguages', "Install extra diffr languages"), f1: true });
-	}
-	override async run(accessor: ServicesAccessor): Promise<void> {
-		const connection = accessor.get(IReviewDesktopConnectionService);
-		const progress = accessor.get(IProgressService);
-		const editors = accessor.get(IEditorService);
-		await progress.withProgress({ location: ProgressLocation.Notification, title: localize('review.diff.installingLanguages', "Installing extra diffr languages..."), delay: 0 }, async () => {
-			const { serverUrl, token } = await connection.getConnection();
-			const response = await fetch(`${serverUrl}/diffr-languages/install`, { method: 'POST', headers: { 'x-review-token': token } });
-			if (!response.ok) throw new Error((await response.json()).error);
-			const pane = editors.activeEditorPane;
-			if (pane instanceof ReviewCanvasEditorPane) await pane.refreshComparison();
-		});
-	}
-}
-registerAction2(InstallExtraDiffLanguagesAction);
diff --git a/apps/review-desktop/code-oss/src/vs/review/services/reviewDiffViewService.ts b/apps/review-desktop/code-oss/src/vs/review/services/reviewDiffViewService.ts
index 7b1136bdb..025931f4c 100644
--- a/apps/review-desktop/code-oss/src/vs/review/services/reviewDiffViewService.ts
+++ b/apps/review-desktop/code-oss/src/vs/review/services/reviewDiffViewService.ts
@@ -37,7 +37,7 @@ import { ReviewFilesDiffView, ReviewFilesEditorInput, type ReviewFilesEditorEntr
 import { ReviewEmbeddedEditors } from "./reviewEmbeddedEditors.js";
 
 import { createStructuralDiffEditors } from "./reviewStructuralDiff.js";
-import { StructuralDiffSession } from "./reviewStructuralDiffSession.js";
+import { StructuralDiffSession, type StructuralSessionChange } from "./reviewStructuralDiffSession.js";
 import type { StructuralDiffStream } from "./reviewStructuralDiffClient.js";
 
 export interface ReviewDiffViewSource {
@@ -360,17 +360,12 @@ class DiffViewController extends Disposable implements ReviewDiffViewHandle {
 
 	private observeSession(session: StructuralDiffSession, entries: readonly ReviewFilesEditorEntry[], view: ReviewFilesDiffView, store: DisposableStore, structuralEnabled: boolean): void {
 		const rendered = new Set<string>();
-		const annotationWarnings = new Set<string>();
-		const renderCurrentState = (change?: import("./reviewStructuralDiffSession.js").StructuralSessionChange) => {
+		const renderCurrentState = (change?: StructuralSessionChange) => {
 			if (this.disposed) return;
 			for (const entry of entries) {
 				const path = entry.file.path;
-				if (change && !change.files.has(path) && !change.labels.has(path)) continue;
+				if (change && !change.files.has(path)) continue;
 				const result = entry.file.status === "unchanged" ? {} : session.getFileResult(path);
-				if (result?.annotationError && !annotationWarnings.has(path)) {
-					annotationWarnings.add(path);
-					this._onDidError.fire(`Summary unavailable for ${path}: ${result.annotationError}`);
-				}
 				if (!result || rendered.has(path)) continue;
 				rendered.add(path);
 				if (structuralEnabled && result.hidden !== undefined) view.hideFile(path, result.hidden);
diff --git a/apps/review-desktop/code-oss/src/vs/review/services/reviewStructuralDiffSession.test.ts b/apps/review-desktop/code-oss/src/vs/review/services/reviewStructuralDiffSession.test.ts
index 16d6b83eb..b183fd5ee 100644
--- a/apps/review-desktop/code-oss/src/vs/review/services/reviewStructuralDiffSession.test.ts
+++ b/apps/review-desktop/code-oss/src/vs/review/services/reviewStructuralDiffSession.test.ts
@@ -1,13 +1,34 @@
 import assert from 'node:assert/strict';
 import test from 'node:test';
 import { StructuralDiffSession } from './reviewStructuralDiffSession.js';
-import type { StructuralEvent } from '../common/reviewStructuralDiff.js';
+import { STRUCTURAL_WIRE_VERSION, type StructuralEvent } from '../common/reviewStructuralDiff.js';
 
 const file = { rhs: { path: 'a.ts', oid: 'abc', mode: '100644' } };
-const start: StructuralEvent = { type: 'start', version: 4, lhs: { type: 'empty_tree' }, rhs: { type: 'revision', rev: 'head' }, files: [{ file, status: 'added' }] };
-const result: StructuralEvent = { type: 'file', file, diff: { type: 'text', structural_changes: { base: [], head: [[0, 1]] }, rhs: { text: 'a', regions: [{ kind: 'leaf', id: 1, fold_state_id: 2, alignment_id: 1, start: { line: 0, column: 0 }, end: { line: 0, column: 1 }, visibility: { collapsed: true } }] }, stats: { textual: { added: 1, removed: 0 }, visible: { added: 0, removed: 0 } } } };
+const start: StructuralEvent = { type: 'start', version: STRUCTURAL_WIRE_VERSION, lhs: { type: 'empty_tree' }, rhs: { type: 'revision', rev: 'head' }, files: [{ file, status: 'added' }] };
+const result: StructuralEvent = { type: 'file', file, diff: { type: 'text', structural_changes: { base: [], head: [[0, 1]] }, rhs: { text: 'a', root: { kind: 'leaf', id: 1, fold_state_id: 2, alignment_id: 1, start: { line: 0, column: 0 }, end: { line: 0, column: 1 }, visibility: { collapsed: true } } }, stats: { textual: { added: 1, removed: 0 }, visible: { added: 0, removed: 0 } } } };
 const complete: StructuralEvent = { type: 'complete', succeeded: 1, failed: 0 };
 
+test('file results supply root visibility and summary labels before comparison completion', async () => {
+	let release!: () => void;
+	const gate = new Promise<void>(resolve => release = resolve);
+	const labeled = structuredClone(result);
+	if (labeled.type !== 'file' || labeled.diff?.type !== 'text') throw new Error('Invalid fixture');
+	labeled.diff.rhs!.root.visibility = { collapsed: true, label: 'Generated file' };
+	const session = new StructuralDiffSession({ async *streamComparison() { yield start; yield labeled; await gate; yield complete; } });
+	const label = session.regionLabel('a.ts', 1);
+	const task = session.start();
+	try {
+		const fileResult = await session.fileResult('a.ts');
+		assert.equal(fileResult.hidden, 'Generated file');
+		assert.equal(label.get(), 'Generated file');
+		assert.equal(session.complete, false);
+		session.setRegionCollapsed('a.ts', 2, false);
+		release(); await task;
+		assert.equal(session.isRegionCollapsed('a.ts', 2), false);
+		assert.equal(session.error, undefined);
+	} finally { release(); session.dispose(); await task; }
+});
+
 test('views detach and reattach without restarting a comparison or losing folds', async () => {
 	let requests = 0;
 	const session = new StructuralDiffSession({ async *streamComparison() { requests++; yield start; yield result; yield complete; } });
@@ -61,117 +82,6 @@ test('truncation and missing manifest results are visible to later subscribers',
 	}
 });
 
-test('deferred annotations retain source identity, counts and user fold choices', async () => {
-	let release!: () => void;
-	const gate = new Promise<void>(resolve => release = resolve);
-	const session = new StructuralDiffSession({
-		async *streamComparison() {
-			yield start; yield structuredClone(result);
-			await gate;
-			yield { type: 'annotations', file, annotations: [{ region_id: 1, label: 'summarized' }] } as StructuralEvent;
-			yield complete;
-		}
-	});
-	const task = session.start();
-	while (!session.getTextDiff('a.ts')) await new Promise(resolve => setTimeout(resolve, 0));
-	try {
-		const initial = session.getTextDiff('a.ts')!;
-		assert.equal(session.complete, false);
-		session.setRegionCollapsed('a.ts', 2, false);
-		release(); await task;
-		assert.equal(session.getTextDiff('a.ts'), initial);
-		assert.equal(initial.rhs!.regions![0].visibility?.label, 'summarized');
-		assert.equal(initial.rhs!.text, 'a');
-		assert.deepEqual(initial.structural_changes, { base: [], head: [[0, 1]] });
-		assert.equal(session.isRegionCollapsed('a.ts', 2), false);
-		assert.equal(session.error, undefined);
-	} finally { release(); session.dispose(); }
-});
-
-test('invalid annotation batches are atomic and enrichment failure keeps the initial diff usable', async () => {
-	for (const invalid of [false, true]) {
-		const session = new StructuralDiffSession({
-			async *streamComparison() {
-				yield start; yield structuredClone(result);
-				yield {
-					type: 'annotations', file,
-					annotations: invalid ? [{ region_id: 1, label: 'must not apply' }, { region_id: 99, label: 'bad' }] : [],
-					error: invalid ? undefined : { code: 'enrichment_failed', message: 'offline' },
-				} as StructuralEvent;
-				yield complete;
-			}
-		});
-		try {
-			await session.start();
-			assert.equal(session.getTextDiff('a.ts')!.rhs!.regions![0].visibility?.label, undefined);
-			assert.equal(session.isRegionCollapsed('a.ts', 2), true);
-			if (invalid) assert.match(session.error!, /Unknown annotation region/);
-			else {
-				assert.equal(session.getFileResult('a.ts')?.annotationError, 'offline');
-				assert.equal(session.error, undefined);
-			}
-		} finally { session.dispose(); }
-	}
-});
-
-test('streamed labels update existing bands without invalidating either file provider', async () => {
-	const { StructuralDiffProvider } = await import('./reviewStructuralDiff.js');
-	const { URI } = await import('../../base/common/uri.js');
-	const { CancellationToken } = await import('../../base/common/cancellation.js');
-	const other = { rhs: { path: 'b.ts', oid: 'def', mode: '100644' } };
-	let release!: () => void;
-	const gate = new Promise<void>(resolve => release = resolve);
-	const session = new StructuralDiffSession({
-		async *streamComparison() {
-			yield { ...start, files: [...start.files, { file: other, status: 'added' as const }] };
-			yield structuredClone(result);
-			yield { ...structuredClone(result), file: other };
-			await gate;
-			yield { type: 'annotations', file, annotations: [{ region_id: 1, label: 'first' }] } as StructuralEvent;
-			yield { type: 'annotations', file, annotations: [{ region_id: 1, label: '// pseudocode\nfinal summary' }] } as StructuralEvent;
-			yield { ...complete, succeeded: 2 };
-		}
-	});
-	const task = session.start();
-	const ready = new Promise<void>(resolve => {
-		const sub = session.onDidChange(change => { if (change.files.has('b.ts')) { sub.dispose(); resolve(); } });
-	});
-	try {
-		await ready;
-		const models = (path: string) => [
-			{ uri: URI.parse(`test:/base/${path}`), getLinesContent: () => [''] },
-			{ uri: URI.parse(`test:/head/${path}`), getLinesContent: () => ['a'] },
-		] as const;
-		const a = models('a.ts'), b = models('b.ts');
-		const pairs = new Map([[`${a[0].uri}\n${a[1].uri}`, 'a.ts'], [`${b[0].uri}\n${b[1].uri}`, 'b.ts']]);
-		const pa = new StructuralDiffProvider(session, pairs, new Set());
-		const pb = new StructuralDiffProvider(session, pairs, new Set());
-		const compute = (provider: typeof pa, pair: ReturnType<typeof models>) => provider.computeDiff(
-			pair[0] as Parameters<typeof provider.computeDiff>[0], pair[1] as Parameters<typeof provider.computeDiff>[1],
-			{ ignoreTrimWhitespace: false, maxComputationTimeMs: 0, computeMoves: false }, CancellationToken.None,
-		);
-		const diff = await compute(pa, a);
-		await compute(pb, b);
-		let invalidationsA = 0, invalidationsB = 0, labelBatches = 0;
-		const subscriptions = [pa.onDidChange(() => invalidationsA++), pb.onDidChange(() => invalidationsB++),
-		session.onDidChange(change => { if (change.labels.has('a.ts')) labelBatches++; })];
-		const band = diff.contextGaps![0];
-		release(); await task;
-		assert.equal(band.labelObservable!.get(), '// pseudocode\nfinal summary');
-		assert.equal(invalidationsA, 0);
-		assert.equal(invalidationsB, 0);
-		assert.equal(labelBatches, 1, 'a burst publishes only the latest presentation state');
-		const folded = new Promise<void>(resolve => {
-			const sub = pa.onDidChange(() => { sub.dispose(); resolve(); });
-		});
-		session.setRegionCollapsed('a.ts', 2, false);
-		await folded;
-		assert.equal(invalidationsA, 1);
-		assert.equal(invalidationsB, 0, 'folding a file does not invalidate unrelated editors');
-		subscriptions.forEach(sub => sub.dispose());
-	} finally { release(); session.dispose(); await task; }
-});
-
 test('structural editor models retain diffr bytes across a live file save', async () => {
 	const { createStructuralDiffEditors, StructuralDiffProvider } = await import('./reviewStructuralDiff.js');
 	const { URI } = await import('../../base/common/uri.js');
@@ -188,7 +98,7 @@ test('structural editor models retain diffr bytes across a live file save', asyn
 		yield { ...start, files: [{ file: changedFile, status: 'modified' }] } as StructuralEvent;
 		await gate;
 		yield { type: 'file', file: changedFile, diff: {
-			type: 'text', lhs: { text: 'base\n' }, rhs: { text: 'saved A\n' },
+			type: 'text', lhs: { text: 'base\n', root: {kind:'leaf',id:3,fold_state_id:3,alignment_id:1,start:{line:0,column:0},end:{line:1,column:0}} }, rhs: { text: 'saved A\n', root: {kind:'leaf',id:4,fold_state_id:4,alignment_id:1,start:{line:0,column:0},end:{line:1,column:0}} },
 			structural_changes: { base: [[0, 1]], head: [[0, 1]] },
 			stats: { textual: { added: 1, removed: 1 }, visible: { added: 1, removed: 1 } },
 		} } as StructuralEvent;
diff --git a/apps/review-desktop/code-oss/src/vs/review/services/reviewStructuralDiffSession.ts b/apps/review-desktop/code-oss/src/vs/review/services/reviewStructuralDiffSession.ts
index 77a58274c..b64888fa0 100644
--- a/apps/review-desktop/code-oss/src/vs/review/services/reviewStructuralDiffSession.ts
+++ b/apps/review-desktop/code-oss/src/vs/review/services/reviewStructuralDiffSession.ts
@@ -1,5 +1,5 @@
 import { RunOnceScheduler } from "../../base/common/async.js";
-import { observableValue, transaction, type IObservable, type ISettableObservable } from "../../base/common/observable.js";
+import { observableValue, type IObservable, type ISettableObservable } from "../../base/common/observable.js";
 import { Emitter } from "../../base/common/event.js";
 import { Disposable } from "../../base/common/lifecycle.js";
 import { CancellationError } from "../../base/common/errors.js";
@@ -11,14 +11,11 @@ export interface StructuralFileResult {
 	diff?: StructuralDiff;
 	error?: string;
 	hidden?: string;
-	annotationError?: string;
 }
 
 export interface StructuralSessionChange {
 	/** Files whose diff or fold state changed. */
 	readonly files: ReadonlySet<string>;
-	/** Files with new summary labels or summary errors; their diff is unchanged. */
-	readonly labels: ReadonlySet<string>;
 	readonly status: boolean;
 }
 
@@ -27,11 +24,9 @@ export class StructuralDiffSession extends Disposable {
 	private readonly changed = this._register(new Emitter<StructuralSessionChange>());
 	readonly onDidChange = this.changed.event;
 	private readonly pendingFiles = new Set<string>();
-	private readonly pendingLabels = new Set<string>();
 	private pendingStatus = false;
 	private readonly regions = new Map<string, StructuralRegion>();
 	private readonly labels = new Map<string, ISettableObservable<string | undefined>>();
-	private readonly pendingLabelValues = new Map<string, string>();
 	private readonly notification = this._register(new RunOnceScheduler(() => this.flushChanges(), 16));
 	private readonly abort = new AbortController();
 	private readonly results = new Map<string, StructuralFileResult>();
@@ -107,14 +102,10 @@ export class StructuralDiffSession extends Disposable {
 			if (event.type !== "start" || event.version !== STRUCTURAL_WIRE_VERSION) throw new Error("Unsupported diffr stream protocol.");
 			this.acceptManifest(event);
 		} else if (event.type === "file") this.storeFileResult(event);
-		else if (event.type === "annotations") this.applyAnnotations(event);
 		else if (event.type === "complete") this.finishLoading(event);
 		else throw new Error(`Unexpected diffr event: ${event.type}`);
 		if (event.type === "file") this.notify(structuralFilePath(event.file));
-		else if (event.type === "annotations") {
-			this.pendingLabels.add(structuralFilePath(event.file));
-			this.notify();
-		} else this.notify(undefined, true);
+		else this.notify(undefined, true);
 	}
 
 	/** Stable presentation state, shared by all editors displaying this region. */
@@ -135,15 +126,11 @@ export class StructuralDiffSession extends Disposable {
 	}
 
 	private flushChanges(): void {
-		if (!this.pendingFiles.size && !this.pendingLabels.size && !this.pendingStatus) return;
+		if (!this.pendingFiles.size && !this.pendingStatus) return;
 		const change: StructuralSessionChange = {
-			files: new Set(this.pendingFiles), labels: new Set(this.pendingLabels), status: this.pendingStatus,
+			files: new Set(this.pendingFiles), status: this.pendingStatus,
 		};
-		const labels = new Map(this.pendingLabelValues);
-		this.pendingFiles.clear(); this.pendingLabels.clear(); this.pendingLabelValues.clear(); this.pendingStatus = false;
-		transaction(tx => {
-			for (const [key, value] of labels) this.labels.get(key)?.set(value, tx);
-		});
+		this.pendingFiles.clear(); this.pendingStatus = false;
 		this.changed.fire(change);
 	}
 
@@ -160,33 +147,17 @@ export class StructuralDiffSession extends Disposable {
 		if (diff.type === "text") {
 			const seed = (region: StructuralRegion) => {
 				this.regions.set(`${path}:${region.id}`, region);
+				this.labels.get(`${path}:${region.id}`)?.set(region.visibility?.label, undefined);
 				const key = `${path}:${region.fold_state_id}`;
 				if (!this.folds.has(key)) this.folds.set(key, region.visibility?.collapsed === true);
 				if (region.kind === "fold") region.children.forEach(seed);
 			};
-			for (const side of [diff.lhs, diff.rhs]) side?.regions?.forEach(seed);
-		}
-		this.results.set(path, {
-			diff,
-			hidden: event.visibility?.collapsed ? event.visibility.label || "Hidden by default" : undefined
-		});
-	}
-
-	private applyAnnotations(event: Extract<StructuralEvent, { type: "annotations" }>): void {
-		const path = structuralFilePath(event.file);
-		const result = this.results.get(path);
-		if (result?.diff?.type !== "text") throw new Error(`Annotations precede a text result: ${path}`);
-		// Validate the entire batch before applying it. Labels do not replace the
-		// source, correspondence, region identities, or the reader's fold choices.
-		for (const annotation of event.annotations) {
-			if (!this.regions.has(`${path}:${annotation.region_id}`)) throw new Error(`Unknown annotation region: ${annotation.region_id}`);
-		}
-		for (const annotation of event.annotations) {
-			const region = this.regions.get(`${path}:${annotation.region_id}`)!;
-			region.visibility = { ...region.visibility, label: annotation.label };
-			this.pendingLabelValues.set(`${path}:${region.id}`, annotation.label);
+			for (const side of [diff.lhs, diff.rhs]) if (side) seed(side.root);
 		}
-		result.annotationError = event.error?.message;
+		const visibility = diff.type === "text"
+			? [diff.rhs, diff.lhs].find(side => side?.root.visibility?.collapsed)?.root.visibility
+			: undefined;
+		this.results.set(path, { diff, hidden: visibility ? visibility.label || "Hidden by default" : undefined });
 	}
 
 	private finishLoading(event: Extract<StructuralEvent, { type: "complete" }>): void {
@@ -203,8 +174,6 @@ export class StructuralDiffSession extends Disposable {
 		this.labels.clear();
 		this.regions.clear();
 		this.pendingFiles.clear();
-		this.pendingLabels.clear();
-		this.pendingLabelValues.clear();
 		super.dispose();
 	}
 }
diff --git a/apps/review-desktop/package.json b/apps/review-desktop/package.json
index 58f467ca9..37690dc7a 100644
--- a/apps/review-desktop/package.json
+++ b/apps/review-desktop/package.json
@@ -29,7 +29,7 @@
     "@dev.fast/whiteboard": "workspace:*"
   },
   "devDependencies": {
-    "@dev.fast/diffr": "0.1.10",
+    "@dev.fast/diffr": "catalog:",
     "@dev.fast/review-canvas": "workspace:*",
     "@types/node": "24.12.2",
     "jsdom": "29.1.1",
diff --git a/apps/review-desktop/scripts/e2e/journeys/diffr-settings.mjs b/apps/review-desktop/scripts/e2e/journeys/diffr-settings.mjs
index 7e5f60d92..fb05d9d60 100644
--- a/apps/review-desktop/scripts/e2e/journeys/diffr-settings.mjs
+++ b/apps/review-desktop/scripts/e2e/journeys/diffr-settings.mjs
@@ -54,7 +54,7 @@ function testFolds(events) {
 
   return events
     .filter((event) => event.type === "file")
-    .flatMap((event) => walk(event.diff?.rhs?.regions))
+    .flatMap((event) => walk(event.diff?.rhs ? [event.diff.rhs.root] : []))
     .filter(
       (region) =>
         region.tags?.includes("test-bodies:test") &&
@@ -117,8 +117,9 @@ export async function run(ctx) {
   await toggle.click();
   await ctx.until(
     async () =>
-      (await ctx.apiOk("/diffr-config")).values.plugins.bundled["test-bodies"]
-        .enabled === false,
+      (await ctx.apiOk("/diffr-config")).values.plugins.shape.bundled[
+        "test-bodies"
+      ].enabled === false,
     "diffr persisted the setting",
   );
   await settings
diff --git a/apps/review-desktop/scripts/e2e/journeys/extra-diff-languages.mjs b/apps/review-desktop/scripts/e2e/journeys/extra-diff-languages.mjs
deleted file mode 100644
index d89c3f684..000000000
--- a/apps/review-desktop/scripts/e2e/journeys/extra-diff-languages.mjs
+++ /dev/null
@@ -1,146 +0,0 @@
-import assert from "node:assert/strict";
-import { writeFile } from "node:fs/promises";
-import path from "node:path";
-
-import { createReview } from "../harness.mjs";
-
-export const name = "extra-diff-languages";
-
-export const phase = 1;
-
-export const options = {
-  settings: { "review.experimental.structuralDiff.enabled": true },
-  env: {
-    REVIEW_DIFFR_BINARY: "",
-    GEMINI_API_KEY: "",
-    GOOGLE_API_KEY: "",
-    OPENAI_API_KEY: "",
-    ANTHROPIC_API_KEY: "",
-  },
-  async beforeLaunch(ctx) {
-    ctx.env.XDG_CACHE_HOME = path.join(ctx.root, "cache");
-    const file = path.join(ctx.repo, "example.jl");
-    await writeFile(file, "function example()\n    value = 1\nend\n");
-    await ctx.git("add", ".");
-    await ctx.git(
-      "-c",
-      "commit.gpgsign=false",
-      "commit",
-      "-qm",
-      "Before optional grammar",
-    );
-    ctx.base = await ctx.git("rev-parse", "HEAD");
-    await writeFile(file, "function example()\n    value = 2\nend\n");
-    await ctx.git(
-      "-c",
-      "commit.gpgsign=false",
-      "commit",
-      "-qam",
-      "After optional grammar",
-    );
-    ctx.head = await ctx.git("rev-parse", "HEAD");
-  },
-};
-
-export async function run(ctx) {
-  const review = await createReview(ctx, {
-    title: "Extra diffr languages",
-    blocks: [
-      {
-        type: "code_peek",
-        source: {
-          file: "example.jl",
-          start: { side: "head", line: 1 },
-          end: { side: "head", line: 1 },
-        },
-      },
-    ],
-  });
-
-  const before = await ctx.apiOk(`/reviews-api/${review.reviewId}?full=true`);
-
-  const compare = async () => {
-    const response = await fetch(
-      new URL(
-        `/reviews-api/${review.reviewId}/structural-diff`,
-        ctx.discovery.url,
-      ),
-      { headers: { "x-review-token": ctx.discovery.token } },
-    );
-
-    assert.equal(response.status, 200);
-
-    return (await response.text())
-      .trim()
-      .split("\n")
-      .map((line) => JSON.parse(line))
-      .find(
-        (event) =>
-          event.type === "file" &&
-          (event.file.rhs ?? event.file.lhs).path === "example.jl",
-      ).diff;
-  };
-
-  assert.ok((await compare()).stats.fallback);
-
-  await review.canvas
-    .getByRole("button", { name: "Diff", exact: true })
-    .click();
-
-  let navigations = 0;
-  let installed = false;
-
-  const installationResponse = (response) => {
-    if (response.url().endsWith("/diffr-languages/install") && response.ok())
-      installed = true;
-  };
-
-  ctx.page.on("response", installationResponse);
-
-  const navigated = (frame) => {
-    if (frame === ctx.page.mainFrame()) navigations++;
-  };
-
-  ctx.page.on("framenavigated", navigated);
-
-  const refreshed = ctx.page.waitForResponse(
-    (response) =>
-      installed &&
-      response
-        .url()
-        .includes(`/reviews-api/${review.reviewId}/structural-diff`),
-    { timeout: 180000 },
-  );
-
-  await ctx.page.keyboard.press("F1");
-  const palette = ctx.page.locator(".quick-input-widget input").first();
-  await palette.fill(">Install extra diffr languages");
-  await ctx.page
-    .locator(".quick-input-list .monaco-list-row")
-    .filter({ hasText: "Install extra diffr languages" })
-    .first()
-    .click();
-  const response = await refreshed;
-  assert.equal(response.status(), 200);
-
-  const structural = await compare();
-
-  assert.equal(structural.stats.fallback, undefined);
-  assert.equal(structural.rhs.text, "function example()\n    value = 2\nend\n");
-  await review.canvas
-    .getByText("example.jl", { exact: true })
-    .first()
-    .waitFor();
-  assert.equal(navigations, 0, "installation must not reload the window");
-  ctx.page.off("framenavigated", navigated);
-  ctx.page.off("response", installationResponse);
-  await ctx.page.screenshot({
-    path: path.join(ctx.root, "extra-diff-languages-ready.png"),
-  });
-  const after = await ctx.apiOk(`/reviews-api/${review.reviewId}?full=true`);
-  assert.deepEqual(after, before);
-  ctx.check(
-    "extra languages: command palette installs the full edition and refreshes the current review without reloading the window",
-    "extra languages: pinned review identity and content remain unchanged",
-  );
-}
diff --git a/apps/review-desktop/scripts/linux/nixos/vm-test.nix b/apps/review-desktop/scripts/linux/nixos/vm-test.nix
index e8c60791d..9de0a7e23 100644
--- a/apps/review-desktop/scripts/linux/nixos/vm-test.nix
+++ b/apps/review-desktop/scripts/linux/nixos/vm-test.nix
@@ -15,7 +15,7 @@ let
     targetPkgs = p: package.runtimePackages p ++ [ p.unzip p.file p.binutils p.cargo p.rustc ];
     runScript = pkgs.writeShellScript "probe-installed-whiteboard" ''
       set -eu
-      ${raw}/resources/app/review-runtime/bin/diffr --version
+      ${raw}/resources/app/review-runtime/node_modules/@dev.fast/diffr-linux-*/diffr --version
       mkdir -p "$HOME/rust-extension"
       unzip -qo ${rustVsix} -d "$HOME/rust-extension"
       chmod +x "$HOME/rust-extension/extension/server/rust-analyzer"
diff --git a/apps/review-desktop/scripts/lsp-e2e.mjs b/apps/review-desktop/scripts/lsp-e2e.mjs
index cb37f91b3..4798c0874 100644
--- a/apps/review-desktop/scripts/lsp-e2e.mjs
+++ b/apps/review-desktop/scripts/lsp-e2e.mjs
@@ -38,9 +38,11 @@ const { values } = parseArgs({
   options: { app: { type: "string" }, keep: { type: "boolean" } },
 });
 
+const diffrPackage = `node_modules/@dev.fast/diffr-${process.platform}-${process.arch}/diffr`;
+
 const bundledDiffr = values.app
-  ? path.join(values.app, "Contents/Resources/app/review-runtime/bin/diffr")
-  : path.join(workspace, "packages/review/bin/diffr");
+  ? path.join(values.app, "Contents/Resources/app/review-runtime", diffrPackage)
+  : path.join(workspace, diffrPackage);
 
 const structuralDiffAvailable =
   !!process.env.REVIEW_DIFFR_BINARY ||
diff --git a/apps/review-desktop/scripts/package-linux.sh b/apps/review-desktop/scripts/package-linux.sh
index f00ec8ecc..c473fd2ab 100755
--- a/apps/review-desktop/scripts/package-linux.sh
+++ b/apps/review-desktop/scripts/package-linux.sh
@@ -42,7 +42,6 @@ node "$APP_DIR/scripts/curated-extensions.mjs" \
 # The installed app embeds its own Review server runtime (server, CLI, and
 # docs) so it never reaches back into this checkout.
 pnpm --dir "$MONOREPO_ROOT" --filter @dev.fast/whiteboard build
-pnpm --dir "$MONOREPO_ROOT" --filter @dev.fast/whiteboard ensure:diffr --required
 node "$APP_DIR/scripts/stage-review-runtime.mjs" --packaged-root "$PACKAGED_ROOT"
 
 node "$APP_DIR/scripts/stage-review-runtime.mjs" --verify --packaged-root "$PACKAGED_ROOT"
diff --git a/apps/review-desktop/scripts/package-macos.sh b/apps/review-desktop/scripts/package-macos.sh
index 82583d3fc..bf9af5f7c 100755
--- a/apps/review-desktop/scripts/package-macos.sh
+++ b/apps/review-desktop/scripts/package-macos.sh
@@ -79,8 +79,6 @@ node "$APP_DIR/scripts/curated-extensions.mjs" \
 #
 # build.sh produces the server dist in local mode. In precompiled mode, the
 # server dist arrives in the darwin payload.
-# Fetch on Darwin: precompiled payloads were built on Linux.
-pnpm --dir "$MONOREPO_ROOT" --filter @dev.fast/whiteboard ensure:diffr --required
 node "$APP_DIR/scripts/stage-review-runtime.mjs" --packaged-root "$PACKAGED_APP"
 
 # Installs Assets.car and rewrites CFBundleIconName, which invalidates any
diff --git a/apps/review-desktop/scripts/package-windows.sh b/apps/review-desktop/scripts/package-windows.sh
index 1f60a339a..4990f04ac 100644
--- a/apps/review-desktop/scripts/package-windows.sh
+++ b/apps/review-desktop/scripts/package-windows.sh
@@ -15,7 +15,6 @@ node "$APP_DIR/scripts/copy-canvas.mjs" --packaged-root "$PACKAGED_ROOT"
 node "$APP_DIR/scripts/curated-extensions.mjs" --target=win32-x64 --copy-to "$PACKAGED_ROOT/resources/app/extensions"
 # ty links the Visual C++ runtime dynamically and a clean Windows install has none, so ship it beside ty.
 cp "$(cygpath -u "$SYSTEMROOT")/System32/vcruntime140.dll" "$PACKAGED_ROOT/resources/app/extensions/astral-sh.ty/bundled/libs/bin/"
-pnpm --dir "$MONOREPO_ROOT" --filter @dev.fast/whiteboard ensure:diffr --required
 node "$APP_DIR/scripts/stage-review-runtime.mjs" --packaged-root "$PACKAGED_ROOT"
 node "$APP_DIR/scripts/stage-review-runtime.mjs" --verify --packaged-root "$PACKAGED_ROOT"
 npm --prefix "$CHECKOUT" run gulp -- vscode-win32-x64-inno-updater
diff --git a/apps/review-desktop/scripts/run.sh b/apps/review-desktop/scripts/run.sh
index 7bad815b0..b5e1fddf4 100755
--- a/apps/review-desktop/scripts/run.sh
+++ b/apps/review-desktop/scripts/run.sh
@@ -71,13 +71,6 @@ if [[ "$(cat "$EXTENSIONS_SELECTION_STAMP" 2>/dev/null)" != "$EXTENSIONS_SELECTI
   echo "$EXTENSIONS_SELECTION" >"$EXTENSIONS_SELECTION_STAMP"
 fi
 
-# Development launches use the checkout runtime, not the staged release bundle.
-# Check the pinned binary even when all compiled outputs are already current.
-# An explicit developer override supplies its own executable.
-if [[ -z "$PACKAGED_ROOT" && -z "${REVIEW_DIFFR_BINARY:-}" ]]; then
-  pnpm --dir "$MONOREPO_ROOT" --filter @dev.fast/whiteboard ensure:diffr --required
-fi
-
 rebuild_review_desktop_outputs "$MONOREPO_ROOT" "$REVIEW_PACKAGE"
 # Names this Desktop as the checkout's dev instance, packaged or not.
 export DEV_FAST_REVIEW_CHECKOUT="$MONOREPO_ROOT"
diff --git a/apps/review-desktop/scripts/runtime-bundler.test.mjs b/apps/review-desktop/scripts/runtime-bundler.test.mjs
index 20d9ba016..22106981b 100644
--- a/apps/review-desktop/scripts/runtime-bundler.test.mjs
+++ b/apps/review-desktop/scripts/runtime-bundler.test.mjs
@@ -13,13 +13,13 @@ import test from "node:test";
 
 import {
   RUNTIME_CLI_ENTRY,
+  RUNTIME_DIFFR_ENTRY,
   assertNoRuntimeBundler,
   assertPackagedArtifacts,
   assertRuntimeClosure,
   assertRuntimeContents,
   requiredPackagedArtifacts,
   runtimeRootForPackagedRoot,
-  stageDiffrBinary,
 } from "./stage-review-runtime.mjs";
 
 test("runtime closure rejects transitive esbuild packages and native binaries", async () => {
@@ -131,7 +131,7 @@ test("final package verification requires the CLI and rechecks archives outside
       await mkdir(path.dirname(artifact), { recursive: true });
 
       if (artifact === path.join(runtime, "node_modules")) {
-        await mkdir(artifact);
+        await mkdir(artifact, { recursive: true });
       } else {
         await writeFile(artifact, artifact.endsWith(".json") ? "{}\n" : "");
       }
@@ -158,12 +158,12 @@ test("final package verification requires the CLI and rechecks archives outside
     await assertRuntimeClosure(runtime);
     await assertPackagedArtifacts(packaged);
 
-    const diffr = path.join(runtime, "bin", "diffr");
+    const diffr = path.join(runtime, RUNTIME_DIFFR_ENTRY);
     await rm(diffr, { force: true });
-    await assert.rejects(assertRuntimeClosure(runtime), /missing bin\/diffr/);
+    await assert.rejects(assertRuntimeClosure(runtime), /missing node_modules\/@dev\.fast\/diffr-/);
     await assert.rejects(
       assertPackagedArtifacts(packaged),
-      /missing .*bin\/diffr/,
+      /missing .*diffr-/,
     );
     await writeFile(diffr, "");
 
@@ -188,31 +188,6 @@ test("final package verification requires the CLI and rechecks archives outside
   }
 });
 
-test("diffr staging rejects missing and stale downloads", async () => {
-  const root = await mkdtemp(path.join(os.tmpdir(), "review-diffr-stage-"));
-  const runtime = path.join(root, "review-runtime");
-  const source = path.join(root, "diffr");
-
-  try {
-    await assert.rejects(stageDiffrBinary(runtime, source), /ensure:diffr/);
-    await writeFile(source, "#!/bin/sh\necho stale\n", { mode: 0o755 });
-    await assert.rejects(
-      stageDiffrBinary(runtime, source),
-      /missing or not diffr/,
-    );
-    await writeFile(
-      path.join(root, "diffr.stamp.json"),
-      JSON.stringify({ version: "0.0.0", target: "wrong-target" }),
-    );
-    await assert.rejects(
-      stageDiffrBinary(runtime, source),
-      /missing or not diffr/,
-    );
-  } finally {
-    await rm(root, { recursive: true, force: true });
-  }
-});
-
 function asarHeader(name) {
   const json = Buffer.from(
     JSON.stringify({ files: { [name]: { files: {} } } }),
diff --git a/apps/review-desktop/scripts/smoke-windows.mjs b/apps/review-desktop/scripts/smoke-windows.mjs
index e7d781f96..3d1d02572 100644
--- a/apps/review-desktop/scripts/smoke-windows.mjs
+++ b/apps/review-desktop/scripts/smoke-windows.mjs
@@ -207,7 +207,7 @@ export async function smokeWindows(app, evidence) {
         assert.match(version, /\d+\.\d+\.\d+/);
 
         const diffr = execFileSync(
-          path.join(runtime, "bin/diffr.exe"),
+          path.join(runtime, "node_modules/@dev.fast/diffr-win32-x64/diffr.exe"),
           ["--version"],
           { encoding: "utf8", timeout: 30000 },
         );
@@ -251,13 +251,12 @@ export async function smokeWindows(app, evidence) {
         const head = git("rev-parse", "HEAD").trim();
 
         const stream = execFileSync(
-          path.join(runtime, "bin/diffr.exe"),
+          path.join(runtime, "node_modules/@dev.fast/diffr-win32-x64/diffr.exe"),
           [
             "--repo",
             repository,
             "--format",
             "ndjson",
-            "--stream-annotations",
             base,
             head,
             "--",
diff --git a/apps/review-desktop/scripts/stage-review-runtime.mjs b/apps/review-desktop/scripts/stage-review-runtime.mjs
index a02fe8543..675b38772 100644
--- a/apps/review-desktop/scripts/stage-review-runtime.mjs
+++ b/apps/review-desktop/scripts/stage-review-runtime.mjs
@@ -2,9 +2,7 @@ import { execFile } from "node:child_process";
 import {
   access,
   chmod,
-  copyFile,
   cp,
-  mkdir,
   open,
   readFile,
   readdir,
@@ -12,7 +10,6 @@ import {
   rm,
   stat,
 } from "node:fs/promises";
-import { createRequire } from "node:module";
 import path from "node:path";
 import { fileURLToPath, pathToFileURL } from "node:url";
 import { promisify } from "node:util";
@@ -21,7 +18,7 @@ import { pruneReviewRuntime } from "./prune-review-runtime.mjs";
 
 const execFileAsync = promisify(execFile);
 
-const diffrName = process.platform === "win32" ? "diffr.exe" : "diffr";
+export const RUNTIME_DIFFR_ENTRY = `node_modules/@dev.fast/diffr-${process.platform}-${process.arch}/${process.platform === "win32" ? "diffr.exe" : "diffr"}`;
 
 const appDirectory = path.resolve(
   path.dirname(fileURLToPath(import.meta.url)),
@@ -48,10 +45,7 @@ export const REQUIRED_RUNTIME_ENTRIES = [
   "THIRD_PARTY_NOTICES.md",
   RUNTIME_SERVER_ENTRY,
   RUNTIME_CLI_ENTRY,
-  `bin/${diffrName}`,
-  "bin/diffr-package/bin/fetch.mjs",
-  "bin/diffr-package/package.json",
-  "bin/diffr-package/pins.json",
+  RUNTIME_DIFFR_ENTRY,
   "dist/cli.js",
   // The build's commit; without it the server reports `commit: null`.
   "dist/build-info.json",
@@ -147,7 +141,6 @@ export async function stageReviewRuntime(packagedRoot) {
   );
 
   await stageReviewDocs(runtimeRoot);
-  await stageDiffrBinary(runtimeRoot);
   await makeTreeOwnerWritable(path.join(runtimeRoot, "tutorial", "git-stub"));
   console.log("[runtime pruning]", await pruneReviewRuntime(runtimeRoot));
   await assertRuntimeClosure(runtimeRoot);
@@ -173,47 +166,6 @@ export async function stageReviewDocs(
   return destination;
 }
 
-export async function stageDiffrBinary(
-  runtimeRoot,
-  source = path.join(monorepoRoot, "packages", "review", "bin", diffrName),
-) {
-  if (!(await stat(source).catch(() => null))?.isFile()) {
-    throw new Error(
-      `Missing ${source}. Run pnpm --filter @dev.fast/whiteboard ensure:diffr before packaging.`,
-    );
-  }
-
-  const require = createRequire(
-    path.join(monorepoRoot, "packages/review/package.json"),
-  );
-
-  const packageRoot = path.dirname(
-    require.resolve("@dev.fast/diffr/package.json"),
-  );
-
-  await execFileAsync(process.execPath, [
-    path.join(packageRoot, "bin/fetch.mjs"),
-    "--check",
-    "--into",
-    path.dirname(source),
-  ]);
-
-  const destination = path.join(runtimeRoot, "bin", diffrName);
-  await mkdir(path.dirname(destination), { recursive: true });
-  await copyFile(source, destination);
-  const installerRoot = path.join(runtimeRoot, "bin/diffr-package");
-  await mkdir(path.join(installerRoot, "bin"), { recursive: true });
-
-  for (const file of ["package.json", "pins.json", "bin/fetch.mjs"]) {
-    await copyFile(
-      path.join(packageRoot, file),
-      path.join(installerRoot, file),
-    );
-  }
-
-  await chmod(destination, 0o755);
-}
-
 async function assertMatchingFileTrees(sourceRoot, destinationRoot) {
   const [sourceFiles, destinationFiles] = await Promise.all([
     listRelativeFiles(sourceRoot),
diff --git a/packages/review-protocol/package.json b/packages/review-protocol/package.json
index 1f9ecfe16..e80336a18 100644
--- a/packages/review-protocol/package.json
+++ b/packages/review-protocol/package.json
@@ -20,7 +20,7 @@
     "typecheck": "pnpm -w exec tsc -p packages/review-protocol/tsconfig.json --noEmit"
   },
   "dependencies": {
-    "@dev.fast/diffr": "0.1.10",
+    "@dev.fast/diffr": "catalog:",
     "@dev.fast/json": "workspace:*",
     "@dev.fast/trace-protocol": "workspace:*",
     "zod": "catalog:"
diff --git a/packages/review-protocol/src/contracts.ts b/packages/review-protocol/src/contracts.ts
index 67e486393..e169540df 100644
--- a/packages/review-protocol/src/contracts.ts
+++ b/packages/review-protocol/src/contracts.ts
@@ -487,6 +487,7 @@ export interface ReviewDiffrConfig {
   credentialSource: "config" | "environment" | "missing";
   providers?: ReviewDiffrProvider[];
   defaultPrompt?: string;
+  defaultHiddenTags?: string[];
   changed?: boolean;
   error?: string;
 }
@@ -522,6 +523,7 @@ const reviewDiffrConfigSchema = z.object({
     )
     .optional(),
   defaultPrompt: z.string().optional(),
+  defaultHiddenTags: z.array(z.string()).optional(),
   changed: z.boolean().optional(),
   error: z.string().optional(),
 });
diff --git a/packages/review-protocol/src/source-alignment.ts b/packages/review-protocol/src/source-alignment.ts
index 572a81d3f..26f987fcb 100644
--- a/packages/review-protocol/src/source-alignment.ts
+++ b/packages/review-protocol/src/source-alignment.ts
@@ -14,9 +14,7 @@ function alignmentRegionLines(region: StructuralRegion) {
   };
 }
 
-function alignmentLeaves(
-  regions: readonly StructuralRegion[] | undefined,
-): AlignmentLeaf[] {
+function alignmentLeaves(root: StructuralRegion | undefined): AlignmentLeaf[] {
   const leaves: AlignmentLeaf[] = [];
 
   const walk = (region: StructuralRegion) => {
@@ -24,7 +22,7 @@ function alignmentLeaves(
     else for (const child of region.children) walk(child);
   };
 
-  for (const region of regions ?? []) walk(region);
+  if (root) walk(root);
 
   return leaves;
 }
@@ -43,8 +41,8 @@ function monacoLineCount(source: StructuralSource | undefined): number {
 export function structuralRows(
   diff: Extract<StructuralDiff, { type: "text" }>,
 ): [number | null, number | null][] {
-  const lhsLeaves = alignmentLeaves(diff.lhs?.regions);
-  const rhsLeaves = alignmentLeaves(diff.rhs?.regions);
+  const lhsLeaves = alignmentLeaves(diff.lhs?.root);
+  const rhsLeaves = alignmentLeaves(diff.rhs?.root);
   const leftCount = monacoLineCount(diff.lhs);
   const rightCount = monacoLineCount(diff.rhs);
   const rows: [number | null, number | null][] = [];
diff --git a/packages/review/app/src/diffr-config-section.browser.test.tsx b/packages/review/app/src/diffr-config-section.browser.test.tsx
index ed7820a79..cdbb393ce 100644
--- a/packages/review/app/src/diffr-config-section.browser.test.tsx
+++ b/packages/review/app/src/diffr-config-section.browser.test.tsx
@@ -44,21 +44,25 @@ function config(): ReviewDiffrConfig {
       keylessCustomEndpoint: id === "openai",
     })),
     defaultPrompt: "Default prompt.",
+    defaultHiddenTags: ["generated", "vendored", "test"],
     values: {
+      version: 2,
       plugins: {
-        bundled: {
-          context: { enabled: true, lines: 3 },
-          "test-bodies": { enabled: true },
-          "deleted-bodies": { enabled: true },
-          "removed-runs": { enabled: true },
-          group: { enabled: true },
-          "hide-files": { enabled: true, deleted: true, tags: ["test"] },
-          summarize: {
-            enabled: false,
-            provider: "gemini",
-            model: "test-model",
-            tests: true,
-            system_prompt: "Default prompt.",
+        classify: { bundled: { hide: ["test"], hide_deleted: true } },
+        // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+        shape: {
+          bundled: {
+            context: { enabled: true, lines: 3 },
+            "test-bodies": { enabled: true },
+            "deleted-bodies": { enabled: true },
+            "removed-runs": { enabled: true },
+            summarize: {
+              enabled: false,
+              provider: "gemini",
+              model: "test-model",
+              tests: true,
+              system_prompt: "Default prompt.",
+            },
           },
         },
       },
@@ -66,6 +70,10 @@ function config(): ReviewDiffrConfig {
   };
 }
 
+function pluginSettings(config: ReviewDiffrConfig): JsonObject {
+  return config.values.plugins as JsonObject;
+}
+
 async function mount(overrides: Partial<ReviewDiffrConfig> = {}) {
   const current = { ...config(), ...overrides };
 
@@ -79,16 +87,22 @@ async function mount(overrides: Partial<ReviewDiffrConfig> = {}) {
       async (input) => ({
         ...current,
         changed: true,
+        defaultHiddenTags: ["generated", "vendored", "test"],
         values: {
+          version: 2,
           plugins: {
-            bundled: {
-              summarize: {
-                enabled: input.enabled,
-                provider: input.provider,
-                model: input.model,
-                endpoint: input.endpoint,
-                system_prompt: input.systemPrompt,
-                tests: input.tests,
+            classify: { bundled: { hide: ["test"], hide_deleted: true } },
+            // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+            shape: {
+              bundled: {
+                summarize: {
+                  enabled: input.enabled,
+                  provider: input.provider,
+                  model: input.model,
+                  endpoint: input.endpoint,
+                  system_prompt: input.systemPrompt,
+                  tests: input.tests,
+                },
               },
             },
           },
@@ -122,6 +136,116 @@ async function open() {
     .toBeVisible();
 }
 
+test("file-hiding controls use classify fields and retain custom tags across off and on", async () => {
+  const { actions, current } = await mount();
+  pluginSettings(current).classify = {
+    bundled: { hide: ["custom"], hide_deleted: true },
+  };
+  vi.mocked(actions.set).mockImplementation(async (key, value) => {
+    const field = key.split(".").at(-1)!;
+    const classify = pluginSettings(current).classify as JsonObject;
+    classify.bundled = {
+      ...(classify.bundled as JsonObject),
+      [field]: value,
+    };
+
+    return { ...current, changed: true };
+  });
+  await open();
+  await act(async () => page.getByLabelText("Hide files by tag").click());
+  expect(pluginSettings(current).classify).toMatchObject({
+    bundled: { hide: [] },
+  });
+  await act(async () => page.getByLabelText("Hide files by tag").click());
+  expect(pluginSettings(current).classify).toMatchObject({
+    bundled: { hide: ["custom"] },
+  });
+  await act(async () => page.getByLabelText("Hide deleted files").click());
+  expect(pluginSettings(current).classify).toMatchObject({
+    bundled: { hide_deleted: false },
+  });
+  expect(actions.set).toHaveBeenCalledWith("plugins.classify.bundled.hide", []);
+  expect(actions.set).toHaveBeenCalledWith("plugins.classify.bundled.hide", [
+    "custom",
+  ]);
+  expect(actions.set).toHaveBeenCalledWith(
+    "plugins.classify.bundled.hide_deleted",
+    false,
+  );
+});
+
+test("enabling tag hiding from an empty list uses the schema defaults", async () => {
+  const { actions, current } = await mount();
+  pluginSettings(current).classify = {
+    bundled: { hide: [], hide_deleted: false },
+  };
+  await open();
+  await act(async () => page.getByLabelText("Hide files by tag").click());
+  expect(actions.set).toHaveBeenCalledWith(
+    "plugins.classify.bundled.hide",
+    current.defaultHiddenTags,
+  );
+});
+
+test("custom classifier controls write its own entry and keep its tags", async () => {
+  const { actions, current } = await mount();
+  pluginSettings(current).classify = {
+    "team-classifier": {
+      path: "/plugins/team-classifier",
+      hide: ["team-generated"],
+      hide_deleted: true,
+    },
+  };
+  vi.mocked(actions.set).mockImplementation(async (key, value) => {
+    const [, , name, field] = key.split(".");
+    const classifiers = pluginSettings(current).classify as JsonObject;
+    const options = classifiers[name] as JsonObject;
+
+    classifiers[name] = { ...options, [field]: value };
+
+    return { ...current, changed: true };
+  });
+  await open();
+  await act(async () => page.getByLabelText("Hide files by tag").click());
+  expect(actions.set).toHaveBeenLastCalledWith(
+    "plugins.classify.team-classifier.hide",
+    [],
+  );
+  await act(async () => page.getByLabelText("Hide files by tag").click());
+  expect(actions.set).toHaveBeenLastCalledWith(
+    "plugins.classify.team-classifier.hide",
+    ["team-generated"],
+  );
+  await act(async () => page.getByLabelText("Hide deleted files").click());
+  expect(actions.set).toHaveBeenLastCalledWith(
+    "plugins.classify.team-classifier.hide_deleted",
+    false,
+  );
+  expect(pluginSettings(current).classify).toEqual({
+    "team-classifier": {
+      path: "/plugins/team-classifier",
+      hide: ["team-generated"],
+      hide_deleted: false,
+    },
+  });
+});
+
+test("custom classifiers only show the hide fields that they support", async () => {
+  const { actions, current } = await mount();
+  pluginSettings(current).classify = {
+    "team-classifier": { path: "/plugins/team-classifier", hide_deleted: true },
+  };
+  await open();
+  expect(
+    document.querySelector('input[aria-label="Hide files by tag"]'),
+  ).toBeNull();
+  await act(async () => page.getByLabelText("Hide deleted files").click());
+  expect(actions.set).toHaveBeenCalledWith(
+    "plugins.classify.team-classifier.hide_deleted",
+    false,
+  );
+});
+
 test("starts collapsed and reads only on first expansion", async () => {
   const { actions } = await mount();
   expect(actions.read).not.toHaveBeenCalled();
@@ -144,7 +268,7 @@ test("writes the selected key and keeps reload visible when collapsed", async ()
     await page.getByLabelText("Collapse test bodies").click();
   });
   expect(actions.set).toHaveBeenCalledWith(
-    "plugins.bundled.test-bodies.enabled",
+    "plugins.shape.bundled.test-bodies.enabled",
     false,
   );
   await expect
@@ -178,8 +302,14 @@ test("rejects invalid context lines without writing", async () => {
   expect(actions.set).not.toHaveBeenCalled();
 });
 
-test("tests draft settings without saving, then saves and clears the key", async () => {
-  const { actions } = await mount();
+test("tests draft settings without saving, then saves the custom prompt and clears the key", async () => {
+  const saved = config();
+
+  const foldPlugins = (pluginSettings(saved).shape as JsonObject)
+    .bundled as JsonObject;
+
+  (foldPlugins.summarize as JsonObject).system_prompt = "Keep my wording.";
+  const { actions } = await mount(saved);
   await open();
   expect(
     (document.querySelector("input[type=password]") as HTMLInputElement).value,
@@ -203,13 +333,16 @@ test("tests draft settings without saving, then saves and clears the key", async
     provider: "gemini",
     model: "test-model",
     endpoint: "",
-    systemPrompt: "Default prompt.",
+    systemPrompt: "Keep my wording.",
     tests: true,
     apiKey: "test-secret",
   });
   await expect
     .element(page.getByLabelText("API key", { exact: true }))
     .toHaveValue("");
+  await expect
+    .element(page.getByLabelText("Prompt", { exact: true }))
+    .toHaveValue("Keep my wording.");
 });
 
 test("confirms discarding unsaved summary edits before reloading", async () => {
@@ -392,7 +525,16 @@ test("switching provider clears a custom endpoint, and a new endpoint warns abou
     system_prompt: "Default prompt.",
   };
 
-  await mount({ values: { ...values, plugins: { bundled: { summarize } } } });
+  await mount({
+    values: {
+      ...values,
+      plugins: {
+        ...(values.plugins as JsonObject),
+        // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+        shape: { bundled: { summarize } },
+      },
+    },
+  });
   await open();
   const endpoint = page.getByLabelText("Endpoint URL", { exact: true });
   await expect.element(endpoint).toHaveValue("https://openrouter.ai/api/v1");
diff --git a/packages/review/app/src/diffr-config-section.tsx b/packages/review/app/src/diffr-config-section.tsx
index 0d2931bdc..edbb573ca 100644
--- a/packages/review/app/src/diffr-config-section.tsx
+++ b/packages/review/app/src/diffr-config-section.tsx
@@ -1,5 +1,6 @@
 import { Button } from "@canvas/ui/button";
 import { TextField, fieldStyles } from "@canvas/ui/text-field";
+import { isBooleanValue, isStringValue } from "@dev.fast/json";
 import {
   type JsonValue,
   type ReviewDiffrConfig,
@@ -13,30 +14,61 @@ import { type ReactNode, useEffect, useRef, useState } from "react";
 import { Choice } from "./settings-choice";
 import { settingsStyles as styles } from "./settings-styles";
 
-const displaySettings = [
-  ["context.enabled", "Collapse unchanged lines"],
-  ["test-bodies.enabled", "Collapse test bodies"],
-  ["deleted-bodies.enabled", "Collapse deleted function bodies"],
-  ["removed-runs.enabled", "Collapse long removed stretches"],
-  ["group.enabled", "Group adjacent folds"],
-  ["hide-files.enabled", "Hide files by tag"],
-  ["hide-files.deleted", "Hide deleted files"],
+const foldSettings = [
+  ["plugins.shape.bundled.context.enabled", "Collapse unchanged lines"],
+  ["plugins.shape.bundled.test-bodies.enabled", "Collapse test bodies"],
+  [
+    "plugins.shape.bundled.deleted-bodies.enabled",
+    "Collapse deleted function bodies",
+  ],
+  [
+    "plugins.shape.bundled.removed-runs.enabled",
+    "Collapse long removed stretches",
+  ],
 ] as const;
 
+type DisplaySetting = readonly [key: string, label: string];
+
+function classifierPrefix(config: ReviewDiffrConfig): string | undefined {
+  const entries = setting(config, "plugins.classify");
+
+  if (!isJsonObject(entries)) return;
+  const names = Object.keys(entries);
+
+  if (names.length === 1) return `plugins.classify.${names[0]}`;
+}
+
+function displaySettings(config: ReviewDiffrConfig): DisplaySetting[] {
+  const settings: DisplaySetting[] = [...foldSettings];
+  const prefix = classifierPrefix(config);
+
+  if (!prefix) return settings;
+
+  if (Array.isArray(setting(config, `${prefix}.hide`)))
+    settings.push([`${prefix}.hide`, "Hide files by tag"]);
+
+  if (isBooleanValue(setting(config, `${prefix}.hide_deleted`)))
+    settings.push([`${prefix}.hide_deleted`, "Hide deleted files"]);
+
+  return settings;
+}
+
 function setting(
   config: ReviewDiffrConfig,
   key: string,
 ): JsonValue | undefined {
   let value: JsonValue | undefined = config.values;
 
-  for (const part of `plugins.bundled.${key}`.split("."))
+  for (const part of key.split("."))
     value = isJsonObject(value) ? value[part] : undefined;
 
   return value;
 }
 
 function provider(config: ReviewDiffrConfig): string {
-  return String(setting(config, "summarize.provider") ?? "");
+  return String(
+    setting(config, "plugins.shape.bundled.summarize.provider") ?? "",
+  );
 }
 
 /** The provider diffr describes as `id`, if any. */
@@ -50,14 +82,21 @@ function title(config: ReviewDiffrConfig, id: string): string {
 
 function summaryDraft(config: ReviewDiffrConfig): ReviewDiffrSummarizerInput {
   return {
-    enabled: setting(config, "summarize.enabled") === true,
+    enabled:
+      setting(config, "plugins.shape.bundled.summarize.enabled") === true,
     provider: provider(config),
-    model: String(setting(config, "summarize.model") ?? ""),
-    endpoint: String(setting(config, "summarize.endpoint") ?? ""),
+    model: String(
+      setting(config, "plugins.shape.bundled.summarize.model") ?? "",
+    ),
+    endpoint: String(
+      setting(config, "plugins.shape.bundled.summarize.endpoint") ?? "",
+    ),
     systemPrompt: String(
-      setting(config, "summarize.system_prompt") ?? config.defaultPrompt ?? "",
+      setting(config, "plugins.shape.bundled.summarize.system_prompt") ??
+        config.defaultPrompt ??
+        "",
     ),
-    tests: setting(config, "summarize.tests") === true,
+    tests: setting(config, "plugins.shape.bundled.summarize.tests") === true,
     apiKey: "",
   };
 }
@@ -74,6 +113,7 @@ export function DiffrConfigSection({
   const [draft, setDraft] = useState<ReviewDiffrSummarizerInput>();
   const [busy, setBusy] = useState(false);
   const pending = useRef(false);
+  const rememberedTags = useRef<string[] | undefined>(undefined);
   const [error, setError] = useState<string>();
   const [summary, setSummary] = useState<string>();
   const [changed, setChanged] = useState(false);
@@ -85,6 +125,7 @@ export function DiffrConfigSection({
     actions.read().then(
       (result) => {
         if (cancelled) return;
+        rememberTags(result);
         setConfig(result);
         setDraft(summaryDraft(result));
       },
@@ -121,7 +162,16 @@ export function DiffrConfigSection({
     }
   }
 
+  function rememberTags(result: ReviewDiffrConfig) {
+    const prefix = classifierPrefix(result);
+    const tags = prefix ? setting(result, `${prefix}.hide`) : undefined;
+
+    if (Array.isArray(tags) && tags.length)
+      rememberedTags.current = tags.filter(isStringValue);
+  }
+
   function saved(result: ReviewDiffrConfig) {
+    rememberTags(result);
     setConfig(result);
 
     if (result.changed) setChanged(true);
@@ -134,11 +184,15 @@ export function DiffrConfigSection({
     JSON.stringify(draft) !== JSON.stringify(summaryDraft(config));
 
   const unavailable =
-    !config || setting(config, "summarize.enabled") === undefined;
+    !config ||
+    setting(config, "plugins.shape.bundled.summarize.enabled") === undefined;
 
   const summaryValid = !!draft?.model.trim();
   const savedDraft = config && summaryDraft(config);
-  const hiddenTags = config ? setting(config, "hide-files.tags") : undefined;
+  const classifier = config && classifierPrefix(config);
+  const hideKey = classifier ? `${classifier}.hide` : undefined;
+
+  const hiddenTags = config && hideKey ? setting(config, hideKey) : undefined;
 
   return (
     <div {...stylex.props(styles.diffr)}>
@@ -158,23 +212,30 @@ export function DiffrConfigSection({
             {config && (
               <>
                 <h3>Display</h3>
-                {displaySettings.map(([key, label]) => (
+                {displaySettings(config).map(([key, label]) => (
                   <div key={key}>
                     <SettingRow label={label}>
                       <input
                         type="checkbox"
                         aria-label={label}
-                        checked={setting(config, key) === true}
+                        checked={
+                          key === hideKey
+                            ? Array.isArray(hiddenTags) && hiddenTags.length > 0
+                            : setting(config, key) === true
+                        }
                         disabled={busy || setting(config, key) === undefined}
                         onChange={(event) => {
-                          const value = event.target.checked;
+                          const value =
+                            key === hideKey
+                              ? event.target.checked
+                                ? (rememberedTags.current ??
+                                  config.defaultHiddenTags ??
+                                  [])
+                                : []
+                              : event.target.checked;
+
                           void run(async () =>
-                            saved(
-                              await actions.set(
-                                `plugins.bundled.${key}`,
-                                value,
-                              ),
-                            ),
+                            saved(await actions.set(key, value)),
                           );
                         }}
                       />
@@ -184,16 +245,19 @@ export function DiffrConfigSection({
                         Not available in this configuration.
                       </p>
                     )}
-                    {key === "context.enabled" && (
+                    {key === "plugins.shape.bundled.context.enabled" && (
                       <SettingRow label="Context lines">
                         <ContextLines
-                          value={setting(config, "context.lines")}
+                          value={setting(
+                            config,
+                            "plugins.shape.bundled.context.lines",
+                          )}
                           disabled={busy || setting(config, key) !== true}
                           commit={(value) =>
                             void run(async () =>
                               saved(
                                 await actions.set(
-                                  "plugins.bundled.context.lines",
+                                  "plugins.shape.bundled.context.lines",
                                   value,
                                 ),
                               ),
@@ -202,12 +266,11 @@ export function DiffrConfigSection({
                         />
                       </SettingRow>
                     )}
-                    {key === "hide-files.enabled" &&
-                      Array.isArray(hiddenTags) && (
-                        <p {...stylex.props(styles.rowDescription)}>
-                          Tags: {hiddenTags.join(", ")}
-                        </p>
-                      )}
+                    {key === hideKey && Array.isArray(hiddenTags) && (
+                      <p {...stylex.props(styles.rowDescription)}>
+                        Tags: {hiddenTags.join(", ")}
+                      </p>
+                    )}
                   </div>
                 ))}
                 <h3>AI summaries</h3>
diff --git a/packages/review/package.json b/packages/review/package.json
index 6f0d6a2aa..8411ecae3 100644
--- a/packages/review/package.json
+++ b/packages/review/package.json
@@ -41,7 +41,6 @@
   },
   "scripts": {
     "prebuild": "pnpm run build:workspace-deps",
-    "ensure:diffr": "diffr-fetch --into bin",
     "build": "node --max-old-space-size=8192 node_modules/tsdown/dist/run.mjs",
     "build:tutorial-assets": "tsx scripts/build-tutorial-assets.ts",
     "ensure:tutorial-assets": "tsx scripts/ensure-tutorial-assets.ts",
@@ -57,13 +56,14 @@
     "test:node": "vitest run --config vitest.config.ts --project shared-module-graph",
     "test:telemetry-privacy": "vitest run --config vitest.config.ts src/ui-telemetry-events.test.ts src/error-telemetry.test.ts",
     "typecheck": "pnpm -w exec tsc --noEmit -p packages/review",
-    "test:integration:diffr": "pnpm run build:workspace-deps && pnpm run ensure:diffr --required && vitest run --config vitest.integration.config.ts",
+    "test:integration:diffr": "pnpm run build:workspace-deps && vitest run --config vitest.integration.config.ts",
     "whiteboard": "tsx src/cli.ts"
   },
   "dependencies": {
     "@agentclientprotocol/claude-agent-acp": "0.84.0",
     "@agentclientprotocol/codex-acp": "2.0.0",
     "@agentclientprotocol/sdk": "1.5.1",
+    "@dev.fast/diffr": "catalog:",
     "@hono/node-server": "2.0.12",
     "@img/sharp-wasm32": "0.35.4",
     "@modelcontextprotocol/sdk": "1.30.0",
@@ -79,10 +79,10 @@
     "semver": "7.8.5",
     "sharp": "0.35.4",
     "smol-toml": "1.8.0",
+    "toml-eslint-parser": "catalog:",
     "zod": "catalog:"
   },
   "devDependencies": {
-    "@dev.fast/diffr": "0.1.10",
     "@dev.fast/json": "workspace:*",
     "@dev.fast/local-vcs": "^0.1.0",
     "@dev.fast/review-protocol": "workspace:*",
diff --git a/packages/review/scripts/bundled-diffr.integration.mjs b/packages/review/scripts/bundled-diffr.integration.mjs
index cc1ff0fee..940d25fa7 100644
--- a/packages/review/scripts/bundled-diffr.integration.mjs
+++ b/packages/review/scripts/bundled-diffr.integration.mjs
@@ -1,15 +1,23 @@
 import assert from "node:assert/strict";
 import { execFileSync } from "node:child_process";
 import { existsSync } from "node:fs";
-import { copyFile, mkdir, readFile, rm, writeFile } from "node:fs/promises";
+import {
+  copyFile,
+  cp,
+  mkdir,
+  readFile,
+  readdir,
+  rm,
+  writeFile,
+} from "node:fs/promises";
 import { createServer } from "node:http";
+import { createRequire } from "node:module";
 import path from "node:path";
 import { pathToFileURL } from "node:url";
 
 import { build } from "tsdown";
 import { afterAll, beforeAll, describe, test } from "vitest";
 
-import { stageDiffrBinary } from "../../../apps/review-desktop/scripts/stage-review-runtime.mjs";
 import {
   cleanupTempDirs,
   gitRepository,
@@ -20,9 +28,43 @@ let structuralDiff,
   readDiffrConfig,
   setDiffrConfigValue,
   saveDiffrSummarizer,
-  testDiffrSummarizer;
+  testDiffrSummarizer,
+  ensureDiffrConfigMigrated,
+  diffrExecutable;
+
+const diffrPackage = path.dirname(
+  createRequire(import.meta.url).resolve("@dev.fast/diffr/package.json"),
+);
+
+const platformPackage = path.dirname(
+  createRequire(path.join(diffrPackage, "package.json")).resolve(
+    `@dev.fast/diffr-${process.platform}-${process.arch}/package.json`,
+  ),
+);
+
+// A local candidate lets this test run before its npm release is published.
+const source =
+  process.env.REVIEW_DIFFR_TEST_BINARY || path.join(platformPackage, "diffr");
+
+async function stageDiffr(runtime) {
+  for (const directory of [diffrPackage, platformPackage])
+    await cp(
+      directory,
+      path.join(runtime, "node_modules/@dev.fast", path.basename(directory)),
+      { recursive: true, dereference: true },
+    );
 
-const source = path.resolve(import.meta.dirname, "../bin/diffr");
+  if (process.env.REVIEW_DIFFR_TEST_BINARY)
+    await copyFile(
+      source,
+      path.join(
+        runtime,
+        "node_modules/@dev.fast",
+        path.basename(platformPackage),
+        "diffr",
+      ),
+    );
+}
 
 async function collect(repositoryPath, base, head, paths, kind = "trees") {
   return Array.fromAsync(
@@ -37,7 +79,7 @@ async function collect(repositoryPath, base, head, paths, kind = "trees") {
 
 function successfulFiles(events, count) {
   assert.equal(events[0].type, "start");
-  assert.equal(events[0].version, 4);
+  assert.equal(events[0].version, 3);
   assert.deepEqual(events.at(-1), {
     type: "complete",
     succeeded: count,
@@ -100,7 +142,7 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
     git("add", "-A");
     git("commit", "-qm", "head");
     head = git("rev-parse", "HEAD");
-    await stageDiffrBinary(runtime, source);
+    await stageDiffr(runtime);
     await build({
       config: false,
       entry: {
@@ -108,6 +150,10 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
           import.meta.dirname,
           "../src/server/structural-diff.ts",
         ),
+        "diffr-config-migration": path.resolve(
+          import.meta.dirname,
+          "../src/server/diffr-config-migration.ts",
+        ),
         "diffr-config": path.resolve(
           import.meta.dirname,
           "../src/server/diffr-config.ts",
@@ -127,7 +173,8 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
         ).href
       );
 
-    ({ structuralDiff } = await load("structural-diff"));
+    ({ structuralDiff, diffrExecutable } = await load("structural-diff"));
+    ({ ensureDiffrConfigMigrated } = await load("diffr-config-migration"));
     ({
       readDiffrConfig,
       setDiffrConfigValue,
@@ -187,25 +234,90 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
     assert.deepEqual(events[0].files, []);
   });
 
+  test("a saved UI config migrates through the staged binary with its overrides intact", async () => {
+    const previous = process.env.XDG_CONFIG_HOME;
+    process.env.XDG_CONFIG_HOME = path.join(root, "migration");
+    const directory = path.join(process.env.XDG_CONFIG_HOME, "diffr");
+    await mkdir(directory, { recursive: true });
+
+    const original = await readFile(
+      new URL(
+        "../src/server/test-fixtures/diffr-ui-overrides.toml",
+        import.meta.url,
+      ),
+      "utf8",
+    );
+
+    await writeFile(path.join(directory, "config.toml"), original, {
+      mode: 0o600,
+    });
+
+    try {
+      assert.equal(await ensureDiffrConfigMigrated(diffrExecutable()), true);
+      const config = await readDiffrConfig(repository);
+      assert.equal(config.values.version, 2);
+      assert.deepEqual(config.values.plugins.classify.bundled.hide, [
+        "test",
+        "generated",
+      ]);
+      assert.equal(config.values.plugins.classify.bundled.hide_deleted, false);
+      assert.equal(config.values.plugins.shape.bundled.context.lines, 17);
+      assert.equal(
+        config.values.plugins.shape.bundled.summarize.system_prompt,
+        "  Use my exact custom instructions.\nKeep # inside the prompt, and answer with JSON if I ask for it.\n",
+      );
+
+      const backup = (await readdir(directory)).find((name) =>
+        name.includes("before-whiteboard-config-v2"),
+      );
+
+      assert.ok(backup);
+      assert.equal(
+        await readFile(path.join(directory, backup), "utf8"),
+        original,
+      );
+
+      const migrated = await readFile(
+        path.join(directory, "config.toml"),
+        "utf8",
+      );
+
+      assert.equal(await ensureDiffrConfigMigrated(diffrExecutable()), false);
+      await readDiffrConfig(repository);
+      assert.equal(
+        await readFile(path.join(directory, "config.toml"), "utf8"),
+        migrated,
+      );
+    } finally {
+      process.env.XDG_CONFIG_HOME = previous;
+    }
+  });
+
   test("settings values and edits round-trip through the staged binary", async () => {
     const config = await readDiffrConfig(repository);
-    assert.ok(Number.isInteger(config.values.plugins.bundled.context.lines));
-    assert.equal(config.values.plugins.bundled.summarize.api_key, undefined);
+    assert.ok(
+      Number.isInteger(config.values.plugins.shape.bundled.context.lines),
+    );
+    assert.equal(
+      config.values.plugins.shape.bundled.summarize.api_key,
+      undefined,
+    );
     assert.ok(
       ["config", "environment", "missing"].includes(config.credentialSource),
     );
 
     const updated = await setDiffrConfigValue(
-      "plugins.bundled.context.lines",
+      "plugins.shape.bundled.context.lines",
       7,
       repository,
     );
 
-    assert.equal(updated.values.plugins.bundled.context.lines, 7);
+    assert.equal(updated.values.plugins.shape.bundled.context.lines, 7);
     assert.equal(updated.changed, true);
     assert.equal(updated.error, undefined);
     assert.equal(
-      (await readDiffrConfig(repository)).values.plugins.bundled.context.lines,
+      (await readDiffrConfig(repository)).values.plugins.shape.bundled.context
+        .lines,
       7,
     );
     assert.equal(existsSync(sentinel), false);
@@ -214,7 +326,7 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
   test("a provider switch saves through the binary, clears the old key and keeps the file sparse", async () => {
     delete process.env.ANTHROPIC_API_KEY;
     await setDiffrConfigValue(
-      "plugins.bundled.summarize.api_key",
+      "plugins.shape.bundled.summarize.api_key",
       "old-secret",
       repository,
     );
@@ -235,7 +347,10 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
     );
 
     assert.equal(saved.error, undefined);
-    assert.equal(saved.values.plugins.bundled.summarize.provider, "anthropic");
+    assert.equal(
+      saved.values.plugins.shape.bundled.summarize.provider,
+      "anthropic",
+    );
     assert.equal(saved.credentialSource, "missing");
 
     const file = await readFile(
@@ -260,19 +375,7 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
           body: JSON.parse(body),
         };
 
-        const id = Number(
-          /fold (\d+):/.exec(received.body.messages[1].content)[1],
-        );
-
-        const content = JSON.stringify({
-          summaries: [
-            {
-              id,
-              summary: "",
-              pseudocode: "count and average positive values",
-            },
-          ],
-        });
+        const content = "count and average positive values";
 
         response.setHeader("content-type", "application/json");
         response.end(JSON.stringify({ choices: [{ message: { content } }] }));
@@ -318,7 +421,10 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
 
   test("an unbundled installation falls back to PATH", async () => {
     delete process.env.REVIEW_DIFFR_BINARY;
-    await rm(path.join(runtime, "bin"), { recursive: true, force: true });
+    await rm(path.join(runtime, "node_modules"), {
+      recursive: true,
+      force: true,
+    });
     await assert.rejects(
       collect(repository, base, head),
       /diffr exited with 97/,
@@ -329,7 +435,7 @@ describe("Relocated runtime diffr integrates with Review streams and settings",
   describe("a working host installation coexists with the Desktop bundle", () => {
     let called, launcher;
     beforeAll(async () => {
-      await stageDiffrBinary(runtime, source);
+      await stageDiffr(runtime);
       const host = path.join(root, "host");
       const traced = path.join(root, "traced-host");
       called = path.join(root, "host-called");
@@ -370,7 +476,10 @@ process.exit(result.status ?? 1);
 
     test("without a bundle the host binary runs real diffs and settings", async () => {
       delete process.env.REVIEW_DIFFR_BINARY;
-      await rm(path.join(runtime, "bin"), { recursive: true, force: true });
+      await rm(path.join(runtime, "node_modules"), {
+        recursive: true,
+        force: true,
+      });
       successfulFiles(await collect(repository, base, head), 3);
       assert.equal(existsSync(called), true);
       await rm(called);
diff --git a/packages/review/src/review-api/comparison-coverage.ts b/packages/review/src/review-api/comparison-coverage.ts
index 12595f89a..ca2ded9cc 100644
--- a/packages/review/src/review-api/comparison-coverage.ts
+++ b/packages/review/src/review-api/comparison-coverage.ts
@@ -4,7 +4,6 @@ import {
   type StructuralDiff,
   type StructuralRegion,
   type StructuralSource,
-  type StructuralVisibility,
   structuralRows,
 } from "@dev.fast/review-protocol";
 import type { AlignmentRow } from "@review/lens-selection.js";
@@ -217,7 +216,7 @@ export async function comparisonCoverage(
         fingerprint,
         changed:
           diff.type === "text" ? diff.structural_changes : emptyCoverage(),
-        folded: foldedChanges(event.visibility, diff),
+        folded: foldedChanges(diff),
         viewed: emptyCoverage(),
       });
       publish?.({
@@ -244,21 +243,17 @@ export async function comparisonCoverage(
  * the lines, not just the counts, are known. A paired leaf contributes its
  * changed spans' lines; an unpaired leaf, all of its lines.
  */
-export function foldedChanges(
-  visibility: StructuralVisibility | undefined,
-  diff: StructuralDiff,
-): Coverage {
+export function foldedChanges(diff: StructuralDiff): Coverage {
   if (diff.type !== "text") return emptyCoverage();
   const all = diff.structural_changes;
 
-  if (visibility?.collapsed)
-    return { base: unionIntervals(all.base), head: unionIntervals(all.head) };
-
   const side = (
     changed: readonly LineInterval[],
     source: StructuralSource | undefined,
     other: StructuralSource | undefined,
   ): LineInterval[] => {
+    if (source?.root.visibility?.collapsed) return unionIntervals(changed);
+
     const paired = new Set<number>();
 
     const pair = (region: StructuralRegion) => {
@@ -266,7 +261,7 @@ export function foldedChanges(
       else region.children.forEach(pair);
     };
 
-    other?.regions?.forEach(pair);
+    if (other) pair(other.root);
 
     const hidden: LineInterval[] = [],
       visible: LineInterval[] = [];
@@ -292,7 +287,7 @@ export function foldedChanges(
         ]);
     };
 
-    for (const region of source?.regions ?? []) collect(region, false);
+    if (source) collect(source.root, false);
 
     return subtractIntervals(intersectIntervals(changed, hidden), visible);
   };
diff --git a/packages/review/src/review-api/folded-progress.test.ts b/packages/review/src/review-api/folded-progress.test.ts
index ef56ad88f..45dc80455 100644
--- a/packages/review/src/review-api/folded-progress.test.ts
+++ b/packages/review/src/review-api/folded-progress.test.ts
@@ -2,10 +2,11 @@ import { mkdtempSync, rmSync } from "node:fs";
 import { tmpdir } from "node:os";
 import path from "node:path";
 
-import type {
-  StructuralDiff,
-  StructuralDiffEvent,
-  StructuralRegion,
+import {
+  STRUCTURAL_DIFF_WIRE_VERSION,
+  type StructuralDiff,
+  type StructuralDiffEvent,
+  type StructuralRegion,
 } from "@dev.fast/review-protocol";
 import { coverageProgress, coverageSources } from "@review/viewed-coverage.js";
 import { afterEach, beforeEach, expect, it, vi } from "vitest";
@@ -18,6 +19,8 @@ import { LocalReviewData } from "./local-data.js";
 import type { ReviewProgress } from "./review-progress.js";
 import { type ReviewProviders, ReviewStore } from "./store.js";
 
+let nextRoot = 100;
+
 const pins = { repositoryId: "repo", base: "base-commit", head: "head-commit" };
 
 const leaf = (
@@ -46,6 +49,7 @@ const fold = (
   id,
   fold_state_id: id,
   kind: "fold",
+  indent: { line: from, column: 0 },
   start: { line: from, column: 0 },
   end: { line: to, column: 0 },
   visibility: { collapsed },
@@ -57,15 +61,15 @@ const text = (lines: number) =>
 
 /** One changed line in a function, and a test module diffr folds whose three
  * added lines pair with nothing. */
-const sourceDiff: StructuralDiff = {
+const sourceDiff: Extract<StructuralDiff, { type: "text" }> = {
   type: "text",
-  lhs: { text: text(2), regions: [leaf(1, 1, [0, 1], [0])] },
+  lhs: { text: text(2), root: root([leaf(1, 1, [0, 1], [0])]) },
   rhs: {
     text: text(6),
-    regions: [
+    root: root([
       leaf(2, 1, [0, 1], [0]),
       fold(3, [2, 5], true, [fold(4, [2, 5], false, [leaf(5, 5, [2, 5])])]),
-    ],
+    ]),
   },
   structural_changes: {
     base: [[0, 1]],
@@ -82,8 +86,8 @@ const sourceDiff: StructuralDiff = {
 
 const plainDiff = (lines: number): StructuralDiff => ({
   type: "text",
-  lhs: { text: text(lines), regions: [leaf(1, 1, [0, lines], [0])] },
-  rhs: { text: text(lines), regions: [leaf(2, 1, [0, lines], [0])] },
+  lhs: { text: text(lines), root: root([leaf(1, 1, [0, lines], [0])]) },
+  rhs: { text: text(lines), root: root([leaf(2, 1, [0, lines], [0])]) },
   structural_changes: { base: [[0, 1]], head: [[0, 1]] },
   stats: {
     textual: { added: 1, removed: 1 },
@@ -92,30 +96,30 @@ const plainDiff = (lines: number): StructuralDiff => ({
 });
 
 it("folds what diffr folds: hidden regions' changed lines, or a hidden file's", () => {
-  expect(foldedChanges(undefined, sourceDiff)).toEqual({
+  expect(foldedChanges(sourceDiff)).toEqual({
     base: [],
     head: [[2, 5]],
   });
   // What stays unfolded is exactly what diffr counts in stats.visible.
-  expect(
-    foldedChanges({ collapsed: true, label: "Test file" }, sourceDiff),
-  ).toEqual(sourceDiff.structural_changes);
-  expect(foldedChanges(undefined, plainDiff(3))).toEqual({
+  expect(foldedChanges(hideFile(sourceDiff))).toEqual(
+    sourceDiff.structural_changes,
+  );
+  expect(foldedChanges(plainDiff(3))).toEqual({
     base: [],
     head: [],
   });
 });
 
 it("a paired leaf folds only its changed lines, and a visible leaf wins a shared line", () => {
-  const diff: StructuralDiff = {
+  const diff: Extract<StructuralDiff, { type: "text" }> = {
     type: "text",
-    lhs: { text: text(4), regions: [leaf(1, 7, [0, 4], [1, 3])] },
+    lhs: { text: text(4), root: root([leaf(1, 7, [0, 4], [1, 3])]) },
     rhs: {
       text: text(4),
-      regions: [
+      root: root([
         fold(2, [0, 3], true, [leaf(3, 7, [0, 3], [0, 2])]),
         leaf(4, 8, [2, 4]),
-      ],
+      ]),
     },
     structural_changes: {
       base: [
@@ -133,7 +137,7 @@ it("a paired leaf folds only its changed lines, and a visible leaf wins a shared
     },
   };
 
-  expect(foldedChanges(undefined, diff)).toEqual({
+  expect(foldedChanges(diff)).toEqual({
     base: [],
     head: [[0, 1]],
   });
@@ -147,19 +151,19 @@ it("any region diffr collapses folds its changed lines, whatever its kind: a doc
     tags: ["summarize:docstring"],
   };
 
-  const diff: StructuralDiff = {
+  const diff: Extract<StructuralDiff, { type: "text" }> = {
     type: "text",
     lhs: {
       text: text(5),
-      regions: [
+      root: root([
         leaf(1, 1, [0, 1]),
         leaf(4, 3, [1, 4], [2]),
         leaf(5, 5, [4, 5], [4]),
-      ],
+      ]),
     },
     rhs: {
       text: text(5),
-      regions: [leaf(6, 1, [0, 1]), docstring, leaf(7, 5, [4, 5], [4])],
+      root: root([leaf(6, 1, [0, 1]), docstring, leaf(7, 5, [4, 5], [4])]),
     },
     structural_changes: {
       base: [
@@ -177,7 +181,7 @@ it("any region diffr collapses folds its changed lines, whatever its kind: a doc
     },
   };
 
-  const folded = foldedChanges(undefined, diff);
+  const folded = foldedChanges(diff);
   expect(folded).toEqual({ base: [], head: [[2, 3]] });
   expect(
     coverageProgress([
@@ -233,17 +237,12 @@ const ref = (path: string) => ({
 const records: {
   path: string;
   diff: StructuralDiff;
-  visibility?: { collapsed: boolean; label: string };
 }[] = [
   { path: "src/api.rs", diff: sourceDiff },
   { path: "src/main.rs", diff: plainDiff(2) },
   {
     path: "Cargo.lock",
-    diff: plainDiff(2),
-    visibility: {
-      collapsed: true,
-      label: "Generated file · hidden by default",
-    },
+    diff: hideFile(plainDiff(2)),
   },
   { path: "docs/readme.md", diff: plainDiff(2) },
 ];
@@ -275,7 +274,7 @@ async function progressApi() {
   vi.spyOn(data, "structuralChanges").mockImplementation(async function* () {
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: "base" },
       rhs: { type: "revision", rev: "head" },
       files: records.map(({ path }) => ({
@@ -284,8 +283,8 @@ async function progressApi() {
       })),
     } satisfies StructuralDiffEvent;
 
-    for (const { path, diff, visibility } of records)
-      yield { type: "file", file: ref(path), diff, visibility };
+    for (const { path, diff } of records)
+      yield { type: "file", file: ref(path), diff };
     yield { type: "complete", succeeded: records.length, failed: 0 };
   });
 
@@ -354,3 +353,28 @@ it("progress counts folded changes as done, overall, per lens and uncategorized"
     ).state,
   ).toBe("viewed");
 });
+
+function root(children: StructuralRegion[]): StructuralRegion {
+  const id = nextRoot++;
+
+  return {
+    kind: "fold",
+    id,
+    fold_state_id: id,
+    start: children[0].start,
+    end: children.at(-1)!.end,
+    indent: children[0].start,
+    children,
+  };
+}
+
+function hideFile(diff: StructuralDiff): StructuralDiff {
+  const hidden = structuredClone(diff);
+
+  if (hidden.type === "text")
+    for (const source of [hidden.lhs, hidden.rhs])
+      if (source)
+        source.root.visibility = { collapsed: true, label: "Test file" };
+
+  return hidden;
+}
diff --git a/packages/review/src/review-api/lenses.test.ts b/packages/review/src/review-api/lenses.test.ts
index 3ab82a4fe..3ce6e661d 100644
--- a/packages/review/src/review-api/lenses.test.ts
+++ b/packages/review/src/review-api/lenses.test.ts
@@ -3,6 +3,10 @@ import { tmpdir } from "node:os";
 import path from "node:path";
 import { DatabaseSync } from "node:sqlite";
 
+import {
+  STRUCTURAL_DIFF_WIRE_VERSION,
+  type StructuralSource,
+} from "@dev.fast/review-protocol";
 import { rangeAnchor } from "@review/lens-selection.js";
 import { afterEach, beforeEach, expect, it, vi } from "vitest";
 
@@ -302,7 +306,7 @@ it("reports the changed lines no lens selects after each lens write", async () =
   vi.spyOn(data, "structuralChanges").mockImplementation(async function* () {
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: "base" },
       rhs: { type: "revision", rev: "head" },
       files: [api, readme].map(({ file }) => ({ file, status: "modified" })),
@@ -314,8 +318,8 @@ it("reports the changed lines no lens selects after each lens write", async () =
         file,
         diff: {
           type: "text",
-          lhs: { text },
-          rhs: { text },
+          lhs: structuralSource(text),
+          rhs: structuralSource(text),
           structural_changes: {
             base: [[0, text.split("\n").length]],
             head: [[0, text.split("\n").length]],
@@ -391,3 +395,19 @@ it("reports the changed lines no lens selects after each lens write", async () =
     await data.close();
   }
 });
+
+function structuralSource(text: string): StructuralSource {
+  const lines = text.split("\n");
+
+  return {
+    text,
+    root: {
+      kind: "leaf",
+      id: 1,
+      fold_state_id: 1,
+      alignment_id: 1,
+      start: { line: 0, column: 0 },
+      end: { line: lines.length - 1, column: lines.at(-1)!.length },
+    },
+  };
+}
diff --git a/packages/review/src/review-api/review-api.test.ts b/packages/review/src/review-api/review-api.test.ts
index 71b662765..64eb82a94 100644
--- a/packages/review/src/review-api/review-api.test.ts
+++ b/packages/review/src/review-api/review-api.test.ts
@@ -4,6 +4,10 @@ import path from "node:path";
 import { DatabaseSync } from "node:sqlite";
 import { fileURLToPath } from "node:url";
 
+import {
+  STRUCTURAL_DIFF_WIRE_VERSION,
+  type StructuralSource,
+} from "@dev.fast/review-protocol";
 import { anchorSelection, rangeAnchor } from "@review/lens-selection.js";
 import { createGlobalReviewServer } from "@review/server/desktop-server.js";
 import { GlobalReviewDesktopVerbRelay } from "@review/server/global-verb-relay.js";
@@ -2088,7 +2092,7 @@ it("keeps reference coverage apart by pins: one path, changed under one comparis
 
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: at.base },
       rhs: { type: "revision", rev: at.head },
       files,
@@ -2100,8 +2104,8 @@ it("keeps reference coverage apart by pins: one path, changed under one comparis
         file: file.file,
         diff: {
           type: "text",
-          lhs: { text: text },
-          rhs: { text: text },
+          lhs: structuralSource(text),
+          rhs: structuralSource(text),
           structural_changes: { base: [], head: [[0, 3]] },
           stats: {
             textual: { added: 3, removed: 0 },
@@ -2176,7 +2180,7 @@ it("preserves unchanged partial file coverage across pins and rejects stale writ
   vi.spyOn(data, "structuralChanges").mockImplementation(async function* () {
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: "base" },
       rhs: { type: "revision", rev: "head" },
       files: [
@@ -2197,8 +2201,8 @@ it("preserves unchanged partial file coverage across pins and rejects stale writ
       },
       diff: {
         type: "text",
-        lhs: { text: base },
-        rhs: { text: head },
+        lhs: structuralSource(base),
+        rhs: structuralSource(head),
         structural_changes: { base: [[1, 2]], head: [[1, 2]] },
         stats: {
           textual: { added: 99, removed: 99 },
@@ -2307,7 +2311,7 @@ it("still reports structural read failures", async () => {
 
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: pins.base },
       rhs: { type: "revision", rev: pins.head },
       files: [{ file, status: "added" }],
@@ -2377,7 +2381,7 @@ it("textual coverage uses Git ranges without launching diffr", async () => {
 
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: "base" },
       rhs: { type: "revision", rev: "head" },
       files: [{ file, status: "modified" }],
@@ -2387,8 +2391,8 @@ it("textual coverage uses Git ranges without launching diffr", async () => {
       file,
       diff: {
         type: "text",
-        lhs: { text: "const x=1;" },
-        rhs: { text: "const x = 1;" },
+        lhs: structuralSource("const x=1;"),
+        rhs: structuralSource("const x = 1;"),
         structural_changes: { base: [], head: [] },
         stats: {
           textual: { added: 1, removed: 1 },
@@ -2447,7 +2451,7 @@ it("resolves file lenses to whole changed files, preserves empty groups, and sha
   vi.spyOn(data, "structuralChanges").mockImplementation(async function* () {
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: "base" },
       rhs: { type: "revision", rev: "head" },
       files: [
@@ -2468,8 +2472,8 @@ it("resolves file lenses to whole changed files, preserves empty groups, and sha
       },
       diff: {
         type: "text",
-        lhs: { text: "base\ncontext\nmore context" },
-        rhs: { text: "head\ncontext\nmore context" },
+        lhs: structuralSource("base\ncontext\nmore context"),
+        rhs: structuralSource("head\ncontext\nmore context"),
         structural_changes: { base: [[0, 1]], head: [[0, 1]] },
         stats: {
           textual: { added: 99, removed: 99 },
@@ -2567,7 +2571,7 @@ it("validates range lens evidence and scopes progress and Uncategorized to disti
   vi.spyOn(data, "structuralChanges").mockImplementation(async function* () {
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: "base" },
       rhs: { type: "revision", rev: "head" },
       files: [
@@ -2588,8 +2592,8 @@ it("validates range lens evidence and scopes progress and Uncategorized to disti
       },
       diff: {
         type: "text",
-        lhs: { text: "base1\nbase2\nbase3" },
-        rhs: { text: "head1\nhead2\nhead3" },
+        lhs: structuralSource("base1\nbase2\nbase3"),
+        rhs: structuralSource("head1\nhead2\nhead3"),
         structural_changes: { base: [[0, 3]], head: [[0, 3]] },
         stats: {
           textual: { added: 99, removed: 99 },
@@ -2693,7 +2697,7 @@ it("returns coverage and lenses after initial files without requesting summary e
   vi.spyOn(data, "structuralChanges").mockImplementation(async function* () {
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "empty_tree" },
       rhs: { type: "revision", rev: "head" },
       files: [{ file, status: "added" }],
@@ -2703,7 +2707,7 @@ it("returns coverage and lenses after initial files without requesting summary e
       file,
       diff: {
         type: "text",
-        rhs: { text: "added" },
+        rhs: structuralSource("added"),
         structural_changes: { base: [], head: [[0, 1]] },
         stats: {
           textual: { added: 1, removed: 0 },
@@ -2955,7 +2959,7 @@ it("shares pending comparison work even when more than 32 reviews are opened", a
     await gate;
     yield {
       type: "start",
-      version: 4,
+      version: STRUCTURAL_DIFF_WIRE_VERSION,
       lhs: { type: "revision", rev: "base" },
       rhs: { type: "revision", rev: "head" },
       files: [],
@@ -3029,3 +3033,19 @@ it("reports a created review with the origin its headers claim", async () => {
     { reviewId: expect.any(String), kind: "review", blocks: 0, via: "other" },
   ]);
 });
+
+function structuralSource(text: string): StructuralSource {
+  const lines = text.split("\n");
+
+  return {
+    text,
+    root: {
+      kind: "leaf",
+      id: 1,
+      fold_state_id: 1,
+      alignment_id: 1,
+      start: { line: 0, column: 0 },
+      end: { line: lines.length - 1, column: lines.at(-1)!.length },
+    },
+  };
+}
diff --git a/packages/review/src/server/desktop-server.ts b/packages/review/src/server/desktop-server.ts
index 9c62c0887..907e133ca 100644
--- a/packages/review/src/server/desktop-server.ts
+++ b/packages/review/src/server/desktop-server.ts
@@ -62,7 +62,7 @@ import {
   setDiffrConfigValue,
   testDiffrSummarizer,
 } from "./diffr-config";
-import { installFullDiffr } from "./diffr-languages.js";
+import { ensureDiffrConfigMigrated } from "./diffr-config-migration.js";
 import {
   GlobalReviewDesktopVerbRelay,
   type ReviewDesktopVerbRelay,
@@ -74,6 +74,7 @@ import { reviewLifecycleTelemetry } from "./review-lifecycle-telemetry";
 import { ReviewOpenWatchdog } from "./review-open-watchdog";
 import { createWhiteboardCore, serverJson } from "./review-server-core";
 import { invalidateStructuralComparisons } from "./structural-comparisons.js";
+import { diffrExecutable } from "./structural-diff.js";
 import { createTutorialService } from "./tutorial-service";
 import { captureSanitizedUiTelemetry } from "./ui-telemetry";
 
@@ -397,18 +398,6 @@ export function createGlobalReviewServer(
 
     return serverJson(200, { ok: true });
   });
-  app.post("/diffr-languages/install", async () => {
-    try {
-      await installFullDiffr();
-      invalidateStructuralComparisons();
-
-      return serverJson(200, { installed: true });
-    } catch (error) {
-      return serverJson(503, {
-        error: error instanceof Error ? error.message : String(error),
-      });
-    }
-  });
 
   app.get("/diffr-config", async () =>
     serverJson(200, await readDiffrConfig()),
@@ -580,6 +569,7 @@ export function createGlobalReviewServer(
       return urlForBoundPort();
     },
     listen: async () => {
+      await ensureDiffrConfigMigrated(diffrExecutable());
       scratchpadEnabled = await readScratchpadEnabled();
       boundPort = await listen(httpServer, input.port);
       discovery.url = urlForBoundPort();
diff --git a/packages/review/src/server/diffr-config-migration.test.ts b/packages/review/src/server/diffr-config-migration.test.ts
new file mode 100644
index 000000000..e264a3a50
--- /dev/null
+++ b/packages/review/src/server/diffr-config-migration.test.ts
@@ -0,0 +1,692 @@
+import {
+  mkdir,
+  mkdtemp,
+  readFile,
+  readdir,
+  rm,
+  stat,
+  writeFile,
+} from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+
+import { parse } from "smol-toml";
+import { afterEach, expect, test } from "vitest";
+import { z } from "zod";
+
+import {
+  ensureDiffrConfigMigrated,
+  migrateDiffrConfig,
+} from "./diffr-config-migration";
+import { TomlEdits } from "./toml-edits";
+
+const roots: string[] = [];
+
+test("rejects a change to a retained credential without exposing its value", () => {
+  const original = 'plugins.bundled.summarize.api_key = "saved-secret"\n';
+  const edits = new TomlEdits(original);
+  edits.set("plugins.bundled.summarize.api_key", "different-secret");
+  expect(() =>
+    edits.assertUnchanged(original, [
+      [
+        "plugins.bundled.summarize.api_key",
+        "plugins.bundled.summarize.api_key",
+      ],
+    ]),
+  ).toThrow(
+    "diffr migration changed a retained setting: plugins.bundled.summarize.api_key",
+  );
+});
+
+afterEach(async () => {
+  await Promise.all(
+    roots.splice(0).map((root) => rm(root, { recursive: true, force: true })),
+  );
+});
+
+test("converts a saved UI config without changing supported overrides or their comments", async () => {
+  const source = await readFile(
+    new URL("./test-fixtures/diffr-ui-overrides.toml", import.meta.url),
+    "utf8",
+  );
+
+  const migrated = migrateDiffrConfig(source);
+  const original = parse(source);
+  const expected = structuredClone(original);
+
+  const plugins = z
+    .object({
+      bundled: z.record(
+        z.string(),
+        z.record(
+          z.string(),
+          z.union([z.string(), z.boolean(), z.number(), z.array(z.string())]),
+        ),
+      ),
+    })
+    .parse(expected.plugins);
+
+  delete plugins.bundled.group;
+  delete plugins.bundled["hide-files"];
+  delete plugins.bundled.summarize.max_concurrency;
+  expected.version = 2;
+  expected.plugins = {
+    // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+    shape: { bundled: plugins.bundled },
+    classify: {
+      bundled: { hide: ["test", "generated"], hide_deleted: false },
+    },
+  };
+  expect(parse(migrated)).toEqual(expected);
+
+  // Source spans for credentials, prompt, context and fold choices are not serialized.
+  for (const line of source
+    .split("\n")
+    .filter((line) =>
+      /# (Collapse|Context|Enable|Provider|API key|Model|Endpoint|Include|Unrelated)/.test(
+        line,
+      ),
+    ))
+    expect(migrated).toContain(line);
+  expect(migrated).toContain(
+    "system_prompt = '''  Use my exact custom instructions.\nKeep # inside the prompt, and answer with JSON if I ask for it.\n''' # Prompt",
+  );
+  expect(migrated).toContain("# Group adjacent folds; retired");
+  expect(migrateDiffrConfig(migrated)).toBe(migrated);
+});
+
+test.each([
+  [true, true, ["test", "generated"], true],
+  [true, false, ["test", "generated"], false],
+  [false, true, [], false],
+  [false, false, [], false],
+])(
+  "preserves hiding for enabled=%s deleted=%s",
+  (enabled, deleted, hide, hideDeleted) => {
+    const migrated = migrateDiffrConfig(
+      `[plugins.bundled.hide-files]\nenabled = ${enabled}\ndeleted = ${deleted}\ntags = ["test", "generated"]\n`,
+    );
+
+    expect(parse(migrated).plugins).toEqual({
+      classify: {
+        bundled: {
+          hide,
+          hide_deleted: hideDeleted,
+        },
+      },
+    });
+  },
+);
+
+test.each([true, false])(
+  "removes retired group=%s without changing context",
+  (enabled) => {
+    const migrated = migrateDiffrConfig(
+      `[plugins.bundled.context]\nenabled = false\nlines = 9\n[plugins.bundled.group]\nenabled = ${enabled}\n`,
+    );
+
+    expect(parse(migrated)).toEqual({
+      version: 2,
+      plugins: {
+        // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+        shape: { bundled: { context: { enabled: false, lines: 9 } } },
+      },
+    });
+  },
+);
+
+test("handles quoted keys, inline tables and dotted keys without touching a custom prompt", () => {
+  const source = `version = 1\nplugins = { bundled = { group = { enabled = false }, "hide-files" = { enabled = false }, summarize = { system_prompt = "Keep me", max_concurrency = 2 } }, order = ["bundled.group", "bundled.hide-files", "bundled.summarize"] }\n`;
+  expect(parse(migrateDiffrConfig(source))).toEqual({
+    version: 2,
+    plugins: {
+      classify: { bundled: { hide: [], hide_deleted: false } },
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: {
+        bundled: { summarize: { system_prompt: "Keep me" } },
+        order: ["bundled.summarize"],
+      },
+    },
+  });
+  const dotted = `plugins.bundled.group.enabled = true\nplugins.bundled."hide-files".deleted = false\nclassifier = { hide = ["vendored"] }\n`;
+  expect(parse(migrateDiffrConfig(dotted)).plugins).toEqual({
+    classify: {
+      bundled: {
+        hide: ["vendored"],
+        hide_deleted: false,
+      },
+    },
+  });
+});
+
+test("retains explicit modern classifier values in a mixed config", () => {
+  const source = `[classifier]\nhide = ["custom"]\nhide_deleted = true\n[plugins.bundled.hide-files]\nenabled = false\n`;
+  expect(parse(migrateDiffrConfig(source))).toEqual({
+    version: 2,
+    plugins: {
+      classify: { bundled: { hide: ["custom"], hide_deleted: true } },
+    },
+  });
+});
+
+test("removes retired names from a custom order without sorting surviving plugins", () => {
+  const source = `[plugins]\norder = ["bundled.context", "bundled.group", "external.custom", "bundled.hide-files", "bundled.summarize"]\n`;
+  expect(parse(migrateDiffrConfig(source))).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: {
+        order: ["bundled.context", "custom", "bundled.summarize"],
+      },
+    },
+  });
+});
+
+test("retains comments inside a rewritten plugin order", () => {
+  const source = `[plugins]\norder = [\n"bundled.context", # keep context first\n"bundled.group", # retired group\n"bundled.summarize",\n]\n`;
+  const migrated = migrateDiffrConfig(source);
+  expect(parse(migrated)).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: { order: ["bundled.context", "bundled.summarize"] },
+    },
+  });
+  expect(migrated.match(/# keep context first/g)).toHaveLength(1);
+  expect(migrated.match(/# retired group/g)).toHaveLength(1);
+});
+
+async function fixture() {
+  const root = await mkdtemp(
+    path.join(tmpdir(), "whiteboard-config-migration-"),
+  );
+
+  roots.push(root);
+  const file = path.join(root, "diffr", "config.toml");
+  await mkdir(path.dirname(file));
+  const executable = path.join(root, "diffr-cli");
+  await writeFile(
+    executable,
+    `#!${process.execPath}\nconst fs = require('node:fs');\nconst path = require('node:path');\nif (process.argv[3] !== 'show') process.exit(3);\n{\n const candidate = fs.readFileSync(path.join(process.env.XDG_CONFIG_HOME,'diffr','config.toml'),'utf8');\n if (process.env.CAPTURE_CANDIDATE) fs.writeFileSync(process.env.CAPTURE_CANDIDATE, candidate);\n if (process.env.REJECT_CANDIDATE) { console.error('synthetic secret'); process.exit(2); }\n if (process.env.CONCURRENT_EDIT) fs.writeFileSync(${JSON.stringify(file)}, 'version = 1 # concurrent edit\\n');\n if (candidate.includes('plugins.bundled.group')) process.exit(2);\n console.log('{}');\n}\n`,
+    { mode: 0o755 },
+  );
+
+  return {
+    root,
+    file,
+    executable,
+    env: { ...process.env, XDG_CONFIG_HOME: root },
+  };
+}
+
+test("validates before writing, backs up privately and is a no-op on a second run", async () => {
+  const { root, file, executable, env } = await fixture();
+  const source = `[plugins.bundled.group]\nenabled = false # retired\n`;
+  await writeFile(file, source);
+  expect(await ensureDiffrConfigMigrated(executable, env)).toBe(true);
+  const migrated = await readFile(file, "utf8");
+  expect(parse(migrated)).toEqual({ version: 2 });
+
+  const backup = (await readdir(path.dirname(file))).find((name) =>
+    name.includes(".before-whiteboard-config-v2."),
+  )!;
+
+  expect(await readFile(path.join(path.dirname(file), backup), "utf8")).toBe(
+    source,
+  );
+
+  expect(await ensureDiffrConfigMigrated(executable, env)).toBe(false);
+  expect(await readFile(file, "utf8")).toBe(migrated);
+  expect(
+    (await readdir(path.join(root, "diffr"))).some((name) =>
+      name.startsWith(".whiteboard-config-"),
+    ),
+  ).toBe(false);
+});
+
+test.skipIf(process.platform === "win32")(
+  "keeps backup credentials private",
+  async () => {
+    const { file, executable, env } = await fixture();
+    await writeFile(file, `[plugins.bundled.group]\nenabled = false\n`);
+    await ensureDiffrConfigMigrated(executable, env);
+
+    const backup = (await readdir(path.dirname(file))).find((name) =>
+      name.includes(".before-whiteboard-config-v2."),
+    )!;
+
+    expect(
+      (await stat(path.join(path.dirname(file), backup))).mode & 0o777,
+    ).toBe(0o600);
+  },
+);
+
+test("does not run the binary or change a version 2 file", async () => {
+  const { file, env } = await fixture();
+
+  const source =
+    "version = 2 # already migrated\n[plugins.shape.bundled.context]\nlines = 8\n";
+
+  await writeFile(file, source);
+  expect(await ensureDiffrConfigMigrated("/no/binary/needed", env)).toBe(false);
+  expect(await readFile(file, "utf8")).toBe(source);
+  expect(await readdir(path.dirname(file))).toEqual(["config.toml"]);
+});
+
+test("keeps an unknown config version unchanged", async () => {
+  const { file, env } = await fixture();
+  const source = "version = 3\n";
+  await writeFile(file, source);
+  await expect(
+    ensureDiffrConfigMigrated("/no/binary/needed", env),
+  ).rejects.toThrow("Unsupported diffr config version: 3");
+  expect(await readFile(file, "utf8")).toBe(source);
+  expect(await readdir(path.dirname(file))).toEqual(["config.toml"]);
+});
+
+test("keeps the original and hides provider output when validation fails", async () => {
+  const { file, executable, env } = await fixture();
+  const source = `[plugins.bundled.group]\nenabled = false\n`;
+  await writeFile(file, source);
+  await expect(
+    ensureDiffrConfigMigrated(executable, { ...env, REJECT_CANDIDATE: "1" }),
+  ).rejects.toThrow("The original file was kept");
+  expect(await readFile(file, "utf8")).toBe(source);
+  expect(await readdir(path.dirname(file))).toEqual(["config.toml"]);
+});
+
+test("does not replace an external edit made during validation", async () => {
+  const { file, executable, env } = await fixture();
+  await writeFile(file, `[plugins.bundled.group]\nenabled = false\n`);
+  await expect(
+    ensureDiffrConfigMigrated(executable, { ...env, CONCURRENT_EDIT: "1" }),
+  ).rejects.toThrow("changed during migration");
+  expect(await readFile(file, "utf8")).toBe("version = 1 # concurrent edit\n");
+});
+
+test("uses the caller directory and preserves relative paths in the saved file", async () => {
+  const { root, file, env } = await fixture();
+  const source = `[theme]\npath = "themes/custom.toml"\n[plugins.bundled.group]\nenabled = true\n`;
+  await writeFile(file, source);
+  const captured = path.join(root, "candidate.toml");
+  expect(
+    await ensureDiffrConfigMigrated(
+      "./diffr-cli",
+      {
+        ...env,
+        XDG_CONFIG_HOME: ".",
+        CAPTURE_CANDIDATE: captured,
+      },
+      undefined,
+      root,
+    ),
+  ).toBe(true);
+  expect(parse(await readFile(captured, "utf8")).theme).toEqual({
+    path: path.join(path.dirname(file), "themes/custom.toml"),
+  });
+  expect(parse(await readFile(file, "utf8")).theme).toEqual({
+    path: "themes/custom.toml",
+  });
+});
+
+test("migrates a version-only config and leaves v2 text unchanged", () => {
+  expect(parse(migrateDiffrConfig("version = 1 # format\n"))).toEqual({
+    version: 2,
+  });
+  const source = "version = 2 # format\n";
+  expect(migrateDiffrConfig(source)).toBe(source);
+  expect(() => migrateDiffrConfig("version = 7\n")).toThrow(
+    "Unsupported diffr config version: 7",
+  );
+});
+
+test("moves plugin options and external paths without rewriting value bytes", () => {
+  const source = `version = 1
+[plugins.bundled.context]
+lines = 0x10 # keep spelling
+extra = { option = 'custom', nested = [1, 2] }
+[plugins.external.custom]
+path = 'plugins/custom' # keep relative
+threshold = 1_000
+[classifier]
+hide = ['custom'] # keep tags
+[diff]
+byte_limit = 1_000_000
+`;
+
+  const migrated = migrateDiffrConfig(source);
+  expect(parse(migrated)).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: {
+        bundled: {
+          context: { lines: 16, extra: { option: "custom", nested: [1, 2] } },
+        },
+        custom: { path: "plugins/custom", threshold: 1000 },
+      },
+      classify: { bundled: { hide: ["custom"] } },
+    },
+    diff: { byte_limit: 1000000 },
+  });
+
+  for (const line of source
+    .split("\n")
+    .filter((line) => line.includes(" = ") && !line.startsWith("version")))
+    expect(migrated).toContain(line);
+});
+
+test("preserves bundled and custom plugins with the same basename", () => {
+  const source = `[plugins.bundled.context]
+enabled = false
+lines = 9
+[plugins.external.context]
+path = "custom/context"
+`;
+
+  const migrated = migrateDiffrConfig(source);
+  expect(parse(migrated)).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: {
+        bundled: { context: { enabled: false, lines: 9 } },
+        context: { path: "custom/context" },
+      },
+    },
+  });
+  expect(migrated).toContain("lines = 9");
+});
+
+test("moves a custom classifier under its manifest name and validates its original path", async () => {
+  const { root, file, executable, env } = await fixture();
+  const directory = path.join(root, "diffr", "custom-classifier");
+  await mkdir(directory);
+  await writeFile(
+    path.join(directory, "plugin.toml"),
+    'name = "team.classifier"\n',
+  );
+
+  const source =
+    '[classifier]\npath = "custom-classifier" # local plugin\nhide = ["team"]\n';
+
+  await writeFile(file, source);
+  const captured = path.join(root, "candidate.toml");
+  await ensureDiffrConfigMigrated(executable, {
+    ...env,
+    CAPTURE_CANDIDATE: captured,
+  });
+  expect(parse(await readFile(file, "utf8"))).toEqual({
+    version: 2,
+    plugins: {
+      classify: {
+        "team.classifier": { path: "custom-classifier", hide: ["team"] },
+      },
+    },
+  });
+  expect(parse(await readFile(captured, "utf8"))).toEqual({
+    version: 2,
+    plugins: {
+      classify: { "team.classifier": { path: directory, hide: ["team"] } },
+    },
+  });
+});
+
+test("keeps a custom classifier config when its manifest cannot be read", async () => {
+  const { file, executable, env } = await fixture();
+  const source = '[classifier]\npath = "missing-plugin"\n';
+  await writeFile(file, source);
+  await expect(ensureDiffrConfigMigrated(executable, env)).rejects.toThrow(
+    "could not read the custom classifier manifest",
+  );
+  expect(await readFile(file, "utf8")).toBe(source);
+});
+
+test("redacts saved credentials from invalid TOML and schema errors", async () => {
+  const { file, executable, env } = await fixture();
+
+  for (const source of [
+    'plugins.bundled.summarize.api_key = "saved-secret" unexpected\n',
+    'plugins.bundled.summarize = "saved-secret"\n',
+  ]) {
+    await writeFile(file, source);
+    const result = ensureDiffrConfigMigrated(executable, env);
+    await expect(result).rejects.toThrow("could not migrate the saved config");
+    await expect(result).rejects.not.toThrow("saved-secret");
+    expect(await readFile(file, "utf8")).toBe(source);
+    expect(await readdir(path.dirname(file))).toEqual(["config.toml"]);
+  }
+});
+
+test("serializes concurrent startup migrations and writes one backup", async () => {
+  const { file, executable, env } = await fixture();
+  const source = "version = 1\n[plugins.bundled.context]\nlines = 11\n";
+  await writeFile(file, source);
+
+  const results = await Promise.all([
+    ensureDiffrConfigMigrated(executable, env),
+    ensureDiffrConfigMigrated(executable, env),
+  ]);
+
+  expect(results.sort()).toEqual([false, true]);
+  expect(parse(await readFile(file, "utf8"))).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: { bundled: { context: { lines: 11 } } },
+    },
+  });
+
+  const backups = (await readdir(path.dirname(file))).filter((name) =>
+    name.includes("before-whiteboard-config-v2"),
+  );
+
+  expect(backups).toHaveLength(1);
+  expect(
+    await readFile(path.join(path.dirname(file), backups[0]), "utf8"),
+  ).toBe(source);
+});
+
+test("migrates same-basename stock and custom entries on disk", async () => {
+  const { file, executable, env } = await fixture();
+
+  const source =
+    '[plugins.bundled.context]\nenabled = false\n[plugins.external.context]\npath = "custom"\n';
+
+  await writeFile(file, source);
+  expect(await ensureDiffrConfigMigrated(executable, env)).toBe(true);
+  expect(parse(await readFile(file, "utf8"))).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: {
+        bundled: { context: { enabled: false } },
+        context: { path: "custom" },
+      },
+    },
+  });
+
+  const backup = (await readdir(path.dirname(file))).find((name) =>
+    name.includes("before-whiteboard-config-v2"),
+  )!;
+
+  expect(await readFile(path.join(path.dirname(file), backup), "utf8")).toBe(
+    source,
+  );
+});
+
+test.each([
+  '[plugins.external."team.custom"]\npath = "plugins/custom"\n"option.name" = 0x10\n',
+  'plugins.external."team.custom".path = "plugins/custom"\nplugins.external."team.custom"."option.name" = 0x10\n',
+  'plugins = { external = { "team.custom" = { path = "plugins/custom", "option.name" = 0x10 } } }\n',
+])("retains literal dots in external plugin and option names", (source) => {
+  const migrated = migrateDiffrConfig(source);
+  expect(parse(migrated)).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: { "team.custom": { path: "plugins/custom", "option.name": 16 } },
+    },
+  });
+  expect(migrated).toContain("0x10");
+});
+
+test.each(["order", "bundled", "bundled.context"])(
+  "refuses reserved custom plugin name %s",
+  (name) => {
+    expect(() =>
+      migrateDiffrConfig(
+        `[plugins.external.${JSON.stringify(name)}]\npath = "plugins/custom"\n`,
+      ),
+    ).toThrow(`custom plugin named ${name}`);
+  },
+);
+
+// Historical literals copied from diffr defaults and config/prune.rs.
+test.each([
+  'For each listed fold, rewrite that function body as short python-flavored pseudocode. Keep the names. No prose, no comments, no code fences. Use as few lines as possible: about one pseudocode line per five source lines, and never more than a third of the body\'s lines. When a fold lists a doc, also set "summary" to one sentence copied verbatim from that doc; otherwise leave it empty. Answer with a JSON array of {"id", "summary", "pseudocode"} objects, one per fold.',
+  'For each listed fold, rewrite that function body as short pseudocode. Keep the names. No prose, no comments, no code fences. Use as few lines as possible: about one pseudocode line per five source lines, and never more than a third of the body\'s lines. When a fold lists a doc, also set "summary" to one sentence copied verbatim from that doc; otherwise leave it empty. Answer with a JSON array of {"id", "summary", "pseudocode"} objects, one per fold.',
+  'For each listed fold, rewrite that function body as short pseudocode. Keep the names. No prose, no comments, no code fences. Use as few lines as possible: about one pseudocode line per five source lines, and never more than a third of the body\'s lines. When a fold lists a doc, also set "summary" to one sentence copied verbatim from that doc; otherwise leave it empty. Answer with a JSON object whose "summaries" array holds one {"id", "summary", "pseudocode"} object per fold.',
+])("resets historical stock prompt %# but retains edits", (stockPrompt) => {
+  const source = `[plugins.bundled.summarize]\nsystem_prompt = ${JSON.stringify(stockPrompt)} # old default\n`;
+  const migrated = migrateDiffrConfig(source);
+  expect(parse(migrated)).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: { bundled: { summarize: {} } },
+    },
+  });
+  expect(migrated).toContain("# old default");
+
+  for (const custom of [
+    " " + stockPrompt,
+    stockPrompt + " Keep my team naming.",
+  ]) {
+    const literal = JSON.stringify(custom);
+
+    const migratedCustom = migrateDiffrConfig(
+      `[plugins.bundled.summarize]\nsystem_prompt = ${literal} # custom prompt\n`,
+    );
+
+    expect(
+      new TomlEdits(migratedCustom).value(
+        "plugins.shape.bundled.summarize.system_prompt",
+      ),
+    ).toBe(custom);
+    expect(migratedCustom).toContain(
+      `system_prompt = ${literal} # custom prompt`,
+    );
+  }
+});
+
+test("moves the old default context-first order to the v2 context-last default", () => {
+  const source =
+    '[plugins]\norder = ["bundled.context", "bundled.hide-files", "bundled.deleted-bodies", "bundled.summarize", "bundled.test-bodies", "bundled.removed-runs", "bundled.group"]\n';
+
+  expect(
+    new TomlEdits(migrateDiffrConfig(source)).value("plugins.shape.order"),
+  ).toEqual([
+    "bundled.deleted-bodies",
+    "bundled.summarize",
+    "bundled.test-bodies",
+    "bundled.removed-runs",
+    "bundled.context",
+  ]);
+});
+
+test("keeps new namespaces while removing only legacy parent tables", () => {
+  const source = `version = 1
+[plugins] # pipeline config
+order = ["bundled.context", "external.team.custom"]
+[plugins.bundled] # built-in plugins
+context = { lines = 0x10 }
+[plugins.external] # custom plugins
+"team.custom" = { path = 'plugins/custom', threshold = 1_000 }
+[classifier] # file tags
+hide = ['team']
+`;
+
+  const migrated = migrateDiffrConfig(source);
+  expect(parse(migrated)).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: {
+        order: ["bundled.context", "team.custom"],
+        bundled: { context: { lines: 16 } },
+        "team.custom": { path: "plugins/custom", threshold: 1000 },
+      },
+      classify: { bundled: { hide: ["team"] } },
+    },
+  });
+  expect(migrated).toContain("lines = 0x10");
+  expect(migrated).toContain("threshold = 1_000");
+
+  for (const comment of [
+    "pipeline config",
+    "built-in plugins",
+    "custom plugins",
+    "file tags",
+  ])
+    expect(migrated).toContain(`# ${comment}`);
+});
+
+test("keeps a custom classifier whose name conflicts with bundled unchanged", async () => {
+  const { root, file, executable, env } = await fixture();
+  const directory = path.join(root, "diffr", "custom-classifier");
+  await mkdir(directory);
+  await writeFile(path.join(directory, "plugin.toml"), 'name = "bundled"\n');
+  const source = '[classifier]\npath = "custom-classifier"\nhide = ["team"]\n';
+  await writeFile(file, source);
+  await expect(ensureDiffrConfigMigrated(executable, env)).rejects.toThrow(
+    "custom classifier named bundled",
+  );
+  expect(await readFile(file, "utf8")).toBe(source);
+  expect(await readdir(path.dirname(file))).toEqual([
+    "config.toml",
+    "custom-classifier",
+  ]);
+});
+
+test("retains order references for bundled and custom plugins with the same basename", () => {
+  const source = `[plugins]
+order = ["external.context", "bundled.context"]
+[plugins.bundled.context]
+enabled = false
+lines = 0x10 # stock override
+[plugins.external.context]
+path = 'custom/context' # custom path
+lines = 1_000 # custom override
+`;
+
+  const migrated = migrateDiffrConfig(source);
+  expect(parse(migrated)).toEqual({
+    version: 2,
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config namespace.
+      shape: {
+        order: ["context", "bundled.context"],
+        bundled: { context: { enabled: false, lines: 16 } },
+        context: { path: "custom/context", lines: 1000 },
+      },
+    },
+  });
+
+  for (const line of source.split("\n").filter((line) => line.includes("#")))
+    expect(migrated).toContain(line);
+});
+
+test("keeps reserved custom plugin entries unchanged on disk", async () => {
+  const { file, executable, env } = await fixture();
+
+  const source =
+    '[plugins.external."bundled.context"]\npath = "custom/context"\n';
+
+  await writeFile(file, source);
+  await expect(ensureDiffrConfigMigrated(executable, env)).rejects.toThrow(
+    "custom plugin named bundled.context",
+  );
+  expect(await readFile(file, "utf8")).toBe(source);
+  expect(await readdir(path.dirname(file))).toEqual(["config.toml"]);
+});
diff --git a/packages/review/src/server/diffr-config-migration.ts b/packages/review/src/server/diffr-config-migration.ts
new file mode 100644
index 000000000..0f6de340b
--- /dev/null
+++ b/packages/review/src/server/diffr-config-migration.ts
@@ -0,0 +1,400 @@
+import { execFile } from "node:child_process";
+import { createHash } from "node:crypto";
+import {
+  mkdir,
+  mkdtemp,
+  readFile,
+  realpath,
+  rm,
+  writeFile,
+} from "node:fs/promises";
+import { homedir } from "node:os";
+import path from "node:path";
+import { promisify } from "node:util";
+
+import { withFileLock, writeFileAtomicAsync } from "@dev.fast/trace-core";
+import { parse } from "smol-toml";
+import { z } from "zod";
+
+import { TomlEdits, tomlKey, tomlKeyParts } from "./toml-edits.js";
+
+const execute = promisify(execFile);
+
+class ConfigMigrationError extends Error {}
+
+const oldOrder = [
+  "bundled.context",
+  "bundled.hide-files",
+  "bundled.deleted-bodies",
+  "bundled.summarize",
+  "bundled.test-bodies",
+  "bundled.removed-runs",
+  "bundled.group",
+];
+
+const newOrder = [
+  "bundled.deleted-bodies",
+  "bundled.summarize",
+  "bundled.test-bodies",
+  "bundled.removed-runs",
+  "bundled.context",
+];
+
+// Exact defaults written by older diffr releases; edited prompts stay intact.
+const stockPrompts = new Set([
+  'For each listed fold, rewrite that function body as short python-flavored pseudocode. Keep the names. No prose, no comments, no code fences. Use as few lines as possible: about one pseudocode line per five source lines, and never more than a third of the body\'s lines. When a fold lists a doc, also set "summary" to one sentence copied verbatim from that doc; otherwise leave it empty. Answer with a JSON array of {"id", "summary", "pseudocode"} objects, one per fold.',
+  'For each listed fold, rewrite that function body as short pseudocode. Keep the names. No prose, no comments, no code fences. Use as few lines as possible: about one pseudocode line per five source lines, and never more than a third of the body\'s lines. When a fold lists a doc, also set "summary" to one sentence copied verbatim from that doc; otherwise leave it empty. Answer with a JSON array of {"id", "summary", "pseudocode"} objects, one per fold.',
+  'For each listed fold, rewrite that function body as short pseudocode. Keep the names. No prose, no comments, no code fences. Use as few lines as possible: about one pseudocode line per five source lines, and never more than a third of the body\'s lines. When a fold lists a doc, also set "summary" to one sentence copied verbatim from that doc; otherwise leave it empty. Answer with a JSON object whose "summaries" array holds one {"id", "summary", "pseudocode"} object per fold.',
+]);
+
+const configVersionSchema = z.object({ version: z.number().int().optional() });
+
+const pluginEntrySchema = z.record(z.string(), z.unknown());
+
+const legacyConfigSchema = z.object({
+  plugins: z
+    .object({
+      order: z.array(z.string()).optional(),
+      bundled: z.record(z.string(), pluginEntrySchema).optional(),
+      external: z.record(z.string(), pluginEntrySchema).optional(),
+    })
+    .optional(),
+  classifier: pluginEntrySchema.optional(),
+});
+
+const legacyHideSchema = z.object({
+  enabled: z.boolean().default(true),
+  tags: z.array(z.string()).default(["generated", "vendored", "test"]),
+  deleted: z.boolean().default(true),
+});
+
+const legacySummarySchema = z.object({ system_prompt: z.string().optional() });
+
+/** Convert v1 paths to v2 without serializing saved plugin option values. */
+export function migrateDiffrConfig(
+  source: string,
+  classifierName = "bundled",
+): string {
+  const parsed = parse(source);
+  const version = configVersionSchema.parse(parsed).version ?? 1;
+
+  if (version === 2) return source;
+
+  if (version !== 1)
+    throw new ConfigMigrationError(
+      `Unsupported diffr config version: ${version}`,
+    );
+
+  const config = legacyConfigSchema.parse(parsed);
+  const bundled = config.plugins?.bundled;
+  const external = config.plugins?.external;
+  const edits = new TomlEdits(source);
+
+  for (const name of Object.keys(external ?? {}))
+    if (name === "order" || name === "bundled" || name.startsWith("bundled."))
+      throw new ConfigMigrationError(
+        `diffr config has a custom plugin named ${name}. Rename that plugin before migration; plugins.shape.${name} is reserved.`,
+      );
+
+  if (config.classifier?.path !== undefined && classifierName === "bundled")
+    throw new ConfigMigrationError(
+      "diffr config has a custom classifier named bundled. Rename that plugin before migration; plugins.classify.bundled is reserved.",
+    );
+
+  // The independent group switch is retired, for either saved boolean value.
+  edits.remove("plugins.bundled.group");
+
+  if (bundled?.["hide-files"] !== undefined) {
+    const hide = legacyHideSchema.parse(bundled["hide-files"]);
+
+    // Explicit classifier settings in a mixed v1 file take precedence.
+    if (config.classifier?.hide === undefined)
+      edits.set("classifier.hide", hide.enabled ? hide.tags : []);
+
+    if (config.classifier?.hide_deleted === undefined)
+      edits.set("classifier.hide_deleted", hide.enabled && hide.deleted);
+    edits.remove("plugins.bundled.hide-files");
+  }
+
+  if (config.plugins?.order) {
+    const order = config.plugins.order;
+
+    const migrated =
+      JSON.stringify(order) === JSON.stringify(oldOrder)
+        ? newOrder
+        : order
+            .filter(
+              (name) =>
+                name !== "bundled.group" && name !== "bundled.hide-files",
+            )
+            .map((name) => name.replace(/^external\./, ""));
+
+    edits.set("plugins.order", migrated);
+    edits.move("plugins.order", "plugins.shape.order");
+  }
+
+  // This old option was accepted but ignored. Do not turn it into --jobs.
+  edits.remove("plugins.bundled.summarize.max_concurrency");
+
+  const summary =
+    bundled?.summarize === undefined
+      ? undefined
+      : legacySummarySchema.parse(bundled.summarize);
+
+  // Keep custom prompts exactly; reset only these historical stock defaults.
+  const resetPrompt =
+    summary?.system_prompt !== undefined &&
+    stockPrompts.has(summary.system_prompt);
+
+  if (resetPrompt) edits.remove("plugins.bundled.summarize.system_prompt");
+
+  for (const name of Object.keys(bundled ?? {}))
+    if (name !== "group" && name !== "hide-files")
+      edits.move(
+        tomlKey("plugins", "bundled", name),
+        tomlKey("plugins", "shape", "bundled", name),
+      );
+
+  for (const name of Object.keys(external ?? {}))
+    edits.move(
+      tomlKey("plugins", "external", name),
+      tomlKey("plugins", "shape", name),
+    );
+
+  edits.remove("plugins.bundled");
+  edits.remove("plugins.external");
+  edits.move("classifier", tomlKey("plugins", "classify", classifierName));
+  edits.set("version", 2);
+
+  const movedValues: [string, string][] = [];
+
+  for (const key of new TomlEdits(source).valueKeys()) {
+    if (
+      key.startsWith("plugins.bundled.group.") ||
+      key.startsWith("plugins.bundled.hide-files.") ||
+      key === "plugins.bundled.summarize.max_concurrency" ||
+      (key === "plugins.bundled.summarize.system_prompt" && resetPrompt)
+    )
+      continue;
+
+    if (key.startsWith("plugins.bundled."))
+      movedValues.push([
+        key,
+        key.replace("plugins.bundled.", "plugins.shape.bundled."),
+      ]);
+
+    if (key.startsWith("plugins.external."))
+      movedValues.push([
+        key,
+        key.replace("plugins.external.", "plugins.shape."),
+      ]);
+
+    if (key.startsWith("classifier."))
+      movedValues.push([
+        key,
+        key.replace(
+          "classifier.",
+          `${tomlKey("plugins", "classify", classifierName)}.`,
+        ),
+      ]);
+  }
+
+  edits.assertUnchanged(source, movedValues);
+
+  return edits.source;
+}
+
+/** Run once at startup; v2 files do not need binary probing or validation. */
+export async function ensureDiffrConfigMigrated(
+  executable: string,
+  env: NodeJS.ProcessEnv = process.env,
+  signal?: AbortSignal,
+  cwd?: string,
+): Promise<boolean> {
+  const file = path.resolve(
+    cwd ?? process.cwd(),
+    env.XDG_CONFIG_HOME || path.join(homedir(), ".config"),
+    "diffr",
+    "config.toml",
+  );
+
+  const target = await realpath(file).catch((error: NodeJS.ErrnoException) => {
+    if (error.code === "ENOENT") return undefined;
+    throw error;
+  });
+
+  if (!target) return false;
+
+  const result = await withFileLock(
+    `${target}.whiteboard-migration.lock`,
+    {
+      retryMs: 25,
+      staleMs: 120_000,
+      timeoutMs: 30_000,
+      unownedGraceMs: 5_000,
+    },
+    async () => {
+      signal?.throwIfAborted();
+      const original = await readFile(target, "utf8");
+      let candidate: string;
+
+      try {
+        const version = configVersionSchema.parse(parse(original)).version ?? 1;
+
+        if (version === 2) return false;
+
+        if (version !== 1)
+          throw new ConfigMigrationError(
+            `Unsupported diffr config version: ${version}`,
+          );
+        const classifierName = await legacyClassifierName(original, file);
+        candidate = migrateDiffrConfig(original, classifierName);
+      } catch (error) {
+        if (error instanceof ConfigMigrationError) throw error;
+        // TOML and schema errors can contain the source and saved credentials.
+        throw new Error(
+          "diffr could not migrate the saved config. The original file was kept.",
+        );
+      }
+
+      if (candidate === original) return false;
+
+      // Validate from a sibling config directory, with relative paths made absolute.
+      await validateDiffrConfig(executable, candidate, file, env, signal, cwd);
+
+      if ((await readFile(target, "utf8")) !== original)
+        throw new Error("diffr config changed during migration. Try again.");
+
+      const hash = createHash("sha256")
+        .update(original)
+        .digest("hex")
+        .slice(0, 16);
+
+      const backup = `${target}.before-whiteboard-config-v2.${hash}`;
+
+      try {
+        await writeFile(backup, original, { flag: "wx", mode: 0o600 });
+      } catch (error) {
+        if (
+          !(
+            error instanceof Error &&
+            "code" in error &&
+            error.code === "EEXIST"
+          )
+        )
+          throw error;
+
+        if ((await readFile(backup, "utf8")) !== original)
+          throw new Error(
+            "diffr migration backup already exists for different config. Keep it and move it before retrying.",
+          );
+      }
+
+      signal?.throwIfAborted();
+
+      if ((await readFile(target, "utf8")) !== original)
+        throw new Error("diffr config changed during migration. Try again.");
+      await writeFileAtomicAsync(target, candidate, {
+        encoding: "utf8",
+        mode: 0o600,
+      });
+
+      return true;
+    },
+  );
+
+  if (!result.acquired) throw new Error("diffr config is busy. Try again.");
+
+  return result.result;
+}
+
+async function legacyClassifierName(
+  source: string,
+  file: string,
+): Promise<string> {
+  const classifier = legacyConfigSchema.parse(parse(source)).classifier;
+
+  if (classifier?.path === undefined) return "bundled";
+
+  const directory = path.resolve(
+    path.dirname(file),
+    z.string().parse(classifier.path),
+  );
+
+  try {
+    const manifest = z
+      .object({ name: z.string().min(1) })
+      .parse(
+        parse(await readFile(path.join(directory, "plugin.toml"), "utf8")),
+      );
+
+    return manifest.name;
+  } catch {
+    throw new ConfigMigrationError(
+      "diffr could not read the custom classifier manifest. The original file was kept.",
+    );
+  }
+}
+
+async function validateDiffrConfig(
+  executable: string,
+  source: string,
+  file: string,
+  env: NodeJS.ProcessEnv,
+  signal?: AbortSignal,
+  cwd?: string,
+): Promise<void> {
+  const directory = await mkdtemp(
+    path.join(path.dirname(file), ".whiteboard-config-"),
+  );
+
+  try {
+    const edits = new TomlEdits(source);
+
+    // Moving the candidate for validation must not move theme or plugin paths.
+    for (const key of edits.keys()) {
+      const parts = tomlKeyParts(key);
+
+      if (
+        key === "theme.path" ||
+        (parts.length === 4 &&
+          parts[0] === "plugins" &&
+          (parts[1] === "shape" || parts[1] === "classify") &&
+          parts[3] === "path") ||
+        (parts.length === 5 &&
+          parts[0] === "plugins" &&
+          parts[1] === "shape" &&
+          parts[2] === "bundled" &&
+          parts[4] === "path")
+      ) {
+        const value = z.string().parse(edits.value(key));
+
+        if (!path.isAbsolute(value))
+          edits.set(key, path.resolve(path.dirname(file), value));
+      }
+    }
+
+    await mkdir(path.join(directory, "diffr"), { mode: 0o700 });
+    await writeFile(
+      path.join(directory, "diffr", "config.toml"),
+      edits.source,
+      { mode: 0o600 },
+    );
+
+    try {
+      await execute(executable, ["config", "show", "--json"], {
+        env: { ...env, XDG_CONFIG_HOME: directory },
+        cwd,
+        signal: signal ?? AbortSignal.timeout(30_000),
+        maxBuffer: 16 * 1024 * 1024,
+      });
+    } catch {
+      signal?.throwIfAborted();
+      throw new Error(
+        "diffr could not validate the migrated config. The original file was kept.",
+      );
+    }
+  } finally {
+    await rm(directory, { recursive: true, force: true });
+  }
+}
diff --git a/packages/review/src/server/diffr-config.test.ts b/packages/review/src/server/diffr-config.test.ts
index 4699803f7..cac9af5d2 100644
--- a/packages/review/src/server/diffr-config.test.ts
+++ b/packages/review/src/server/diffr-config.test.ts
@@ -114,7 +114,11 @@ const draft = {
   tests: true,
 };
 
-async function fakeDiffr(key = "", summarize: JsonObject = {}) {
+async function fakeDiffr(
+  key = "",
+  summarize: JsonObject = {},
+  classifier?: JsonObject,
+) {
   const root = await mkdtemp(path.join(tmpdir(), "review-diffr-config-"));
   roots.push(root);
 
@@ -125,18 +129,23 @@ async function fakeDiffr(key = "", summarize: JsonObject = {}) {
   await writeFile(
     state,
     JSON.stringify({
+      version: 2,
       plugins: {
-        bundled: {
-          summarize: {
-            enabled: false,
-            provider: "gemini",
-            model: "old",
-            tests: false,
-            system_prompt: DEFAULT_PROMPT,
-            ...(key && { api_key: key }),
-            ...summarize,
+        ...(classifier && { classify: { bundled: classifier } }),
+        // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+        shape: {
+          bundled: {
+            summarize: {
+              enabled: false,
+              provider: "gemini",
+              model: "old",
+              tests: false,
+              system_prompt: DEFAULT_PROMPT,
+              ...(key && { api_key: key }),
+              ...summarize,
+            },
+            context: { lines: 3, enabled: true },
           },
-          context: { lines: 3, enabled: true },
         },
       },
     }),
@@ -153,23 +162,24 @@ if (args[0] === 'config' && args[1] === 'schema' && process.env.FAIL_SCHEMA) {
   process.exit(2);
 } else if (args[0] === 'config' && args[1] === 'schema') {
   const summarize = ${JSON.stringify(SUMMARIZE_SCHEMA)};
-  console.log(JSON.stringify({ properties: { plugins: { properties: { bundled: { properties: { summarize } } } } } }));
+  // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+  console.log(JSON.stringify({ properties: { plugins: { properties: { ${classifier ? 'classify: { properties: { bundled: { properties: { hide: { default: ["generated", "vendored"] } } } } },' : ""} shape: { properties: { bundled: { properties: { summarize } } } } } } } }));
 } else if (args[0] === 'config' && args[1] === 'show') {
-  if (!args.includes('--reveal') && config.plugins.bundled.summarize.api_key) config.plugins.bundled.summarize.api_key = '<redacted>';
+  if (!args.includes('--reveal') && config.plugins.shape.bundled.summarize.api_key) config.plugins.shape.bundled.summarize.api_key = '<redacted>';
   console.log(JSON.stringify(config));
 } else if (args[0] === 'config' && args[1] === 'set') {
   if (args[2] === process.env.FAIL_KEY) { console.error('command leaked secret: ' + args.join(' ')); process.exit(2); }
   const keys = args[2].split('.'); let object = config;
   for (const part of keys.slice(0,-1)) object = object[part];
   let value = args[3]; try { value = JSON.parse(value); } catch {}
-  // diffr 0.1.10 clears a provider's own settings when the provider changes.
+  // diffr clears a provider's own settings when the provider changes.
   if (process.env.FAKE_RESET && args[2].endsWith('.provider') && object.provider !== value) {
     for (const option of ['api_key', 'endpoint', 'model']) delete object[option];
   }
   object[keys.at(-1)] = value;
   fs.writeFileSync(state, JSON.stringify(config));
  } else if (!args.includes('--no-index')) {
-  console.log(JSON.stringify({type:'start',version:4,lhs:{type:'revision',rev:'base'},rhs:{type:'revision',rev:'head'},files:[]}));
+  console.log(JSON.stringify({type:'start',version:3,lhs:{type:'revision',rev:'base'},rhs:{type:'revision',rev:'head'},files:[]}));
   console.log(JSON.stringify({type:'complete',succeeded:0,failed:0}));
 } else {
   const temporary = require('node:path').join(process.env.XDG_CONFIG_HOME, 'diffr', 'config.toml');
@@ -181,7 +191,7 @@ if (args[0] === 'config' && args[1] === 'schema' && process.env.FAIL_SCHEMA) {
   if (mode === 'hang') { setTimeout(() => {}, 10000); }
   else {
     const file = {rhs:{path:'after.rs',oid:'',mode:''}};
-    console.log(JSON.stringify({type:'annotations',file,annotations:mode === 'empty' ? [] : [{region_id:1,label:'count positive values'}]}));
+    console.log(JSON.stringify({type:'file',file,diff:{type:'text',rhs:{text:'sample',root:{kind:'leaf',id:1,fold_state_id:1,alignment_id:1,start:{line:0,column:0},end:{line:0,column:6},visibility:mode === 'empty' ? undefined : {collapsed:true,label:'count positive values'}}},structural_changes:{base:[],head:[[0,1]]},stats:{textual:{added:1,removed:0},visible:{added:0,removed:0}}}}));
     console.log(JSON.stringify({type:'complete',succeeded:1,failed:0}));
   }
 }
@@ -190,6 +200,8 @@ if (args[0] === 'config' && args[1] === 'schema' && process.env.FAIL_SCHEMA) {
   );
   vi.stubEnv("REVIEW_DIFFR_BINARY", file);
 
+  vi.stubEnv("XDG_CONFIG_HOME", path.join(root, "xdg"));
+
   return {
     root,
     state,
@@ -211,6 +223,28 @@ test("reads resolved values and reports credentials without exposing keys", asyn
   );
 });
 
+test("redacts credentials in bundled and custom shape entries", async () => {
+  const fake = await fakeDiffr("bundled-secret");
+  const state = JSON.parse(await readFile(fake.state, "utf8"));
+  state.plugins.shape.custom = {
+    path: "plugins/custom",
+    api_key: "custom-secret",
+    enabled: true,
+  };
+  await writeFile(fake.state, JSON.stringify(state));
+
+  const config = await readDiffrConfig();
+  expect(JSON.stringify(config)).not.toMatch(
+    /bundled-secret|custom-secret|api_key/,
+  );
+  expect(config.values).toMatchObject({
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+      shape: { custom: { path: "plugins/custom", enabled: true } },
+    },
+  });
+});
+
 test("detects host environment credentials and missing credentials", async () => {
   await fakeDiffr();
   expect((await readDiffrConfig()).credentialSource).toBe("missing");
@@ -218,15 +252,88 @@ test("detects host environment credentials and missing credentials", async () =>
   expect((await readDiffrConfig()).credentialSource).toBe("environment");
 });
 
+test("reads classifier values and schema defaults without old plugin keys", async () => {
+  await fakeDiffr(
+    "saved-secret",
+    {},
+    { hide: ["test", "custom"], hide_deleted: false },
+  );
+  const config = await readDiffrConfig();
+  expect(config.values).toMatchObject({
+    plugins: {
+      classify: { bundled: { hide: ["test", "custom"], hide_deleted: false } },
+    },
+  });
+  expect(config.defaultHiddenTags).toEqual(["generated", "vendored"]);
+  expect(JSON.stringify(config)).not.toContain("saved-secret");
+});
+
+test("writes classifier values without changing credentials", async () => {
+  const fake = await fakeDiffr(
+    "saved-secret",
+    {},
+    { hide: ["custom"], hide_deleted: true },
+  );
+
+  expect(
+    (await setDiffrConfigValue("plugins.classify.bundled.hide", ["custom"]))
+      .changed,
+  ).toBe(false);
+  await setDiffrConfigValue("plugins.classify.bundled.hide", []);
+  await setDiffrConfigValue("plugins.classify.bundled.hide_deleted", false);
+  const disabled = JSON.parse(await readFile(fake.state, "utf8"));
+  expect(disabled.plugins.classify.bundled).toEqual({
+    hide: [],
+    hide_deleted: false,
+  });
+  await setDiffrConfigValue("plugins.classify.bundled.hide", ["custom"]);
+  const enabled = JSON.parse(await readFile(fake.state, "utf8"));
+  expect(enabled.plugins.classify.bundled).toEqual({
+    hide: ["custom"],
+    hide_deleted: false,
+  });
+  expect(enabled.plugins.shape.bundled.summarize.api_key).toBe("saved-secret");
+  expect(enabled.plugins.shape.bundled["hide-files"]).toBeUndefined();
+});
+
+test("writes the native path of a custom classifier whose name contains spaces", async () => {
+  const fake = await fakeDiffr("saved-secret", {}, { hide: ["team"] });
+  const state = JSON.parse(await readFile(fake.state, "utf8"));
+  state.plugins.classify = {
+    "team classifier": state.plugins.classify.bundled,
+  };
+  await writeFile(fake.state, JSON.stringify(state));
+
+  const result = await setDiffrConfigValue(
+    "plugins.classify.team classifier.hide",
+    [],
+  );
+
+  expect(result.error).toBeUndefined();
+  expect(result.values).toMatchObject({
+    plugins: { classify: { "team classifier": { hide: [] } } },
+  });
+  const saved = JSON.parse(await readFile(fake.state, "utf8"));
+  expect(Object.keys(saved.plugins.classify)).toEqual(["team classifier"]);
+  expect(JSON.stringify(result)).not.toContain("saved-secret");
+});
+
 test("writes a setting, rereads it, and avoids invalidation for a no-op", async () => {
   await fakeDiffr();
   expect(
-    (await setDiffrConfigValue("plugins.bundled.context.lines", 3)).changed,
+    (await setDiffrConfigValue("plugins.shape.bundled.context.lines", 3))
+      .changed,
   ).toBe(false);
-  const result = await setDiffrConfigValue("plugins.bundled.context.lines", 8);
+
+  const result = await setDiffrConfigValue(
+    "plugins.shape.bundled.context.lines",
+    8,
+  );
+
   expect(result).toMatchObject({
     changed: true,
-    values: { plugins: { bundled: { context: { lines: 8 } } } },
+    // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+    values: { plugins: { shape: { bundled: { context: { lines: 8 } } } } },
   });
 });
 
@@ -236,13 +343,13 @@ test("saves credentials and options before enabling and preserves blank keys", a
   const writes = (await fake.calls()).filter((args) => args[1] === "set");
   expect(writes.map((args) => args[2])).toEqual(
     ["api_key", "model", "tests", "enabled"].map(
-      (key) => `plugins.bundled.summarize.${key}`,
+      (key) => `plugins.shape.bundled.summarize.${key}`,
     ),
   );
   await saveDiffrSummarizer({ ...draft, apiKey: "" });
   expect(
-    JSON.parse(await readFile(fake.state, "utf8")).plugins.bundled.summarize
-      .api_key,
+    JSON.parse(await readFile(fake.state, "utf8")).plugins.shape.bundled
+      .summarize.api_key,
   ).toBe("test-secret");
 });
 
@@ -251,7 +358,7 @@ test("disables first and serializes concurrent saves", async () => {
   await saveDiffrSummarizer(draft);
   await Promise.all([
     saveDiffrSummarizer({ ...draft, enabled: false, model: "next" }),
-    setDiffrConfigValue("plugins.bundled.context.lines", 9),
+    setDiffrConfigValue("plugins.shape.bundled.context.lines", 9),
   ]);
 
   const writes = (await fake.calls())
@@ -259,27 +366,30 @@ test("disables first and serializes concurrent saves", async () => {
     .slice(-3);
 
   expect(writes.map((args) => args[2])).toEqual([
-    "plugins.bundled.summarize.enabled",
-    "plugins.bundled.summarize.model",
-    "plugins.bundled.context.lines",
+    "plugins.shape.bundled.summarize.enabled",
+    "plugins.shape.bundled.summarize.model",
+    "plugins.shape.bundled.context.lines",
   ]);
 });
 
 test("partial failure returns current values and invalidates without leaking the key", async () => {
   await fakeDiffr();
-  vi.stubEnv("FAIL_KEY", "plugins.bundled.summarize.model");
+  vi.stubEnv("FAIL_KEY", "plugins.shape.bundled.summarize.model");
   const result = await saveDiffrSummarizer({ ...draft, apiKey: "test-secret" });
   expect(result.changed).toBe(true);
   expect(result.error).toContain("Some settings were saved");
   expect(result.values).toMatchObject({
-    plugins: { bundled: { summarize: { enabled: false, model: "old" } } },
+    plugins: {
+      // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+      shape: { bundled: { summarize: { enabled: false, model: "old" } } },
+    },
   });
   expect(JSON.stringify(result)).not.toContain("test-secret");
 });
 
 test("failed key saves do not leak args or stderr and do not invalidate", async () => {
   await fakeDiffr();
-  vi.stubEnv("FAIL_KEY", "plugins.bundled.summarize.api_key");
+  vi.stubEnv("FAIL_KEY", "plugins.shape.bundled.summarize.api_key");
   const result = await saveDiffrSummarizer({ ...draft, apiKey: "test-secret" });
   expect(result.changed).toBe(false);
   expect(result.error).toBeDefined();
@@ -380,12 +490,12 @@ test("saved changes invalidate cached comparisons while no-op saves reuse them",
 
   try {
     await consume();
-    await setDiffrConfigValue("plugins.bundled.context.lines", 3);
+    await setDiffrConfigValue("plugins.shape.bundled.context.lines", 3);
     await consume();
     expect(
       (await fake.calls()).filter((args) => args[0] === "--repo"),
     ).toHaveLength(1);
-    await setDiffrConfigValue("plugins.bundled.context.lines", 8);
+    await setDiffrConfigValue("plugins.shape.bundled.context.lines", 8);
     await consume();
     expect(
       (await fake.calls()).filter((args) => args[0] === "--repo"),
@@ -414,8 +524,8 @@ test("saves a changed prompt and leaves an unchanged one alone", async () => {
     systemPrompt: "Be terse.",
   });
   expect(
-    JSON.parse(await readFile(fake.state, "utf8")).plugins.bundled.summarize
-      .system_prompt,
+    JSON.parse(await readFile(fake.state, "utf8")).plugins.shape.bundled
+      .summarize.system_prompt,
   ).toBe("Be terse.");
 });
 
@@ -423,7 +533,8 @@ test("switching providers clears the saved key unless a new one is entered", asy
   const fake = await fakeDiffr("gemini-secret");
 
   const state = async () =>
-    JSON.parse(await readFile(fake.state, "utf8")).plugins.bundled.summarize;
+    JSON.parse(await readFile(fake.state, "utf8")).plugins.shape.bundled
+      .summarize;
 
   await saveDiffrSummarizer({
     ...draft,
@@ -502,7 +613,7 @@ test("reads the environment key of the saved provider", async () => {
 
 test("a switch clears the saved key before naming the new provider", async () => {
   const fake = await fakeDiffr("gemini-secret");
-  vi.stubEnv("FAIL_KEY", "plugins.bundled.summarize.provider");
+  vi.stubEnv("FAIL_KEY", "plugins.shape.bundled.summarize.provider");
 
   const result = await saveDiffrSummarizer({
     ...draft,
@@ -512,8 +623,8 @@ test("a switch clears the saved key before naming the new provider", async () =>
 
   expect(result.error).toBeDefined();
 
-  const state = JSON.parse(await readFile(fake.state, "utf8")).plugins.bundled
-    .summarize;
+  const state = JSON.parse(await readFile(fake.state, "utf8")).plugins.shape
+    .bundled.summarize;
 
   // The failure left the old provider, and no key for it to send.
   expect(state).toMatchObject({ provider: "gemini", api_key: "" });
@@ -525,7 +636,8 @@ test("a new endpoint is treated like a new provider", async () => {
   await expect(testDiffrSummarizer(moved)).rejects.toThrow("Add an API key");
   await saveDiffrSummarizer({ ...moved, enabled: false });
   expect(
-    JSON.parse(await readFile(fake.state, "utf8")).plugins.bundled.summarize,
+    JSON.parse(await readFile(fake.state, "utf8")).plugins.shape.bundled
+      .summarize,
   ).toMatchObject({ api_key: "", endpoint: "https://proxy.example/v1" });
 });
 
@@ -619,7 +731,8 @@ test("a custom endpoint kept across a provider switch survives diffr clearing it
     apiKey: "openai-key",
   });
   expect(
-    JSON.parse(await readFile(fake.state, "utf8")).plugins.bundled.summarize,
+    JSON.parse(await readFile(fake.state, "utf8")).plugins.shape.bundled
+      .summarize,
   ).toMatchObject({
     provider: "openai",
     endpoint: "https://gateway.example/v1",
diff --git a/packages/review/src/server/diffr-config.ts b/packages/review/src/server/diffr-config.ts
index c7e137875..6538667bb 100644
--- a/packages/review/src/server/diffr-config.ts
+++ b/packages/review/src/server/diffr-config.ts
@@ -15,6 +15,7 @@ import {
   type ReviewDiffrConfig,
   type ReviewDiffrProvider,
   type ReviewDiffrSummarizerInput,
+  type StructuralRegion,
   decodeStructuralDiffEvent,
   reviewDiffrSummarizerInputSchema,
 } from "@dev.fast/review-protocol";
@@ -36,13 +37,39 @@ function serialized<T>(operation: () => Promise<T>): Promise<T> {
   return next;
 }
 
+type DiffrArguments =
+  | { command: "schema" }
+  | { command: "show"; reveal: boolean }
+  | { command: "set"; key: string; value: JsonValue }
+  | { command: "diff"; before: string; after: string };
+
+function diffrArgv(args: DiffrArguments): string[] {
+  switch (args.command) {
+    case "schema":
+      return ["config", "schema"];
+    case "show":
+      return ["config", "show", "--json", ...(args.reveal ? ["--reveal"] : [])];
+    case "set":
+      return ["config", "set", args.key, diffrConfigValueText(args.value)];
+    case "diff":
+      return [
+        "--no-index",
+        "--format",
+        "ndjson",
+        "--",
+        args.before,
+        args.after,
+      ];
+  }
+}
+
 async function diffr(
-  args: string[],
+  args: DiffrArguments,
   rootPath?: string,
   options: { signal?: AbortSignal; env?: NodeJS.ProcessEnv } = {},
 ): Promise<string> {
   try {
-    const { stdout } = await execFileAsync(diffrExecutable(), args, {
+    const { stdout } = await execFileAsync(diffrExecutable(), diffrArgv(args), {
       cwd: rootPath,
       maxBuffer: 16 * 1024 * 1024,
       signal: options.signal ?? AbortSignal.timeout(30_000),
@@ -70,13 +97,7 @@ async function values(
   reveal = false,
   signal?: AbortSignal,
 ): Promise<JsonObject> {
-  return json(
-    await diffr(
-      ["config", "show", "--json", ...(reveal ? ["--reveal"] : [])],
-      rootPath,
-      { signal },
-    ),
-  );
+  return json(await diffr({ command: "show", reveal }, rootPath, { signal }));
 }
 
 function json(output: string): JsonObject {
@@ -100,7 +121,7 @@ function valueAt(object: JsonObject, key: string): JsonValue | undefined {
   return value;
 }
 
-const prefix = "plugins.bundled.summarize";
+const prefix = "plugins.shape.bundled.summarize";
 
 function savedProvider(config: JsonObject): string {
   const value = valueAt(config, `${prefix}.provider`);
@@ -151,27 +172,35 @@ function strings(value: JsonValue | undefined): string[] {
 }
 
 /**
- * What diffr's schema says about summaries: each provider's defaults, and
- * the default prompt with the link its description gives. Nothing when
- * diffr cannot describe its schema: the rest of Settings still works.
+ * Defaults supplied by diffr's schema for tag hiding and summary controls.
+ * If the schema cannot be read, resolved settings still work.
  */
-async function summaryDefaults(
+async function configDefaults(
   rootPath?: string,
-): Promise<Pick<ReviewDiffrConfig, "providers" | "defaultPrompt">> {
+): Promise<
+  Pick<ReviewDiffrConfig, "providers" | "defaultPrompt" | "defaultHiddenTags">
+> {
   let schema: JsonObject;
 
   try {
-    schema = json(await diffr(["config", "schema"], rootPath));
+    schema = json(await diffr({ command: "schema" }, rootPath));
   } catch {
     return {};
   }
 
   const options = valueAt(
     schema,
-    "properties.plugins.properties.bundled.properties.summarize.properties",
+    "properties.plugins.properties.shape.properties.bundled.properties.summarize.properties",
+  );
+
+  const defaultHiddenTags = strings(
+    valueAt(
+      schema,
+      "properties.plugins.properties.classify.properties.bundled.properties.hide.default",
+    ),
   );
 
-  if (!isJsonObject(options)) return {};
+  if (!isJsonObject(options)) return { defaultHiddenTags };
 
   const option = (name: string) =>
     isJsonObject(options[name]) ? options[name] : {};
@@ -200,6 +229,7 @@ async function summaryDefaults(
   const prompt = option("system_prompt");
 
   return {
+    defaultHiddenTags,
     providers,
     defaultPrompt: isStringValue(prompt.default) ? prompt.default : undefined,
   };
@@ -207,7 +237,7 @@ async function summaryDefaults(
 
 async function read(rootPath?: string): Promise<ReviewDiffrConfig> {
   const config = await values(rootPath);
-  const defaults = await summaryDefaults(rootPath);
+  const defaults = await configDefaults(rootPath);
   const saved = valueAt(config, `${prefix}.api_key`);
 
   const credentialSource =
@@ -217,16 +247,15 @@ async function read(rootPath?: string): Promise<ReviewDiffrConfig> {
         ? "environment"
         : "missing";
 
-  const plugins = config.plugins;
+  const plugins = valueAt(config, "plugins.shape");
 
   if (isJsonObject(plugins)) {
-    for (const namespace of Object.values(plugins)) {
-      if (!isJsonObject(namespace)) continue;
+    const entries = isJsonObject(plugins.bundled)
+      ? [...Object.values(plugins), ...Object.values(plugins.bundled)]
+      : Object.values(plugins);
 
-      for (const plugin of Object.values(namespace)) {
-        if (isJsonObject(plugin)) delete plugin.api_key;
-      }
-    }
+    for (const plugin of entries)
+      if (isJsonObject(plugin)) delete plugin.api_key;
   }
 
   return { values: config, credentialSource, ...defaults };
@@ -250,11 +279,9 @@ async function writeSettings(
 
   try {
     for (const [key, value] of entries) {
-      if (valueAt(current, key) === value) continue;
-      await diffr(
-        ["config", "set", key, diffrConfigValueText(value)],
-        rootPath,
-      );
+      if (JSON.stringify(valueAt(current, key)) === JSON.stringify(value))
+        continue;
+      await diffr({ command: "set", key, value }, rootPath);
       changed = true;
       // A write can clear others, such as a provider's endpoint and key.
       current = await values(rootPath);
@@ -275,9 +302,7 @@ export function setDiffrConfigValue(
   value: JsonValue,
   rootPath?: string,
 ): Promise<ReviewDiffrConfig> {
-  if (
-    !/^[A-Za-z0-9_][A-Za-z0-9_-]*(\.[A-Za-z0-9_][A-Za-z0-9_-]*)*$/.test(key)
-  ) {
+  if (!/^[A-Za-z0-9_][A-Za-z0-9_-]*(\.[^.\r\n\0]+)*$/u.test(key)) {
     throw new Error("Invalid diffr config key.");
   }
 
@@ -373,7 +398,7 @@ export async function testDiffrSummarizer(
       throw new Error("The summarizer is not available in this configuration.");
 
     const { provider, endpoint, model, systemPrompt } = parsed.data;
-    const providers = (await summaryDefaults(rootPath)).providers ?? [];
+    const providers = (await configDefaults(rootPath)).providers ?? [];
 
     const variables =
       providers.find((known) => known.id === provider)?.keyVariables ?? [];
@@ -410,10 +435,13 @@ export async function testDiffrSummarizer(
     await writeFile(
       join(directory, "diffr", "config.toml"),
       stringify({
-        version: 1,
+        version: 2,
         plugins: {
-          order: ["bundled.summarize"],
-          bundled: { summarize: options },
+          // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+          shape: {
+            order: ["bundled.summarize"],
+            bundled: { summarize: options },
+          },
         },
       }),
       { mode: 0o600 },
@@ -425,56 +453,47 @@ export async function testDiffrSummarizer(
     await writeFile(before, "");
     await writeFile(after, SUMMARY_SAMPLE);
 
-    const output = await diffr(
-      [
-        "--no-index",
-        "--format",
-        "ndjson",
-        "--stream-annotations",
-        "--",
-        before,
-        after,
-      ],
-      directory,
-      {
-        env: {
-          ...process.env,
-          ...Object.fromEntries(
-            providers
-              .flatMap((known) => known.keyVariables)
-              .map((name) => [name, ""]),
-          ),
-          ...(apiKey && variables[0] && { [variables[0]]: apiKey }),
-          XDG_CONFIG_HOME: directory,
-        },
-        signal: deadline,
+    const output = await diffr({ command: "diff", before, after }, directory, {
+      env: {
+        ...process.env,
+        ...Object.fromEntries(
+          providers
+            .flatMap((known) => known.keyVariables)
+            .map((name) => [name, ""]),
+        ),
+        ...(apiKey && variables[0] && { [variables[0]]: apiKey }),
+        XDG_CONFIG_HOME: directory,
       },
-    );
+      signal: deadline,
+    });
 
     try {
       const events = output.trim().split("\n").map(decodeStructuralDiffEvent);
       const complete = events.at(-1);
 
-      const annotation = events
+      const labels = (region: StructuralRegion): string[] => [
+        ...(region.visibility?.label ? [region.visibility.label] : []),
+        ...(region.kind === "fold" ? region.children.flatMap(labels) : []),
+      ];
+
+      const summary = events
         .flatMap((event) =>
-          event.type === "annotations" ? event.annotations : [],
+          event.type === "file" && event.diff?.type === "text"
+            ? [event.diff.rhs, event.diff.lhs].flatMap((source) =>
+                source ? labels(source.root) : [],
+              )
+            : [],
         )
-        .find((item) => item.label.trim());
+        .find((label) => label.trim());
 
       if (
         complete?.type === "complete" &&
         complete.failed === 0 &&
         !complete.aborted &&
-        !events.some(
-          (event) =>
-            (event.type === "annotations" || event.type === "file") &&
-            event.error,
-        ) &&
-        annotation
+        !events.some((event) => event.type === "file" && event.error) &&
+        summary
       ) {
-        return apiKey
-          ? annotation.label.split(apiKey).join("[redacted]")
-          : annotation.label;
+        return apiKey ? summary.split(apiKey).join("[redacted]") : summary;
       }
     } catch {
       /* Never return provider output or parser causes. */
diff --git a/packages/review/src/server/diffr-languages.test.ts b/packages/review/src/server/diffr-languages.test.ts
deleted file mode 100644
index ac3efe9c9..000000000
--- a/packages/review/src/server/diffr-languages.test.ts
+++ /dev/null
@@ -1,54 +0,0 @@
-import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
-import os from "node:os";
-import path from "node:path";
-
-import { afterEach, expect, test, vi } from "vitest";
-
-import { installFullDiffr } from "./diffr-languages.js";
-import { diffrExecutable } from "./structural-diff.js";
-
-let temporary: string;
-
-afterEach(async () => {
-  vi.unstubAllEnvs();
-
-  if (temporary) await rm(temporary, { recursive: true, force: true });
-});
-
-test("delegates full installation once and selects its cache outside the runtime", async () => {
-  temporary = await mkdtemp(path.join(os.tmpdir(), "whiteboard-diffr-"));
-  vi.stubEnv("XDG_CACHE_HOME", path.join(temporary, "cache"));
-  vi.stubEnv("REVIEW_DIFFR_BINARY", "");
-  const root = path.join(temporary, "runtime");
-  const installer = path.join(root, "bin/diffr-package");
-  await mkdir(path.join(installer, "bin"), { recursive: true });
-  await writeFile(
-    path.join(installer, "package.json"),
-    JSON.stringify({ version: "0.1.10" }),
-  );
-  const calls = path.join(temporary, "calls");
-  await writeFile(
-    path.join(installer, "bin/fetch.mjs"),
-    `
-    import { appendFileSync, chmodSync, mkdirSync, writeFileSync } from "node:fs";
-    import path from "node:path";
-    if (!process.argv.includes("--full") || !process.argv.includes("--required")) throw new Error("full verified installation required");
-    appendFileSync(${JSON.stringify(calls)}, "install\\n");
-    const directory = process.argv[process.argv.indexOf("--into") + 1];
-    mkdirSync(directory, { recursive: true });
-    const binary = path.join(directory, process.platform === "win32" ? "diffr.exe" : "diffr");
-    writeFileSync(binary, "installed");
-    chmodSync(binary, 0o755);
-    writeFileSync(path.join(directory, "diffr.stamp.json"), JSON.stringify({ version: "0.1.10", full: true }));
-  `,
-  );
-  expect(diffrExecutable(root)).toBe("diffr");
-  await Promise.all([installFullDiffr(root), installFullDiffr(root)]);
-  expect(await readFile(calls, "utf8")).toBe("install\n");
-  const binary = diffrExecutable(root);
-  expect(binary.startsWith(root)).toBe(false);
-  expect(await readFile(binary, "utf8")).toBe("installed");
-  vi.stubEnv("REVIEW_DIFFR_BINARY", "/explicit/diffr");
-  expect(diffrExecutable(root)).toBe("/explicit/diffr");
-  await expect(installFullDiffr(root)).rejects.toThrow("explicitly selected");
-});
diff --git a/packages/review/src/server/diffr-languages.ts b/packages/review/src/server/diffr-languages.ts
deleted file mode 100644
index dc9a992f5..000000000
--- a/packages/review/src/server/diffr-languages.ts
+++ /dev/null
@@ -1,97 +0,0 @@
-import { execFile } from "node:child_process";
-import { lstatSync, readFileSync } from "node:fs";
-import os from "node:os";
-import path from "node:path";
-import { promisify } from "node:util";
-
-import { findReviewPackageRoot } from "@review/package-paths";
-import { z } from "zod";
-
-const exec = promisify(execFile);
-
-const versionSchema = z.object({ version: z.string() });
-
-const stampSchema = z.object({ version: z.string(), full: z.boolean() });
-
-const pending = new Map<string, Promise<void>>();
-
-function configuration(root: string) {
-  const installer = path.join(root, "bin/diffr-package/bin/fetch.mjs");
-
-  const { version } = versionSchema.parse(
-    JSON.parse(
-      readFileSync(path.join(root, "bin/diffr-package/package.json"), "utf8"),
-    ),
-  );
-
-  const directory = path.join(
-    process.env.XDG_CACHE_HOME || path.join(os.homedir(), ".cache"),
-    "diffr",
-    version,
-    `${process.platform}-${process.arch}`,
-    "full",
-  );
-
-  return {
-    installer,
-    version,
-    directory,
-    binary: path.join(
-      directory,
-      process.platform === "win32" ? "diffr.exe" : "diffr",
-    ),
-  };
-}
-
-export function installedFullDiffr(root: string): string | undefined {
-  try {
-    const { binary, directory, version } = configuration(root);
-    const stat = lstatSync(binary);
-
-    const stamp = stampSchema.parse(
-      JSON.parse(
-        readFileSync(path.join(directory, "diffr.stamp.json"), "utf8"),
-      ),
-    );
-
-    if (
-      stat.isFile() &&
-      (process.platform === "win32" || stat.mode & 0o111) &&
-      stamp.full &&
-      stamp.version === version
-    )
-      return binary;
-  } catch {}
-
-  return undefined;
-}
-
-export function installFullDiffr(
-  root = findReviewPackageRoot(import.meta.url),
-): Promise<void> {
-  if (process.env.REVIEW_DIFFR_BINARY)
-    return Promise.reject(
-      new Error(
-        "An explicitly selected diffr executable is in use. Install its full edition separately.",
-      ),
-    );
-  const { installer, directory } = configuration(root);
-  const current = pending.get(directory);
-
-  if (current) return current;
-
-  const task = exec(
-    process.execPath,
-    [installer, "--full", "--required", "--into", directory],
-    {
-      env: { ...process.env, ELECTRON_RUN_AS_NODE: "1" },
-      timeout: 180_000,
-    },
-  )
-    .then(() => {})
-    .finally(() => pending.delete(directory));
-
-  pending.set(directory, task);
-
-  return task;
-}
diff --git a/packages/review/src/server/diffr-startup.test.ts b/packages/review/src/server/diffr-startup.test.ts
new file mode 100644
index 000000000..c1a5a516a
--- /dev/null
+++ b/packages/review/src/server/diffr-startup.test.ts
@@ -0,0 +1,109 @@
+import { readFileSync } from "node:fs";
+import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+
+import { openLocalReviewStore } from "@review/review-api/local-data.js";
+import { parse } from "smol-toml";
+import { afterEach, expect, test, vi } from "vitest";
+
+import { createGlobalReviewServer } from "./desktop-server.js";
+import { runHeadlessServer } from "./headless-host.js";
+
+const roots: string[] = [];
+
+afterEach(async () => {
+  vi.unstubAllEnvs();
+  await Promise.all(
+    roots.splice(0).map((root) => rm(root, { recursive: true, force: true })),
+  );
+});
+
+test.each(["desktop", "headless"] as const)(
+  "%s startup migrates saved settings before ready and skips migration on restart",
+  async (host) => {
+    const root = await mkdtemp(path.join(tmpdir(), "review-diffr-startup-"));
+    roots.push(root);
+    vi.stubEnv("DEV_REVIEW_HOME", root);
+    vi.stubEnv("XDG_CONFIG_HOME", root);
+    vi.stubEnv("DEV_FAST_REVIEW_TELEMETRY_DISABLED", "1");
+    const file = path.join(root, "diffr", "config.toml");
+    await mkdir(path.dirname(file));
+    await writeFile(
+      file,
+      "version = 1\n[plugins.bundled.context]\nlines = 17\nenabled = false\n",
+    );
+    const executable = path.join(root, "diffr-cli");
+    const log = path.join(root, "validations");
+    await writeFile(
+      executable,
+      `#!${process.execPath}
+const fs = require('node:fs');
+const path = require('node:path');
+const source = fs.readFileSync(path.join(process.env.XDG_CONFIG_HOME, 'diffr', 'config.toml'), 'utf8');
+if (!/version = 2/.test(source)) process.exit(2);
+fs.appendFileSync(${JSON.stringify(log)}, 'validated\\n');
+console.log('{}');
+`,
+      { mode: 0o755 },
+    );
+    vi.stubEnv("REVIEW_DIFFR_BINARY", executable);
+
+    const ready = async () => {
+      expect(parse(await readFile(file, "utf8"))).toMatchObject({
+        version: 2,
+        plugins: {
+          // oxlint-disable-next-line anti-slop/no-shape-in-symbol-names -- Native diffr v2 config key.
+          shape: { bundled: { context: { lines: 17, enabled: false } } },
+        },
+      });
+    };
+
+    const start = async () => {
+      let configAtReady: string | undefined;
+
+      if (host === "headless") {
+        const controller = new AbortController();
+
+        const running = runHeadlessServer({
+          stateDir: path.join(root, "server"),
+          signal: controller.signal,
+          onReady: () => {
+            configAtReady = readFileSync(file, "utf8");
+            controller.abort();
+          },
+        });
+
+        await running;
+        await ready();
+      } else {
+        const local = openLocalReviewStore(path.join(root, "reviews.db"));
+
+        const server = createGlobalReviewServer({
+          reviewStore: local.store,
+          reviewData: local.data,
+          appPid: process.pid,
+          packageRoot: root,
+          toolingRoot: root,
+          port: 0,
+        });
+
+        try {
+          await server.listen();
+          configAtReady = readFileSync(file, "utf8");
+          await ready();
+        } finally {
+          await server.close();
+          await local.data.close();
+          await local.store.close();
+        }
+      }
+
+      expect(parse(configAtReady!)).toMatchObject({ version: 2 });
+    };
+
+    await start();
+    await start();
+    expect(await readFile(log, "utf8")).toBe("validated\n");
+  },
+);
diff --git a/packages/review/src/server/headless-host.ts b/packages/review/src/server/headless-host.ts
index 34815d86b..045c1788a 100644
--- a/packages/review/src/server/headless-host.ts
+++ b/packages/review/src/server/headless-host.ts
@@ -12,6 +12,7 @@ import {
   reviewServerDiscoveryPath,
 } from "@review/server-discovery.js";
 
+import { ensureDiffrConfigMigrated } from "./diffr-config-migration.js";
 import { GlobalReviewDesktopVerbRelay } from "./global-verb-relay.js";
 import { createNodeRequestListener } from "./hono-http.js";
 import {
@@ -19,6 +20,7 @@ import {
   installProcessErrorTelemetry,
 } from "./process-error-telemetry.js";
 import { createWhiteboardCore } from "./review-server-core.js";
+import { diffrExecutable } from "./structural-diff.js";
 import type { ReviewTelemetryCapture } from "./ui-telemetry.js";
 
 interface HeadlessServerInput {
@@ -72,6 +74,8 @@ export function withHeadlessServerLock<T>(
 async function serve(input: HeadlessServerInput) {
   if (input.signal.aborted) return;
 
+  await ensureDiffrConfigMigrated(diffrExecutable(), process.env, input.signal);
+
   if (input.telemetry) await drainServerCrashReport(input.telemetry);
 
   const local = await openReviewProfile(input.stateDir, {
diff --git a/packages/review/src/server/structural-diff-workspace.test.ts b/packages/review/src/server/structural-diff-workspace.test.ts
index 8964486aa..9e7459a53 100644
--- a/packages/review/src/server/structural-diff-workspace.test.ts
+++ b/packages/review/src/server/structural-diff-workspace.test.ts
@@ -73,18 +73,22 @@ const {execFileSync} = require('node:child_process');
 const args = process.argv.slice(2);
 const repo = args[args.indexOf('--repo') + 1];
 const revisions = args
-  .slice(args.indexOf('ndjson') + 1, args.indexOf('--'))
-  .filter(arg => arg !== '--stream-annotations');
+  .slice(args.indexOf('ndjson') + 1, args.indexOf('--'));
 const range = revisions.length === 1 ? revisions[0].split('...') : revisions;
 const file = args[args.indexOf('--') + 1];
-const read = rev => execFileSync('git', ['-C', repo, 'show', rev + ':' + file], {encoding:'utf8'});
-console.log(JSON.stringify({type:'start',version:4,lhs:{type:'revision',rev:range[0]},rhs:{type:'revision',rev:range[1]},files:[{file:{rhs:{path:file,oid:range[1],mode:'100644'}},status:'modified'}]}));
-console.log(JSON.stringify({type:'file',file:{rhs:{path:file,oid:range[1],mode:'100644'}},diff:{type:'text',lhs:{text:read(range[0])},rhs:{text:read(range[1])},stats:{textual:{added:1,removed:1},visible:{added:1,removed:1}},structural_changes:{base:[[0,1]],head:[[0,1]]}}}));
+const read = rev => {
+  const text = execFileSync('git', ['-C', repo, 'show', rev + ':' + file], {encoding:'utf8'});
+  const lines = text.split('\\n');
+  return {text,root:{kind:'leaf',id:1,fold_state_id:1,alignment_id:1,start:{line:0,column:0},end:{line:lines.length-1,column:lines.at(-1).length}}};
+};
+console.log(JSON.stringify({type:'start',version:3,lhs:{type:'revision',rev:range[0]},rhs:{type:'revision',rev:range[1]},files:[{file:{rhs:{path:file,oid:range[1],mode:'100644'}},status:'modified'}]}));
+console.log(JSON.stringify({type:'file',file:{rhs:{path:file,oid:range[1],mode:'100644'}},diff:{type:'text',lhs:read(range[0]),rhs:read(range[1]),stats:{textual:{added:1,removed:1},visible:{added:1,removed:1}},structural_changes:{base:[[0,1]],head:[[0,1]]}}}));
 console.log(JSON.stringify({type:'complete',succeeded:1,failed:0}));
 `,
       { mode: 0o755 },
     );
     vi.stubEnv("REVIEW_DIFFR_BINARY", executable);
+    vi.stubEnv("XDG_CONFIG_HOME", path.join(root, "config"));
     const local = openLocalReviewStore(path.join(root, "reviews.db"));
 
     try {
diff --git a/packages/review/src/server/structural-diff.test.ts b/packages/review/src/server/structural-diff.test.ts
index 9ed12d9f4..5b22b20ae 100644
--- a/packages/review/src/server/structural-diff.test.ts
+++ b/packages/review/src/server/structural-diff.test.ts
@@ -1,15 +1,12 @@
-import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
+import { mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import path from "node:path";
 
 import type { JsonValue } from "@dev.fast/json";
+import { STRUCTURAL_DIFF_WIRE_VERSION } from "@dev.fast/review-protocol";
 import { afterEach, expect, test, vi } from "vitest";
 
-import {
-  type StructuralDiffRequest,
-  diffrExecutable,
-  structuralDiff,
-} from "./structural-diff";
+import { type StructuralDiffRequest, structuralDiff } from "./structural-diff";
 
 const roots: string[] = [];
 
@@ -27,13 +24,14 @@ async function executable(script: string) {
   const file = path.join(root, "diffr");
   await writeFile(file, `#!${process.execPath}\n${script}`, { mode: 0o755 });
   vi.stubEnv("REVIEW_DIFFR_BINARY", file);
+  vi.stubEnv("XDG_CONFIG_HOME", path.join(root, "config"));
 
   return root;
 }
 
 const START = {
   type: "start",
-  version: 4,
+  version: STRUCTURAL_DIFF_WIRE_VERSION,
   lhs: { type: "revision", rev: "base" },
   rhs: { type: "revision", rev: "head" },
   files: [
@@ -96,7 +94,6 @@ test.each(["trees", "merge-base"] as const)(
       root,
       "--format",
       "ndjson",
-      "--stream-annotations",
       ...(kind === "trees" ? ["base", "head"] : ["base...head"]),
       "--",
       "space name.ts",
@@ -189,7 +186,7 @@ test("streams a large comparison without treating accumulated file bytes as one
       for (const { file } of files) await write({
         type: 'file', file,
         diff: {
-          type: 'text', rhs: { text: 'x'.repeat(1024 * 1024), regions: [] },
+          type: 'text', rhs: { text: 'x'.repeat(1024 * 1024), root: {kind:'leaf',id:1,fold_state_id:1,alignment_id:1,start:{line:0,column:0},end:{line:0,column:1024*1024}} },
           structural_changes: { base: [], head: [[0, 1]] },
           stats: { textual: { added: 1, removed: 0 }, visible: { added: 1, removed: 0 } },
         },
@@ -322,70 +319,6 @@ test("rendering and coverage share a stream; cancelling one reader preserves the
   }
 });
 
-test("annotation failure is data, preserves files, and explains exit 2", async () => {
-  const annotation = {
-    type: "annotations",
-    file: FILE,
-    annotations: [],
-    error: { code: "enrichment_failed", message: "offline" },
-  };
-
-  const root = await executable(
-    `${emit(START)} ${emit(BINARY)} ${emit(annotation)} ${emit(COMPLETE)} process.exitCode = 2;`,
-  );
-
-  expect(await collect(request(root))).toEqual([
-    START,
-    BINARY,
-    annotation,
-    COMPLETE,
-  ]);
-});
-
-test("coverage can detach after initial files while summaries continue for later readers", async () => {
-  const { StructuralComparisons } = await import("./structural-comparisons.js");
-
-  const annotation = {
-    type: "annotations",
-    file: FILE,
-    annotations: [{ region_id: 1, label: "summary" }],
-  };
-
-  const root = await executable(`
-    require('node:fs').appendFileSync('runs', 'x');
-    ${emit(START)} ${emit(BINARY)}
-    const timer = setInterval(() => { if(require('node:fs').existsSync('continue')) { clearInterval(timer); ${emit(annotation)} ${emit(COMPLETE)} } }, 10);
-  `);
-
-  const cache = new StructuralComparisons();
-
-  try {
-    for await (const event of cache.stream(request(root)))
-      if (event.type === "file") break;
-    await writeFile(path.join(root, "continue"), "");
-    const events = [];
-
-    for await (const event of cache.stream(request(root))) events.push(event);
-    expect(events).toEqual([START, BINARY, annotation, COMPLETE]);
-    expect(await readFile(path.join(root, "runs"), "utf8")).toBe("x");
-  } finally {
-    cache.close();
-  }
-});
-
-test("uses the bundled binary only when present and no override is set", async () => {
-  const root = await mkdtemp(path.join(tmpdir(), "review-bundled-diffr-"));
-  roots.push(root);
-  vi.stubEnv("REVIEW_DIFFR_BINARY", "");
-  expect(diffrExecutable(root)).toBe("diffr");
-  await mkdir(path.join(root, "bin"));
-  const binary = path.join(root, "bin", "diffr");
-  await writeFile(binary, "#!/bin/sh\n", { mode: 0o755 });
-  expect(diffrExecutable(root)).toBe(binary);
-  vi.stubEnv("REVIEW_DIFFR_BINARY", "/elsewhere/diffr");
-  expect(diffrExecutable(root)).toBe("/elsewhere/diffr");
-});
-
 test("keeps the ten most recently read idle comparisons", async () => {
   const { StructuralComparisons } = await import("./structural-comparisons.js");
 
diff --git a/packages/review/src/server/structural-diff.ts b/packages/review/src/server/structural-diff.ts
index 586d55225..e787323f1 100644
--- a/packages/review/src/server/structural-diff.ts
+++ b/packages/review/src/server/structural-diff.ts
@@ -1,17 +1,13 @@
 import { spawn } from "node:child_process";
-import { existsSync } from "node:fs";
-import path from "node:path";
 import { createInterface } from "node:readline";
 
+import { diffrBinaryPath } from "@dev.fast/diffr";
 import {
   STRUCTURAL_DIFF_WIRE_VERSION,
   type StructuralDiffEvent,
   type StructuralProblem,
   decodeStructuralDiffEvent,
 } from "@dev.fast/review-protocol";
-import { findReviewPackageRoot } from "@review/package-paths";
-
-import { installedFullDiffr } from "./diffr-languages.js";
 
 export type DiffComparison =
   | { kind: "trees"; base: string; head: string }
@@ -26,27 +22,13 @@ export interface StructuralDiffRequest {
   signal: AbortSignal;
 }
 
-export function diffrExecutable(
-  packageRoot = findReviewPackageRoot(import.meta.url),
-): string {
-  if (process.env.REVIEW_DIFFR_BINARY) return process.env.REVIEW_DIFFR_BINARY;
-
-  const full = installedFullDiffr(packageRoot);
-
-  if (full) return full;
-
-  const bundled = path.join(
-    packageRoot,
-    "bin",
-    process.platform === "win32" ? "diffr.exe" : "diffr",
-  );
-
-  return existsSync(bundled) ? bundled : "diffr";
+export function diffrExecutable(): string {
+  return process.env.REVIEW_DIFFR_BINARY || diffrBinaryPath() || "diffr";
 }
 
 export function diffrMissingError(): Error {
   return new Error(
-    `Cannot find diffr at ${diffrExecutable()}. Whiteboard Desktop bundles it at bin/diffr under its runtime; in a checkout, run \`pnpm --filter @dev.fast/whiteboard ensure:diffr\` or install diffr on PATH, or set REVIEW_DIFFR_BINARY to its executable.`,
+    `Cannot find diffr at ${diffrExecutable()}. Install diffr on PATH, or set REVIEW_DIFFR_BINARY to its executable.`,
   );
 }
 
@@ -61,13 +43,7 @@ export async function* structuralDiff(
   input.signal.throwIfAborted();
   const comparison = input.comparison;
 
-  const args = [
-    "--repo",
-    input.repositoryPath,
-    "--format",
-    "ndjson",
-    "--stream-annotations",
-  ];
+  const args = ["--repo", input.repositoryPath, "--format", "ndjson"];
 
   switch (comparison.kind) {
     case "worktree":
@@ -120,7 +96,6 @@ export async function* structuralDiff(
   let completed = false;
   let aborted: StructuralProblem | undefined;
   let failed = 0;
-  let annotationFailed = false;
   const lines = createInterface({ input: child.stdout, crlfDelay: Infinity });
 
   try {
@@ -152,8 +127,6 @@ export async function* structuralDiff(
 
         failed = event.failed;
         aborted = event.aborted;
-      } else if (event.type === "annotations") {
-        annotationFailed ||= event.error !== undefined;
       } else if (event.type !== "file") {
         throw new Error(`Unexpected diffr event: ${event.type}`);
       }
@@ -168,13 +141,10 @@ export async function* structuralDiff(
       throw new Error("diffr stream ended before completion.");
     }
 
-    // diffr exits 2 for file or enrichment failures already reported by the stream.
+    // diffr exits 2 for file failures already reported by the stream.
     const code = await exited;
 
-    if (
-      code !== 0 &&
-      !(code === 2 && (failed > 0 || annotationFailed || aborted !== undefined))
-    )
+    if (code !== 0 && !(code === 2 && (failed > 0 || aborted !== undefined)))
       throw exitError(code);
   } finally {
     clearTimeout(idle);
diff --git a/packages/review/src/server/test-fixtures/diffr-ui-overrides.toml b/packages/review/src/server/test-fixtures/diffr-ui-overrides.toml
new file mode 100644
index 000000000..ee58a441a
--- /dev/null
+++ b/packages/review/src/server/test-fixtures/diffr-ui-overrides.toml
@@ -0,0 +1,38 @@
+# Overrides saved by Whiteboard 0.1.10. Migration must retain these comments.
+version = 1
+
+[plugins.bundled.context]
+enabled = false # Collapse unchanged lines
+lines = 17 # Context lines
+
+[plugins.bundled.test-bodies]
+enabled = false # Collapse test bodies
+
+[plugins.bundled.deleted-bodies]
+enabled = false # Collapse deleted function bodies
+
+[plugins.bundled.removed-runs]
+enabled = false # Collapse long removed stretches
+
+[plugins.bundled.group]
+enabled = false # Group adjacent folds; retired
+
+[plugins.bundled.hide-files]
+enabled = true # Hide files by tag
+tags = ["test", "generated"]
+deleted = false # Hide deleted files
+
+[plugins.bundled.summarize]
+enabled = true # Enable summaries
+provider = "openai" # Provider
+api_key = "synthetic-key" # API key
+model = "custom-model" # Model
+endpoint = "http://127.0.0.1:9/v1" # Endpoint URL
+system_prompt = '''  Use my exact custom instructions.
+Keep # inside the prompt, and answer with JSON if I ask for it.
+''' # Prompt
+tests = false # Include tests
+max_concurrency = 2 # Old ignored option
+
+[diff]
+byte_limit = 123456 # Unrelated file-only override
diff --git a/packages/review/src/server/toml-edits.ts b/packages/review/src/server/toml-edits.ts
new file mode 100644
index 000000000..c5012f8de
--- /dev/null
+++ b/packages/review/src/server/toml-edits.ts
@@ -0,0 +1,266 @@
+import { type AST, getStaticTOMLValue, parseTOML } from "toml-eslint-parser";
+
+export function tomlKey(...parts: string[]): string {
+  return parts
+    .map((part) =>
+      /^[A-Za-z0-9_-]+$/.test(part) ? part : JSON.stringify(part),
+    )
+    .join(".");
+}
+
+export function tomlKeyParts(key: string): string[] {
+  const node = parseTOML(`${key} = 0`, { tomlVersion: "1.0" }).body[0].body[0];
+
+  if (node.type !== "TOMLKeyValue")
+    throw new Error("Expected a TOML config key.");
+
+  return getStaticTOMLValue(node.key);
+}
+
+/** Small source edits through TOML's AST; do not serialize unrelated user values. */
+export class TomlEdits {
+  constructor(public source: string) {}
+
+  private index() {
+    const ast = parseTOML(this.source, { tomlVersion: "1.0" });
+    const fields = new Map<string, AST.TOMLKeyValue>();
+    const tables = new Map<string, AST.TOMLTable>();
+
+    const field = (node: AST.TOMLKeyValue, prefix: string[]) => {
+      const key = [...prefix, ...getStaticTOMLValue(node.key)];
+      fields.set(tomlKey(...key), node);
+
+      if (node.value.type === "TOMLInlineTable")
+        for (const child of node.value.body) field(child, key);
+    };
+
+    for (const node of ast.body[0].body) {
+      if (node.type === "TOMLKeyValue") field(node, []);
+      else {
+        const key = node.resolvedKey.map(String);
+        tables.set(tomlKey(...key), node);
+
+        for (const child of node.body) field(child, key);
+      }
+    }
+
+    return { ast, fields, tables };
+  }
+
+  keys(): string[] {
+    return [...this.index().fields.keys()];
+  }
+
+  valueKeys(): string[] {
+    return [...this.index().fields].flatMap(([key, node]) =>
+      node.value.type === "TOMLInlineTable" ? [] : [key],
+    );
+  }
+
+  value(key: string) {
+    const node = this.index().fields.get(key);
+
+    return node && getStaticTOMLValue(node.value);
+  }
+
+  /** Retained settings must keep their exact saved value, including prompt spacing. */
+  assertUnchanged(
+    original: string,
+    keys: readonly (readonly [string, string])[],
+  ): void {
+    const before = new TomlEdits(original).index().fields;
+    const after = this.index().fields;
+
+    for (const [from, to] of keys) {
+      const previous = before.get(from);
+      const current = after.get(to);
+      const previousText = previous && original.slice(...previous.value.range);
+      const currentText = current && this.source.slice(...current.value.range);
+
+      if (previousText !== currentText)
+        throw new Error(`diffr migration changed a retained setting: ${from}`);
+    }
+  }
+
+  /** Move a config subtree without serializing any of its saved values. */
+  move(from: string, to: string): void {
+    const { fields, tables } = this.index();
+    const matches = (key: string) => key === from || key.startsWith(`${from}.`);
+
+    if (
+      [...fields.keys(), ...tables.keys()].some(
+        (key) => key === to || key.startsWith(`${to}.`),
+      )
+    )
+      throw new Error(`diffr migration has conflicting config entries: ${to}`);
+
+    const direct = fields.get(from);
+
+    if (direct) {
+      const literal = this.source.slice(...direct.value.range);
+      this.remove(from, false);
+      this.setLiteral(to, literal);
+
+      return;
+    }
+
+    const moves: { start: number; end: number; text: string }[] = [];
+    const movedTables = [...tables].filter(([key]) => matches(key));
+
+    for (const [key, table] of movedTables)
+      moves.push({
+        start: table.key.range[0],
+        end: table.key.range[1],
+        text: `${to}${key.slice(from.length)}`,
+      });
+
+    const dotted: [string, string][] = [];
+
+    for (const [key, field] of fields) {
+      if (!matches(key) || field.parent.type === "TOMLInlineTable") continue;
+
+      // Fields in a moved table keep their original spelling and comments.
+      if (
+        field.parent.type === "TOMLTable" &&
+        movedTables.some(([, table]) => table === field.parent)
+      )
+        continue;
+      dotted.push([
+        `${to}${key.slice(from.length)}`,
+        this.source.slice(...field.value.range),
+      ]);
+      moves.push({ start: field.range[0], end: field.range[1], text: "" });
+    }
+
+    for (const edit of moves.sort((a, b) => b.start - a.start))
+      this.replace(edit.start, edit.end, edit.text);
+
+    for (const [key, literal] of dotted) this.setLiteral(key, literal);
+  }
+
+  remove(key: string, retainComments = true): void {
+    while (true) {
+      const { ast, fields, tables } = this.index();
+
+      const matches = (name: string) =>
+        name === key || name.startsWith(`${key}.`);
+
+      const node =
+        fields.get(key) ??
+        [...tables].find(([name]) => matches(name))?.[1] ??
+        [...fields].find(([name]) => matches(name))?.[1];
+
+      if (!node) return;
+      let [start, end] = node.range;
+
+      if (
+        node.type === "TOMLKeyValue" &&
+        node.parent.type === "TOMLInlineTable"
+      ) {
+        const siblings = node.parent.body;
+        const position = siblings.indexOf(node);
+        const next = siblings[position + 1];
+        const previous = siblings[position - 1];
+
+        if (next) {
+          const comma = ast.tokens.find(
+            (token) =>
+              token.value === "," &&
+              token.range[0] >= end &&
+              token.range[0] < next.range[0],
+          );
+
+          if (comma) end = comma.range[1];
+        } else if (previous) {
+          const comma = ast.tokens.find(
+            (token) =>
+              token.value === "," &&
+              token.range[0] >= previous.range[1] &&
+              token.range[0] < start,
+          );
+
+          if (comma) start = comma.range[0];
+        }
+      }
+
+      const comments = retainComments
+        ? ast.comments
+            .filter(
+              (comment) => comment.range[0] >= start && comment.range[1] <= end,
+            )
+            .map((comment) => this.source.slice(...comment.range))
+            .join("\n")
+        : "";
+
+      this.replace(start, end, comments);
+    }
+  }
+
+  set(key: string, value: boolean | number | string | string[]): void {
+    this.setLiteral(key, JSON.stringify(value), Array.isArray(value));
+  }
+
+  private setLiteral(key: string, input: string, retainComments = false): void {
+    const { ast, fields, tables } = this.index();
+    let literal = input;
+    const existing = fields.get(key);
+
+    if (existing) {
+      // Keep notes between entries when a plugin order is rewritten.
+      if (retainComments) {
+        const comments = ast.comments
+          .filter(
+            (comment) =>
+              comment.range[0] >= existing.value.range[0] &&
+              comment.range[1] <= existing.value.range[1],
+          )
+          .map((comment) => this.source.slice(...comment.range));
+
+        if (comments.length)
+          literal = `[\n${comments.join("\n")}\n${literal.slice(1)}`;
+      }
+
+      this.replace(...existing.value.range, literal);
+
+      return;
+    }
+
+    const parts = tomlKeyParts(key);
+
+    for (let length = parts.length - 1; length > 0; length--) {
+      const parent = tomlKey(...parts.slice(0, length));
+      const suffix = tomlKey(...parts.slice(length));
+      const inline = fields.get(parent)?.value;
+
+      if (inline?.type === "TOMLInlineTable") {
+        this.replace(
+          inline.range[1] - 1,
+          inline.range[1] - 1,
+          `${inline.body.length ? ", " : ""}${suffix} = ${literal}`,
+        );
+
+        return;
+      }
+
+      const table = tables.get(parent);
+
+      if (table) {
+        const newline = this.source.indexOf("\n", table.key.range[1]);
+        const at = newline < 0 ? this.source.length : newline + 1;
+        this.replace(
+          at,
+          at,
+          `${newline < 0 ? "\n" : ""}${suffix} = ${literal}\n`,
+        );
+
+        return;
+      }
+    }
+
+    this.source = `${key} = ${literal}\n${this.source}`;
+  }
+
+  private replace(start: number, end: number, text: string): void {
+    this.source = this.source.slice(0, start) + text + this.source.slice(end);
+  }
+}
diff --git a/packages/review/vitest.config.ts b/packages/review/vitest.config.ts
index 2ea18dcf4..a34e006d4 100644
--- a/packages/review/vitest.config.ts
+++ b/packages/review/vitest.config.ts
@@ -12,6 +12,10 @@ export default defineConfig({
         os.tmpdir(),
         `progressive-review-tests-${process.pid}`,
       ),
+      XDG_CONFIG_HOME: path.join(
+        os.tmpdir(),
+        `progressive-review-config-tests-${process.pid}`,
+      ),
       // GitHub Actions exports the repository slug, which the trace code
       // honors over a checkout's remote; scratch repositories in tests must
       // resolve to their own remotes.
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index dbf356132..6e3d187b7 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -6,6 +6,12 @@ settings:
 
 catalogs:
   default:
+    '@dev.fast/diffr':
+      specifier: 0.1.13
+      version: 0.1.13
+    toml-eslint-parser:
+      specifier: ^1.0.3
+      version: 1.0.3
     zod:
       specifier: 4.6.5
       version: 4.6.5
@@ -51,8 +57,8 @@ importers:
         version: link:../../packages/review
     devDependencies:
       '@dev.fast/diffr':
-        specifier: 0.1.10
-        version: 0.1.10(zod@4.6.5)
+        specifier: 'catalog:'
+        version: 0.1.13(zod@4.6.5)
       '@dev.fast/review-canvas':
         specifier: workspace:*
         version: link:../../packages/review/app
@@ -119,6 +125,9 @@ importers:
       '@agentclientprotocol/sdk':
         specifier: 1.5.1
         version: 1.5.1(zod@4.6.5)
+      '@dev.fast/diffr':
+        specifier: 'catalog:'
+        version: 0.1.13(zod@4.6.5)
       '@hono/node-server':
         specifier: 2.0.12
         version: 2.0.12(hono@4.13.5)
@@ -164,13 +173,13 @@ importers:
       smol-toml:
         specifier: 1.8.0
         version: 1.8.0
+      toml-eslint-parser:
+        specifier: 'catalog:'
+        version: 1.0.3
       zod:
         specifier: 'catalog:'
         version: 4.6.5
     devDependencies:
-      '@dev.fast/diffr':
-        specifier: 0.1.10
-        version: 0.1.10(zod@4.6.5)
       '@dev.fast/json':
         specifier: workspace:*
         version: link:../json
@@ -217,8 +226,8 @@ importers:
   packages/review-protocol:
     dependencies:
       '@dev.fast/diffr':
-        specifier: 0.1.10
-        version: 0.1.10(zod@4.6.5)
+        specifier: 'catalog:'
+        version: 0.1.13(zod@4.6.5)
       '@dev.fast/json':
         specifier: workspace:*
         version: link:../json
@@ -554,10 +563,36 @@ packages:
     resolution: {integrity: sha512-QxULHAm7cNu72w97JUNCBFODFaXpbDg+dP8b/oWFAZ2MTRppA3U00Y2L1HqaS4J6yBqxwa/Y3nMBaxVKbB/NsA==}
     engines: {node: '>=20.19.0'}
 
-  '@dev.fast/diffr@0.1.10':
-    resolution: {integrity: sha512-C5bU+lmZ5LRWt3HsgW37lp4cXU+7RVERGmD+50Rwf9+Vi368fYfiP9Brx1o8O13TQui5uTp6fsP8FrpgpOQ/Vw==}
+  '@dev.fast/diffr-darwin-arm64@0.1.13':
+    resolution: {integrity: sha512-xTXaa4PHjgbFgSuW+Ery5lvsNwIG9HbliqnmaUxrG4U9yxPtDSsi7hPpJnYfEB+0XO43s090ihiNtzLGfC3BNQ==}
+    cpu: [arm64]
+    os: [darwin]
+
+  '@dev.fast/diffr-darwin-x64@0.1.13':
+    resolution: {integrity: sha512-XgZ22QRmK8vfRZHsHs9s0wZDkzS4IL1rQaVAizjuIGG+AubYkabqRzFqy/JE2M+MpXSS+fbw1W8r9e/9TulOnA==}
+    cpu: [x64]
+    os: [darwin]
+
+  '@dev.fast/diffr-linux-arm64@0.1.13':
+    resolution: {integrity: sha512-tmTQLx9j3JW9mYh5YJ/JJES03c8j/BNJ5PnvEwSsd9FfS7K7+pHD+Lfk2jtzvaROzF2MZCEDI57TDq3b5zhvaQ==}
+    cpu: [arm64]
+    os: [linux]
+    libc: [glibc]
+
+  '@dev.fast/diffr-linux-x64@0.1.13':
+    resolution: {integrity: sha512-xD60m46hDobsG+kJx3kulI/NEpGWw7B1OB4h9tAItjwOrPsh9mMcXlQfJYPGtlZha6CfE1+Ympc7Lexr/QTqfw==}
+    cpu: [x64]
+    os: [linux]
+    libc: [glibc]
+
+  '@dev.fast/diffr-win32-x64@0.1.13':
+    resolution: {integrity: sha512-c9oaND+TyqrFVccOAmoWfg/25+pDKBnYNzoi4t5pdStKSFjcNSYgltoGIoS+GV1aFNdXOo/6qk3wdDDqKccR/g==}
+    cpu: [x64]
+    os: [win32]
+
+  '@dev.fast/diffr@0.1.13':
+    resolution: {integrity: sha512-0awUVjvSWRv1oQu3prCrKvqPBH64Eqk+AtqUT67a3AxcKdvm4CrGeF+cPVy9D0PVhbXePPeqV0spjCwKShO0gw==}
     engines: {node: '>=20'}
-    hasBin: true
     peerDependencies:
       zod: ^4.0.0
 
@@ -2021,6 +2056,10 @@ packages:
     resolution: {integrity: sha512-/veY75JbMK4j1yjvuUxuVsiS/hr/4iHs9FTT6cgTexxdE0Ly/glccBAkloH/DofkjRbZU3bnoj38mOmhkZ0lHw==}
     engines: {node: '>=12'}
 
+  eslint-visitor-keys@5.0.1:
+    resolution: {integrity: sha512-tD40eHxA35h0PEIZNeIjkHoDR4YjjJp34biM0mDvplBe//mB+IHCqHDGV7pxF+7MklTvighcCPPZC7ynWyjdTA==}
+    engines: {node: ^20.19.0 || ^22.13.0 || >=24}
+
   estree-walker@3.0.3:
     resolution: {integrity: sha512-7RUKfXgSMMkzt6ZuXmqapOurLGPPfgj6l9uRZ7lRGolvk0y2yocc35LdcxKC5PQZdn2DMqioAQ2NoWcrTKmm6g==}
 
@@ -2894,6 +2933,10 @@ packages:
     resolution: {integrity: sha512-o5sSPKEkg/DIQNmH43V0/uerLrpzVedkUh8tGNvaeXpfpuwjKenlSox/2O/BTlZUtEe+JG7s5YhEz608PlAHRA==}
     engines: {node: '>=0.6'}
 
+  toml-eslint-parser@1.0.3:
+    resolution: {integrity: sha512-A5F0cM6+mDleacLIEUkmfpkBbnHJFV1d2rprHU2MXNk7mlxHq2zGojA+SRvQD1RoMo9gqjZPWEaKG4v1BQ48lw==}
+    engines: {node: ^20.19.0 || ^22.13.0 || >=24}
+
   totalist@3.0.1:
     resolution: {integrity: sha512-sf4i37nQ2LBx4m3wB74y+ubopq6W/dIzXg0FDGjsYnZHVa1Da8FH853wlL2gtUhg+xJXjfk3kUZS3BRoQeoQBQ==}
     engines: {node: '>=6'}
@@ -3426,9 +3469,30 @@ snapshots:
 
   '@csstools/css-tokenizer@4.0.0': {}
 
-  '@dev.fast/diffr@0.1.10(zod@4.6.5)':
+  '@dev.fast/diffr-darwin-arm64@0.1.13':
+    optional: true
+
+  '@dev.fast/diffr-darwin-x64@0.1.13':
+    optional: true
+
+  '@dev.fast/diffr-linux-arm64@0.1.13':
+    optional: true
+
+  '@dev.fast/diffr-linux-x64@0.1.13':
+    optional: true
+
+  '@dev.fast/diffr-win32-x64@0.1.13':
+    optional: true
+
+  '@dev.fast/diffr@0.1.13(zod@4.6.5)':
     dependencies:
       zod: 4.6.5
+    optionalDependencies:
+      '@dev.fast/diffr-darwin-arm64': 0.1.13
+      '@dev.fast/diffr-darwin-x64': 0.1.13
+      '@dev.fast/diffr-linux-arm64': 0.1.13
+      '@dev.fast/diffr-linux-x64': 0.1.13
+      '@dev.fast/diffr-win32-x64': 0.1.13
 
   '@dual-bundle/import-meta-resolve@4.2.1': {}
 
@@ -4478,6 +4542,8 @@ snapshots:
 
   escape-string-regexp@5.0.0: {}
 
+  eslint-visitor-keys@5.0.1: {}
+
   estree-walker@3.0.3:
     dependencies:
       '@types/estree': 1.0.8
@@ -5572,6 +5638,10 @@ snapshots:
 
   toidentifier@1.0.1: {}
 
+  toml-eslint-parser@1.0.3:
+    dependencies:
+      eslint-visitor-keys: 5.0.1
+
   totalist@3.0.1: {}
 
   tough-cookie@6.0.2:
diff --git a/pnpm-workspace.yaml b/pnpm-workspace.yaml
index ed99b113c..4d86bd16b 100644
--- a/pnpm-workspace.yaml
+++ b/pnpm-workspace.yaml
@@ -5,6 +5,8 @@ packages:
   - "apps/*"
 
 catalog:
+  '@dev.fast/diffr': 0.1.13
+  toml-eslint-parser: ^1.0.3
   zod: "4.6.5"
 
 catalogMode: strict
@@ -17,7 +19,12 @@ verifyDepsBeforeRun: false
 minimumReleaseAge: 10080
 minimumReleaseAgeStrict: true
 minimumReleaseAgeExclude:
-  - "@dev.fast/diffr@0.1.10"
+  - "@dev.fast/diffr@0.1.13"
+  - "@dev.fast/diffr-darwin-arm64@0.1.13"
+  - "@dev.fast/diffr-darwin-x64@0.1.13"
+  - "@dev.fast/diffr-linux-arm64@0.1.13"
+  - "@dev.fast/diffr-linux-x64@0.1.13"
+  - "@dev.fast/diffr-win32-x64@0.1.13"
   # Ask tracks the latest ACP SDK and adapters, and the CLI packages they pin.
   - "@agentclientprotocol/sdk@1.5.1"
   - "@agentclientprotocol/claude-agent-acp@0.84.0"