--- before
+++ after
@@ -1,2048 +0,0 @@
-import { runInNewContext } from "node:vm";
-
-import { McpUiInitializeResultSchema } from "@modelcontextprotocol/ext-apps";
-import { describe, expect, it, vi } from "vitest";
-
-import {
-  createHostScientificSequenceDataClient,
-  MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-  MAX_SEQUENCE_SOURCE_RANGE_BYTES,
-  refreshHostScientificSequenceDataClient,
-  ScientificSequenceDataClient,
-  type SequencePersistentDataSession,
-  type SequenceScientificDataTransport,
-} from "./scientific-data-client";
-
-const session: SequencePersistentDataSession = {
-  family: "sequence",
-  logicalSessionId: "logical-sequence-1",
-  backendInstanceId: "sequence-instance-1",
-  backendGeneration: 4,
-  sourceRevision: "source-revision-1",
-  canEditApprovedSource: true,
-};
-
-describe("host-mediated persistent Sequence data client", () => {
-  it("activates the live first-party host gateway without exposing a source grant", async () => {
-    const callServerTool = vi.fn(async () => ({
-      content: [],
-      structuredContent: {
-        cursor: "0",
-        nextCursor: null,
-        sourceRevision: session.sourceRevision,
-        complete: true,
-        records: [{ id: "source-record", description: "", sequenceLength: 4 }],
-      },
-    }));
-    const app = {
-      getHostCapabilities: () => ({
-        serverTools: {},
-        scientificViewers: {
-          protocolVersion: 1,
-          processIsolation: "family-process",
-          binaryTransfer: "bounded-process-ipc",
-          familyScopedChannels: true,
-          transportSupportsRangeReads: true,
-          attachment: {
-            family: "sequence",
-            logicalSessionId: session.logicalSessionId,
-            backendInstanceId: session.backendInstanceId,
-            backendGeneration: session.backendGeneration,
-            frameId: "sequence-frame-1",
-            channelId: "sequence-channel-1",
-            expiresAtMs: Date.now() + 60_000,
-          },
-          effectiveCapabilities: {
-            ...session,
-            canReadRanges: true,
-          },
-        },
-      }),
-      callServerTool,
-    };
-    const client = createHostScientificSequenceDataClient(app);
-    expect(client).not.toBeNull();
-    await expect(client?.listRecords({ limit: 1 })).resolves.toMatchObject({
-      records: [{ id: "source-record" }],
-    });
-    expect(callServerTool).toHaveBeenCalledWith(
-      {
-        name: "ui/scientific/sequence/records",
-        arguments: {
-          family: "sequence",
-          logicalSessionId: session.logicalSessionId,
-          backendInstanceId: session.backendInstanceId,
-          backendGeneration: session.backendGeneration,
-          sourceRevision: session.sourceRevision,
-          frameId: "sequence-frame-1",
-          channelId: "sequence-channel-1",
-          resourceUri: "ui://sequence-viewer/viewer",
-          cursor: "0",
-          limit: 1,
-        },
-      },
-      undefined,
-    );
-    expect(JSON.stringify(callServerTool.mock.calls)).not.toContain(
-      "sourceGrantId",
-    );
-  });
-
-  it("keeps its existing client and never replays a write when a restarted backend renews its channel", async () => {
-    const callServerTool = vi.fn(async ({ name }: { name: string }) => ({
-      content: [],
-      structuredContent:
-        name === "ui/scientific/sequence/checkpoint"
-          ? {
-              checkpointVersion: 1,
-              lastAcknowledgedRevision: 7,
-              logicalSessionId: session.logicalSessionId,
-              recoveryReference: "sequence-recovery-1",
-            }
-          : {
-              complete: true,
-              cursor: "0",
-              nextCursor: null,
-              records: [
-                { id: "source-record", description: "", sequenceLength: 4 },
-              ],
-              sourceRevision: session.sourceRevision,
-            },
-    }));
-    const initial = sequenceHostContext();
-    let hostContext = initial;
-    const app = {
-      callServerTool,
-      getHostCapabilities: () => ({}),
-      getHostContext: () => hostContext,
-    };
-    const client = createHostScientificSequenceDataClient(app);
-    if (client == null)
-      throw new Error("Expected an authenticated Sequence client.");
-    await client.checkpoint({
-      checkpoint: new Uint8Array([1]),
-      lastAcknowledgedRevision: 7,
-    });
-
-    hostContext = sequenceHostContext({
-      backendGeneration: session.backendGeneration + 1,
-      backendInstanceId: "restarted-sequence-instance",
-      channelId: "restarted-sequence-channel",
-    });
-    expect(
-      refreshHostScientificSequenceDataClient(app, client, hostContext),
-    ).toBe(true);
-    expect(callServerTool).toHaveBeenCalledTimes(1);
-    expect(client.session).toMatchObject({
-      backendGeneration: session.backendGeneration + 1,
-      backendInstanceId: "restarted-sequence-instance",
-      logicalSessionId: session.logicalSessionId,
-      sourceRevision: session.sourceRevision,
-    });
-
-    await client.listRecords({ limit: 1 });
-    expect(callServerTool).toHaveBeenCalledTimes(2);
-    expect(callServerTool).toHaveBeenLastCalledWith(
-      expect.objectContaining({
-        arguments: expect.objectContaining({
-          backendGeneration: session.backendGeneration + 1,
-          backendInstanceId: "restarted-sequence-instance",
-          channelId: "restarted-sequence-channel",
-          frameId: "sequence-frame-1",
-        }),
-        name: "ui/scientific/sequence/records",
-      }),
-      undefined,
-    );
-  });
-
-  it("renews an expired channel after more than five idle minutes without advancing generation", async () => {
-    let now = 1_800_000_000_000;
-    const clock = vi.spyOn(Date, "now").mockImplementation(() => now);
-    try {
-      let hostContext = sequenceHostContext({ expiresAtMs: now + 60_000 });
-      const callServerTool = vi.fn(async () => ({
-        content: [],
-        structuredContent: {
-          complete: true,
-          cursor: "0",
-          nextCursor: null,
-          records: [
-            { id: "source-record", description: "", sequenceLength: 4 },
-          ],
-          sourceRevision: session.sourceRevision,
-        },
-      }));
-      const app = {
-        callServerTool,
-        getHostCapabilities: () => ({}),
-        getHostContext: () => hostContext,
-      };
-      const client = createHostScientificSequenceDataClient(app);
-      if (client == null)
-        throw new Error("Expected an authenticated Sequence client.");
-
-      hostContext = sequenceHostContext({
-        channelId: "rotated-sequence-channel",
-        expiresAtMs: now + 60_000,
-      });
-      expect(
-        refreshHostScientificSequenceDataClient(app, client, hostContext),
-      ).toBe(true);
-
-      now += 6 * 60_000;
-      hostContext = sequenceHostContext({
-        channelId: "renewed-sequence-channel",
-        expiresAtMs: now + 60_000,
-      });
-      expect(
-        refreshHostScientificSequenceDataClient(app, client, hostContext),
-      ).toBe(true);
-      expect(client.session.backendGeneration).toBe(session.backendGeneration);
-      await client.listRecords({ limit: 1 });
-      expect(callServerTool).toHaveBeenCalledWith(
-        expect.objectContaining({
-          arguments: expect.objectContaining({
-            backendGeneration: session.backendGeneration,
-            channelId: "renewed-sequence-channel",
-          }),
-        }),
-        undefined,
-      );
-    } finally {
-      clock.mockRestore();
-    }
-  });
-
-  it("rejects stale, forged, expired, and widened renewed native authority", async () => {
-    const initial = sequenceHostContext({ expiresAtMs: Date.now() + 60_000 });
-    let hostContext = initial;
-    const callServerTool = vi.fn(async () => ({
-      content: [],
-      structuredContent: {
-        complete: true,
-        cursor: "0",
-        nextCursor: null,
-        records: [{ id: "source-record", description: "", sequenceLength: 4 }],
-        sourceRevision: session.sourceRevision,
-      },
-    }));
-    const app = {
-      callServerTool,
-      getHostCapabilities: () => ({}),
-      getHostContext: () => hostContext,
-    };
-    const client = createHostScientificSequenceDataClient(app);
-    if (client == null)
-      throw new Error("Expected an authenticated Sequence client.");
-
-    for (const overrides of [
-      { backendGeneration: session.backendGeneration - 1 },
-      { backendInstanceId: "substituted-instance" },
-      { logicalSessionId: "substituted-session" },
-      { sourceRevision: "substituted-source" },
-      { frameId: "substituted-frame" },
-      { expiresAtMs: Date.now() - 1 },
-      { canEditApprovedSource: false },
-    ]) {
-      hostContext = sequenceHostContext(overrides);
-      expect(
-        refreshHostScientificSequenceDataClient(app, client, hostContext),
-      ).toBe(false);
-      expect(client.session).toEqual(session);
-    }
-
-    await client.listRecords({ limit: 1 });
-    expect(callServerTool).toHaveBeenCalledWith(
-      expect.objectContaining({
-        arguments: expect.objectContaining({
-          backendGeneration: session.backendGeneration,
-          backendInstanceId: session.backendInstanceId,
-          channelId: "sequence-channel-1",
-          frameId: "sequence-frame-1",
-        }),
-      }),
-      undefined,
-    );
-  });
-
-  it("recovers native authority from host context after the real SDK strips scientific capabilities", async () => {
-    const scientificViewers = {
-      protocolVersion: 1,
-      processIsolation: "family-process",
-      binaryTransfer: "bounded-process-ipc",
-      familyScopedChannels: true,
-      transportSupportsRangeReads: true,
-      attachment: {
-        family: "sequence",
-        logicalSessionId: session.logicalSessionId,
-        backendInstanceId: session.backendInstanceId,
-        backendGeneration: session.backendGeneration,
-        frameId: "sdk-sequence-frame",
-        channelId: "sdk-sequence-channel",
-        expiresAtMs: Date.now() + 60_000,
-      },
-      effectiveCapabilities: {
-        ...session,
-        canReadRanges: true,
-      },
-    };
-    const initialized = McpUiInitializeResultSchema.parse({
-      protocolVersion: "2026-01-26",
-      hostInfo: { name: "Installed Sequence host", version: "1.0.0" },
-      hostCapabilities: { serverTools: {}, scientificViewers },
-      hostContext: {
-        availableDisplayModes: ["inline"],
-        displayMode: "inline",
-        scientificViewers,
-      },
-    });
-    expect(
-      Object.hasOwn(initialized.hostCapabilities, "scientificViewers"),
-    ).toBe(false);
-    expect(Object.hasOwn(initialized.hostContext, "scientificViewers")).toBe(
-      true,
-    );
-
-    const callServerTool = vi.fn(async () => ({
-      content: [],
-      structuredContent: {
-        complete: true,
-        cursor: "0",
-        nextCursor: null,
-        records: [{ id: "source-record", description: "", sequenceLength: 4 }],
-        sourceRevision: session.sourceRevision,
-      },
-    }));
-    const client = createHostScientificSequenceDataClient({
-      getHostCapabilities: () => initialized.hostCapabilities,
-      getHostContext: () => initialized.hostContext,
-      callServerTool,
-    });
-
-    expect(client?.session).toMatchObject({
-      ...session,
-      canEditApprovedSource: true,
-    });
-    await expect(client?.listRecords({ limit: 1 })).resolves.toMatchObject({
-      records: [{ id: "source-record" }],
-    });
-    expect(callServerTool).toHaveBeenCalledWith(
-      expect.objectContaining({
-        arguments: expect.objectContaining({
-          frameId: "sdk-sequence-frame",
-          channelId: "sdk-sequence-channel",
-          resourceUri: "ui://sequence-viewer/viewer",
-        }),
-        name: "ui/scientific/sequence/records",
-      }),
-      undefined,
-    );
-  });
-
-  it("rejects a malformed host-context capability without falling back to a substituted host", () => {
-    const scientificViewers = {
-      protocolVersion: 1,
-      processIsolation: "family-process",
-      binaryTransfer: "bounded-process-ipc",
-      familyScopedChannels: true,
-      transportSupportsRangeReads: true,
-      attachment: {
-        family: "sequence",
-        logicalSessionId: session.logicalSessionId,
-        backendInstanceId: session.backendInstanceId,
-        backendGeneration: session.backendGeneration,
-        frameId: "sequence-frame-1",
-        channelId: "sequence-channel-1",
-        expiresAtMs: Date.now() + 60_000,
-      },
-      effectiveCapabilities: {
-        ...session,
-        canReadRanges: true,
-      },
-    };
-    const callServerTool = vi.fn();
-    const client = createHostScientificSequenceDataClient({
-      getHostCapabilities: () => ({ serverTools: {}, scientificViewers }),
-      getHostContext: () => ({
-        scientificViewers: {
-          ...scientificViewers,
-          attachment: {
-            ...scientificViewers.attachment,
-            logicalSessionId: "substituted-sequence-session",
-          },
-        },
-      }),
-      callServerTool,
-    });
-
-    expect(client).toBeNull();
-    expect(callServerTool).not.toHaveBeenCalled();
-  });
-
-  it("keeps range reads available but refuses source writes without the explicit host capability", async () => {
-    const callServerTool = vi.fn(async () => ({
-      content: [],
-      structuredContent: {
-        cursor: "0",
-        nextCursor: null,
-        sourceRevision: session.sourceRevision,
-        complete: true,
-        records: [{ id: "source-record", description: "", sequenceLength: 4 }],
-      },
-    }));
-    for (const canEditApprovedSource of [undefined, false]) {
-      callServerTool.mockClear();
-      const app = {
-        getHostCapabilities: () => ({
-          serverTools: {},
-          scientificViewers: {
-            protocolVersion: 1,
-            processIsolation: "family-process",
-            binaryTransfer: "bounded-process-ipc",
-            familyScopedChannels: true,
-            transportSupportsRangeReads: true,
-            attachment: {
-              family: "sequence",
-              logicalSessionId: session.logicalSessionId,
-              backendInstanceId: session.backendInstanceId,
-              backendGeneration: session.backendGeneration,
-              frameId: "sequence-frame-1",
-              channelId: "sequence-channel-1",
-              expiresAtMs: Date.now() + 60_000,
-            },
-            effectiveCapabilities: {
-              family: session.family,
-              logicalSessionId: session.logicalSessionId,
-              backendInstanceId: session.backendInstanceId,
-              backendGeneration: session.backendGeneration,
-              sourceRevision: session.sourceRevision,
-              canReadRanges: true,
-              ...(canEditApprovedSource == null
-                ? {}
-                : { canEditApprovedSource }),
-            },
-          },
-        }),
-        callServerTool,
-      };
-      const client = createHostScientificSequenceDataClient(app);
-      expect(client?.session.canEditApprovedSource).toBe(false);
-      await expect(client?.listRecords({ limit: 1 })).resolves.toMatchObject({
-        records: [{ id: "source-record" }],
-      });
-      await expect(
-        client?.beginSourceEdit({
-          approvedOperation: "replace-source",
-          expectedSourceRevision: session.sourceRevision,
-        }),
-      ).rejects.toThrow(/authorized/u);
-      expect(callServerTool).toHaveBeenCalledTimes(1);
-      expect(callServerTool).toHaveBeenCalledWith(
-        expect.objectContaining({
-          name: "ui/scientific/sequence/records",
-        }),
-        undefined,
-      );
-    }
-  });
-
-  it("never dispatches any source-edit operation from an unapproved native session", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient(
-      { request },
-      { ...session, canEditApprovedSource: false },
-    );
-
-    await expect(
-      client.beginSourceEdit({
-        approvedOperation: "replace-source",
-        expectedSourceRevision: session.sourceRevision,
-      }),
-    ).rejects.toThrow(/authorized/u);
-    await expect(
-      client.appendSourceEdit({
-        editId: "source-edit-1",
-        offsetDecimal: "0",
-        bytes: new Uint8Array([65]),
-      }),
-    ).rejects.toThrow(/safe|authorized/u);
-    await expect(
-      client.commitSourceEdit({ editId: "source-edit-1" }),
-    ).rejects.toThrow(/authorized/u);
-    await expect(
-      client.abortSourceEdit({ editId: "source-edit-1" }),
-    ).rejects.toThrow(/authorized/u);
-    await expect(
-      client.resumeSourceEdit({ editId: "source-edit-1" }),
-    ).rejects.toThrow(/authorized/u);
-    expect(request).not.toHaveBeenCalled();
-  });
-
-  it("reads authenticated original source windows at exact offsets beyond four GiB", async () => {
-    const bytes = new Uint8Array([65, 67, 71, 84]);
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValue({ structuredContent: { bytes, eof: false } });
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.readOriginalSourceRange({
-        length: MAX_SEQUENCE_SOURCE_RANGE_BYTES,
-        offsetDecimal: "4294967317",
-      }),
-    ).resolves.toEqual({ bytes, eof: false });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/read-range",
-        payload: {
-          length: MAX_SEQUENCE_SOURCE_RANGE_BYTES,
-          offsetDecimal: "4294967317",
-        },
-        sourceRevision: session.sourceRevision,
-      }),
-    );
-  });
-
-  it("rejects unsafe raw-source ranges before dispatching authenticated filesystem access", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient({ request }, session);
-    for (const invalid of [
-      { length: 0, offsetDecimal: "0" },
-      { length: -1, offsetDecimal: "0" },
-      { length: MAX_SEQUENCE_SOURCE_RANGE_BYTES + 1, offsetDecimal: "0" },
-      { length: 1.5, offsetDecimal: "0" },
-      { length: 1, offsetDecimal: "-1" },
-      { length: 1, offsetDecimal: "01" },
-      { length: 1, offsetDecimal: "1e8" },
-    ]) {
-      await expect(client.readOriginalSourceRange(invalid)).rejects.toThrow(
-        /safe/iu,
-      );
-    }
-    expect(request).not.toHaveBeenCalled();
-  });
-
-  it("rejects forged, stalled, or oversized source range results and propagates authorization refusal", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient({ request }, session);
-    for (const structuredContent of [
-      { bytes: new Uint8Array(5), eof: false },
-      { bytes: new Uint8Array(), eof: false },
-      { bytes: [1, 2], eof: true },
-      { bytes: new Uint8Array([1]), eof: "true" },
-    ]) {
-      request.mockResolvedValueOnce({ structuredContent });
-      await expect(
-        client.readOriginalSourceRange({ length: 4, offsetDecimal: "0" }),
-      ).rejects.toThrow();
-    }
-    request.mockRejectedValueOnce(
-      new Error("PERMISSION_DENIED: source grant revoked"),
-    );
-    await expect(
-      client.readOriginalSourceRange({ length: 4, offsetDecimal: "0" }),
-    ).rejects.toThrow(/permission.denied|revoked/iu);
-  });
-
-  it("refuses an expired or differently bound first-party host attachment", () => {
-    const callServerTool = vi.fn();
-    for (const overrides of [
-      { expiresAtMs: Date.now() - 1 },
-      { logicalSessionId: "another-sequence-session" },
-      { family: "structure" },
-    ]) {
-      const app = {
-        getHostCapabilities: () => ({
-          serverTools: {},
-          scientificViewers: {
-            protocolVersion: 1,
-            processIsolation: "family-process",
-            binaryTransfer: "bounded-process-ipc",
-            familyScopedChannels: true,
-            transportSupportsRangeReads: true,
-            attachment: {
-              ...session,
-              frameId: "sequence-frame-1",
-              channelId: "sequence-channel-1",
-              expiresAtMs: Date.now() + 60_000,
-              ...overrides,
-            },
-            effectiveCapabilities: { ...session, canReadRanges: true },
-          },
-        }),
-        callServerTool,
-      };
-      expect(createHostScientificSequenceDataClient(app)).toBeNull();
-    }
-    expect(callServerTool).not.toHaveBeenCalled();
-  });
-
-  it("rejects unauthenticated loopback and unknown scientific transports", () => {
-    const callServerTool = vi.fn();
-    for (const binaryTransfer of [
-      "host-private-loopback",
-      "http://127.0.0.1",
-      "localhost",
-      undefined,
-    ]) {
-      const app = {
-        getHostCapabilities: () => ({
-          serverTools: {},
-          scientificViewers: {
-            protocolVersion: 1,
-            processIsolation: "family-process",
-            binaryTransfer,
-            familyScopedChannels: true,
-            transportSupportsRangeReads: true,
-            attachment: {
-              ...session,
-              frameId: "sequence-frame-1",
-              channelId: "sequence-channel-1",
-              expiresAtMs: Date.now() + 60_000,
-            },
-            effectiveCapabilities: { ...session, canReadRanges: true },
-          },
-        }),
-        callServerTool,
-      };
-      expect(createHostScientificSequenceDataClient(app)).toBeNull();
-    }
-    expect(callServerTool).not.toHaveBeenCalled();
-  });
-
-  it("persists and restores the exact Sequence checkpoint through the authenticated native host", async () => {
-    const checkpoint = new TextEncoder().encode(
-      '{"version":1,"viewport":{"start1":4294967301}}',
-    );
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValueOnce({
-        structuredContent: {
-          recoveryReference: "sequence-recovery-1",
-          logicalSessionId: session.logicalSessionId,
-          lastAcknowledgedRevision: 12,
-          checkpointVersion: 1,
-        },
-      })
-      .mockResolvedValueOnce({
-        structuredContent: {
-          checkpoint,
-          lastAcknowledgedRevision: 12,
-          sourceRevision: session.sourceRevision,
-          recoveryReference: "sequence-recovery-1",
-          hasCheckpoint: true,
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.checkpoint({ checkpoint, lastAcknowledgedRevision: 12 }),
-    ).resolves.toMatchObject({
-      logicalSessionId: session.logicalSessionId,
-      lastAcknowledgedRevision: 12,
-      checkpointVersion: 1,
-    });
-    await expect(client.restoreCheckpoint()).resolves.toMatchObject({
-      checkpoint,
-      sourceRevision: session.sourceRevision,
-      hasCheckpoint: true,
-    });
-    expect(request.mock.calls.map(([input]) => input.operation)).toEqual([
-      "ui/scientific/sequence/checkpoint",
-      "ui/scientific/sequence/restore_checkpoint",
-    ]);
-    expect(request).toHaveBeenNthCalledWith(
-      1,
-      expect.objectContaining({
-        logicalSessionId: session.logicalSessionId,
-        sourceRevision: session.sourceRevision,
-        payload: { checkpoint, lastAcknowledgedRevision: 12 },
-      }),
-    );
-    expect(request).toHaveBeenNthCalledWith(
-      2,
-      expect.objectContaining({ payload: {} }),
-    );
-  });
-
-  it("rejects oversized, stale, substituted, and malformed recovery checkpoints", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.checkpoint({
-        checkpoint: new Uint8Array(256 * 1024 + 1),
-        lastAcknowledgedRevision: 1,
-      }),
-    ).rejects.toThrow(/checkpoint|bounded/u);
-    await expect(
-      client.checkpoint({
-        checkpoint: new Uint8Array([1]),
-        lastAcknowledgedRevision: -1,
-      }),
-    ).rejects.toThrow();
-    expect(request).not.toHaveBeenCalled();
-
-    request.mockResolvedValueOnce({
-      structuredContent: {
-        recoveryReference: "sequence-recovery-1",
-        logicalSessionId: "different-sequence-session",
-        lastAcknowledgedRevision: 2,
-        checkpointVersion: 1,
-      },
-    });
-    await expect(
-      client.checkpoint({
-        checkpoint: new Uint8Array([1]),
-        lastAcknowledgedRevision: 2,
-      }),
-    ).rejects.toThrow(/different session/u);
-
-    request.mockResolvedValueOnce({
-      structuredContent: {
-        checkpoint: new Uint8Array([1]),
-        lastAcknowledgedRevision: 2,
-        sourceRevision: "different-source-revision",
-        recoveryReference: "sequence-recovery-1",
-        hasCheckpoint: true,
-      },
-    });
-    await expect(client.restoreCheckpoint()).rejects.toThrow(/revision/u);
-  });
-
-  it("opens a new native viewer without mistaking its bootstrap marker for a recovered scene", async () => {
-    const bootstrap = new TextEncoder().encode(
-      JSON.stringify({
-        version: 1,
-        family: "sequence",
-        logicalSessionId: session.logicalSessionId,
-        sourceRevision: session.sourceRevision,
-        lastAcknowledgedRevision: 0,
-        stateStatus: "not-captured",
-      }),
-    );
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValueOnce({
-        structuredContent: {
-          checkpoint: bootstrap,
-          lastAcknowledgedRevision: 0,
-          sourceRevision: session.sourceRevision,
-          recoveryReference: "sequence-recovery-1",
-          hasCheckpoint: false,
-        },
-      })
-      .mockResolvedValueOnce({
-        structuredContent: { hasCheckpoint: false },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(client.restoreCheckpoint()).resolves.toMatchObject({
-      checkpoint: bootstrap,
-      sourceRevision: session.sourceRevision,
-      hasCheckpoint: false,
-    });
-    await expect(client.restoreCheckpoint()).resolves.toEqual({
-      hasCheckpoint: false,
-    });
-    expect(request.mock.calls.map(([input]) => input.operation)).toEqual([
-      "ui/scientific/sequence/restore_checkpoint",
-      "ui/scientific/sequence/restore_checkpoint",
-    ]);
-  });
-
-  it("restores genuine cross-realm Electron checkpoint bytes without accepting other views", async () => {
-    const crossRealmCheckpoint: Uint8Array = runInNewContext(
-      "new Uint8Array([123, 34, 118, 34, 58, 49, 125])",
-    );
-    expect(crossRealmCheckpoint).not.toBeInstanceOf(Uint8Array);
-    expect(ArrayBuffer.isView(crossRealmCheckpoint)).toBe(true);
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValueOnce({
-        structuredContent: {
-          checkpoint: crossRealmCheckpoint,
-          lastAcknowledgedRevision: 3,
-          sourceRevision: session.sourceRevision,
-          recoveryReference: "sequence-recovery-1",
-          hasCheckpoint: true,
-        },
-      })
-      .mockResolvedValueOnce({
-        structuredContent: {
-          checkpoint: new DataView(new ArrayBuffer(8)),
-          lastAcknowledgedRevision: 3,
-          sourceRevision: session.sourceRevision,
-          recoveryReference: "sequence-recovery-1",
-          hasCheckpoint: true,
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(client.restoreCheckpoint()).resolves.toMatchObject({
-      checkpoint: crossRealmCheckpoint,
-      hasCheckpoint: true,
-    });
-    await expect(client.restoreCheckpoint()).rejects.toThrow(/bytes/u);
-  });
-
-  it("preserves bounded page-and-record continuations without dropping records", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          cursor: "0:2",
-          nextCursor: "0:4",
-          sourceRevision: session.sourceRevision,
-          complete: false,
-          records: [
-            { id: "record-3", description: "", sequenceLength: 8 },
-            { id: "record-4", description: "", sequenceLength: 9 },
-          ],
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.listRecords({ cursor: "0:2", limit: 2 }),
-    ).resolves.toMatchObject({
-      cursor: "0:2",
-      nextCursor: "0:4",
-      records: [{ id: "record-3" }, { id: "record-4" }],
-    });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({ payload: { cursor: "0:2", limit: 2 } }),
-    );
-  });
-
-  it("writes the original source only through an explicitly approved bounded native transaction", async () => {
-    const expiresAtMs = Date.now() + 60_000;
-    const bytes = new TextEncoder().encode(">updated\nAACCGGTT\n");
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValueOnce({
-        structuredContent: {
-          editId: "sequence-source-edit-1",
-          expiresAtMs,
-          sourceRevision: session.sourceRevision,
-          bytesWrittenDecimal: "0",
-        },
-      })
-      .mockResolvedValueOnce({
-        structuredContent: {
-          editId: "sequence-source-edit-1",
-          expiresAtMs,
-          sourceRevision: session.sourceRevision,
-          bytesWrittenDecimal: String(bytes.byteLength),
-        },
-      })
-      .mockResolvedValueOnce({
-        structuredContent: {
-          editId: "sequence-source-edit-1",
-          sourceRevision: "updated-source-revision-2",
-          bytesWrittenDecimal: String(bytes.byteLength),
-          sourceIdentity: {
-            fileId: "source-file-1",
-            etag: "updated-source-etag-2",
-            rootId: "workspace-root-1",
-            sizeBytesDecimal: String(bytes.byteLength),
-          },
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    expect(request).not.toHaveBeenCalled();
-    const lease = await client.beginSourceEdit({
-      approvedOperation: "replace-source",
-      expectedSourceRevision: session.sourceRevision,
-      maxOutputBytesDecimal: String(bytes.byteLength),
-    });
-    await client.appendSourceEdit({
-      editId: lease.editId,
-      offsetDecimal: "0",
-      bytes,
-    });
-    await expect(
-      client.commitSourceEdit({ editId: lease.editId }),
-    ).resolves.toMatchObject({
-      sourceRevision: "updated-source-revision-2",
-      bytesWrittenDecimal: String(bytes.byteLength),
-    });
-    expect(request.mock.calls.map(([input]) => input.operation)).toEqual([
-      "ui/scientific/sequence/source_edit/begin",
-      "ui/scientific/sequence/source_edit/append",
-      "ui/scientific/sequence/source_edit/commit",
-    ]);
-    expect(request).toHaveBeenNthCalledWith(
-      1,
-      expect.objectContaining({
-        payload: {
-          approvedOperation: "replace-source",
-          expectedSourceRevision: session.sourceRevision,
-          maxOutputBytesDecimal: String(bytes.byteLength),
-        },
-      }),
-    );
-  });
-
-  it("rejects stale, oversized, or substituted source edits before writing the original file", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.beginSourceEdit({
-        approvedOperation: "replace-source",
-        expectedSourceRevision: "substituted-source-revision",
-      }),
-    ).rejects.toThrow(/authorized/u);
-    await expect(
-      client.appendSourceEdit({
-        editId: "source-edit-1",
-        offsetDecimal: "0",
-        bytes: new Uint8Array(64 * 1024 + 1),
-      }),
-    ).rejects.toThrow(/safe/u);
-    expect(request).not.toHaveBeenCalled();
-
-    request.mockResolvedValueOnce({
-      structuredContent: {
-        editId: "source-edit-1",
-        expiresAtMs: Date.now() + 60_000,
-        sourceRevision: "substituted-source-revision",
-        bytesWrittenDecimal: "0",
-      },
-    });
-    await expect(
-      client.beginSourceEdit({
-        approvedOperation: "replace-source",
-        expectedSourceRevision: session.sourceRevision,
-      }),
-    ).rejects.toThrow(/stale|invalid/u);
-  });
-
-  it("negotiates bounded one-MiB original-source writes with stable idempotency keys", async () => {
-    const bytes = new Uint8Array(MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES);
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValueOnce({
-        structuredContent: {
-          bytesWrittenDecimal: "0",
-          editId: "large-source-edit",
-          expiresAtMs: Date.now() + 60_000,
-          maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-          sourceRevision: session.sourceRevision,
-        },
-      })
-      .mockResolvedValueOnce({
-        structuredContent: {
-          bytesWrittenDecimal: String(bytes.byteLength),
-          editId: "large-source-edit",
-          expiresAtMs: Date.now() + 60_000,
-          maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-          sourceRevision: session.sourceRevision,
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-    const lease = await client.beginSourceEdit({
-      approvedOperation: "replace-source",
-      expectedSourceRevision: session.sourceRevision,
-    });
-    expect(lease.maxChunkBytes).toBe(MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES);
-    await client.appendSourceEdit({
-      bytes,
-      editId: lease.editId,
-      offsetDecimal: "0",
-      requestId: "stable-one-mib-chunk",
-    });
-    const appendedChunk = request.mock.calls[1]?.[0].payload;
-    expect(appendedChunk?.bytes).toBe(bytes);
-    expect(appendedChunk?.requestId).toBe("stable-one-mib-chunk");
-    await expect(
-      client.appendSourceEdit({
-        bytes: new Uint8Array(MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES + 1),
-        editId: lease.editId,
-        offsetDecimal: String(bytes.byteLength),
-        requestId: "oversized-chunk",
-      }),
-    ).rejects.toThrow(/safe/u);
-    expect(request).toHaveBeenCalledTimes(2);
-  });
-
-  it("resumes a durable original-source edit at its authenticated committed offset", async () => {
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValue({
-        structuredContent: {
-          bytesWrittenDecimal: "1048576",
-          editId: "durable-source-edit",
-          expiresAtMs: Date.now() + 60_000,
-          maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-          sourceRevision: session.sourceRevision,
-          state: "staging",
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await expect(
-      client.resumeSourceEdit({ editId: "durable-source-edit" }),
-    ).resolves.toMatchObject({
-      bytesWrittenDecimal: "1048576",
-      maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-      state: "staging",
-    });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/source_edit/resume",
-        payload: { editId: "durable-source-edit" },
-      }),
-    );
-  });
-
-  it("rejects renewed source edits with substituted authority or unsafe negotiated chunks", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient({ request }, session);
-    for (const invalid of [
-      { sourceRevision: "substituted-source" },
-      { editId: "substituted-edit" },
-      { expiresAtMs: Date.now() - 1 },
-      { maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES + 1 },
-    ]) {
-      request.mockResolvedValueOnce({
-        structuredContent: {
-          bytesWrittenDecimal: "0",
-          editId: "durable-source-edit",
-          expiresAtMs: Date.now() + 60_000,
-          maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-          sourceRevision: session.sourceRevision,
-          state: "staging",
-          ...invalid,
-        },
-      });
-      await expect(
-        client.resumeSourceEdit({ editId: "durable-source-edit" }),
-      ).rejects.toThrow();
-    }
-  });
-
-  it("recovers an exactly-once published original when the commit response was lost", async () => {
-    const committedResult = {
-      bytesWrittenDecimal: "1048576",
-      editId: "published-source-edit",
-      sourceIdentity: {
-        etag: "source-etag-v2",
-        fileId: "source-file-1",
-        rootId: "workspace-root-1",
-        sizeBytesDecimal: "1048576",
-      },
-      sourceRevision: "source-revision-v2",
-    };
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValue({
-        structuredContent: {
-          bytesWrittenDecimal: "1048576",
-          committedResult,
-          editId: "published-source-edit",
-          expiresAtMs: Date.now() + 60_000,
-          maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-          sourceRevision: session.sourceRevision,
-          state: "published",
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await expect(
-      client.resumeSourceEdit({ editId: "published-source-edit" }),
-    ).resolves.toMatchObject({ committedResult, state: "published" });
-  });
-
-  it("rejects forged cached publications before trusting a resumed original-source commit", async () => {
-    const committedResult = {
-      bytesWrittenDecimal: "1048576",
-      editId: "published-source-edit",
-      sourceIdentity: {
-        etag: "independently-validated-physical-etag-v2",
-        fileId: "source-file-1",
-        rootId: "workspace-root-1",
-        sizeBytesDecimal: "1048576",
-      },
-      sourceRevision: "distinct-logical-source-revision-v2",
-    };
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient({ request }, session);
-    for (const forgery of [
-      { ...committedResult, editId: "substituted-source-edit" },
-      { ...committedResult, bytesWrittenDecimal: "1048575" },
-      {
-        ...committedResult,
-        sourceIdentity: {
-          ...committedResult.sourceIdentity,
-          sizeBytesDecimal: "1048575",
-        },
-      },
-      {
-        ...committedResult,
-        sourceIdentity: { ...committedResult.sourceIdentity, etag: "" },
-      },
-      { ...committedResult, sourceRevision: session.sourceRevision },
-      undefined,
-    ]) {
-      request.mockResolvedValueOnce({
-        structuredContent: {
-          bytesWrittenDecimal: "1048576",
-          committedResult: forgery,
-          editId: "published-source-edit",
-          expiresAtMs: Date.now() + 60_000,
-          maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-          sourceRevision: session.sourceRevision,
-          state: "published",
-        },
-      });
-      await expect(
-        client.resumeSourceEdit({ editId: "published-source-edit" }),
-      ).rejects.toThrow();
-    }
-  });
-
-  it("renews the same durable source edit after more than thirty minutes of streaming", async () => {
-    let now = 1_800_000_000_000;
-    const clock = vi.spyOn(Date, "now").mockImplementation(() => now);
-    try {
-      const request = vi
-        .fn<SequenceScientificDataTransport["request"]>()
-        .mockResolvedValueOnce({
-          structuredContent: {
-            bytesWrittenDecimal: "0",
-            editId: "long-running-source-edit",
-            expiresAtMs: now + 5 * 60_000,
-            maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-            sourceRevision: session.sourceRevision,
-          },
-        });
-      const client = new ScientificSequenceDataClient({ request }, session);
-      await client.beginSourceEdit({
-        approvedOperation: "replace-source",
-        expectedSourceRevision: session.sourceRevision,
-      });
-
-      now += 31 * 60_000;
-      request.mockResolvedValueOnce({
-        structuredContent: {
-          bytesWrittenDecimal: "1048576",
-          editId: "long-running-source-edit",
-          expiresAtMs: now + 5 * 60_000,
-          maxChunkBytes: MAX_SEQUENCE_SOURCE_EDIT_CHUNK_BYTES,
-          sourceRevision: session.sourceRevision,
-          state: "staging",
-        },
-      });
-      await expect(
-        client.resumeSourceEdit({ editId: "long-running-source-edit" }),
-      ).resolves.toMatchObject({
-        bytesWrittenDecimal: "1048576",
-        editId: "long-running-source-edit",
-      });
-      expect(request.mock.calls.map(([call]) => call.operation)).toEqual([
-        "ui/scientific/sequence/source_edit/begin",
-        "ui/scientific/sequence/source_edit/resume",
-      ]);
-    } finally {
-      clock.mockRestore();
-    }
-  });
-
-  it("aborts only the authenticated, explicitly selected original-file transaction", async () => {
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValueOnce({
-        structuredContent: {
-          editId: "source-edit-1",
-          aborted: true,
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.abortSourceEdit({ editId: "source-edit-1" }),
-    ).resolves.toBeUndefined();
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/source_edit/abort",
-        payload: { editId: "source-edit-1" },
-      }),
-    );
-  });
-
-  it("asks the isolated backend to stream every source record without a full-file payload", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          transactionId: "source-transaction-1",
-          publicationId: "source-publication-1",
-          state: "published",
-          bytesWrittenDecimal: "22",
-          manifest: {
-            entries: [
-              {
-                relativeName: "all-records.fasta",
-                sizeBytesDecimal: "22",
-                sha256: `sha256:${"a".repeat(64)}`,
-              },
-            ],
-          },
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.exportOpenedSource({
-        artifactKind: "sequence-fasta",
-        collisionPolicy: "fail",
-        format: "fasta",
-        idempotencyKey: "source-export-1",
-        memberName: "all-records.fasta",
-        relativePath: "results/all-records.fasta",
-      }),
-    ).resolves.toMatchObject({ state: "published" });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/export/source",
-        payload: {
-          artifactKind: "sequence-fasta",
-          collisionPolicy: "fail",
-          format: "fasta",
-          idempotencyKey: "source-export-1",
-          memberName: "all-records.fasta",
-          pluginVersion: "0.1.43",
-          relativePath: "results/all-records.fasta",
-        },
-      }),
-    );
-  });
-
-  it("stages a source export for one atomic data-and-provenance publication", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          bytesWrittenDecimal: "22",
-          publicationId: "source-publication-1",
-          sha256: "a".repeat(64),
-          state: "staging",
-          transactionId: "source-transaction-1",
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.stageOpenedSource({
-        artifactKind: "sequence-fasta",
-        collisionPolicy: "fail",
-        format: "fasta",
-        idempotencyKey: "source-export-1",
-        memberName: "all-records.fasta",
-        relativePath: "results/all-records.fasta",
-      }),
-    ).resolves.toMatchObject({
-      bytesWrittenDecimal: "22",
-      publicationId: "source-publication-1",
-      state: "staging",
-    });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/export/source",
-        payload: expect.objectContaining({
-          deferCommit: true,
-          pluginVersion: "0.1.43",
-        }),
-      }),
-    );
-  });
-
-  it("stages genuine native rich generation without receiving source bytes in the renderer", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          bytesWrittenDecimal: "247",
-          publicationId: "rich-publication-1",
-          sha256: "b".repeat(64),
-          state: "staging",
-          transactionId: "rich-transaction-1",
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.stageNativeRichSource({
-        artifactKind: "sequence-genbank",
-        collisionPolicy: "fail",
-        format: "genbank",
-        idempotencyKey: "rich-export-1",
-        memberName: "reference.gb",
-        recordNumber: 1,
-        relativePath: "results/reference.gb",
-      }),
-    ).resolves.toMatchObject({
-      bytesWrittenDecimal: "247",
-      publicationId: "rich-publication-1",
-      sha256: "b".repeat(64),
-      state: "staging",
-    });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/export/rich",
-        payload: {
-          artifactKind: "sequence-genbank",
-          collisionPolicy: "fail",
-          deferCommit: true,
-          format: "genbank",
-          idempotencyKey: "rich-export-1",
-          memberName: "reference.gb",
-          pluginVersion: "0.1.43",
-          recordNumber: 1,
-          relativePath: "results/reference.gb",
-        },
-      }),
-    );
-    expect(request.mock.calls[0]?.[0].payload).not.toHaveProperty("bytes");
-
-    await expect(
-      client.stageNativeRichSource({
-        artifactKind: "sequence-genbank",
-        collisionPolicy: "fail",
-        format: "genbank",
-        idempotencyKey: "rich-export-1",
-        memberName: "reference.gb",
-        recordNumber: 0,
-        relativePath: "results/reference.gb",
-      }),
-    ).rejects.toThrow("not valid");
-    expect(request).toHaveBeenCalledTimes(1);
-  });
-
-  it("restores the authenticated independent data and provenance offsets", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          bytesWrittenDecimal: "44",
-          memberOffsets: [
-            {
-              bytesWrittenDecimal: "33",
-              memberName: "all-records.fasta",
-              role: "data",
-            },
-            {
-              bytesWrittenDecimal: "11",
-              memberName: "all-records.fasta.provenance.json",
-              role: "provenance",
-            },
-          ],
-          publicationId: "source-publication-1",
-          state: "staging",
-          transactionId: "source-transaction-1",
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.resumeArtifactExport({
-        artifactKind: "sequence-fasta",
-        collisionPolicy: "fail",
-        memberName: "all-records.fasta",
-        relativePath: "results/all-records.fasta",
-        transactionId: "source-transaction-1",
-      }),
-    ).resolves.toMatchObject({
-      bytesWrittenDecimal: "44",
-      memberOffsets: [
-        { bytesWrittenDecimal: "33", role: "data" },
-        { bytesWrittenDecimal: "11", role: "provenance" },
-      ],
-    });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/export/resume",
-        payload: expect.objectContaining({
-          artifactKind: "sequence-fasta",
-          collisionPolicy: "fail",
-          pluginVersion: "0.1.43",
-          relativePath: "results/all-records.fasta",
-        }),
-      }),
-    );
-  });
-
-  it("rejects resumed artifact totals that conflate different durable members", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          bytesWrittenDecimal: "33",
-          memberOffsets: [
-            {
-              bytesWrittenDecimal: "33",
-              memberName: "all-records.fasta",
-              role: "data",
-            },
-            {
-              bytesWrittenDecimal: "11",
-              memberName: "all-records.fasta.provenance.json",
-              role: "provenance",
-            },
-          ],
-          state: "staging",
-          transactionId: "source-transaction-1",
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.resumeArtifactExport({
-        artifactKind: "sequence-fasta",
-        collisionPolicy: "fail",
-        memberName: "all-records.fasta",
-        relativePath: "results/all-records.fasta",
-        transactionId: "source-transaction-1",
-      }),
-    ).rejects.toThrow(/inconsistent member offsets/u);
-  });
-
-  it("uses the host-allowed canonical Sequence alignment tile operation", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          rowStart1: 1,
-          rowEnd1: 1,
-          columnStart1: 1,
-          columnEnd1: 4,
-          rows: [{ id: "row-1", row1: 1, aligned: "A-CG" }],
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await client.readAlignmentTile({
-      rowStart1: 1,
-      rowEnd1: 1,
-      columnStart1: 1,
-      columnEnd1: 4,
-    });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/alignment/tile",
-      }),
-    );
-  });
-
-  it("publishes only a real user-selected relative destination through the host-owned artifact route", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          transactionId: "host-transaction-1",
-          publicationId: "host-publication-1",
-          state: "published",
-          bytesWrittenDecimal: "15",
-          manifest: { artifactKind: "sequence-fasta" },
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await expect(
-      client.exportDerivedCopy({
-        recordNumber: 1,
-        idempotencyKey: "user-export-1",
-        memberName: "derived.fasta",
-        format: "fasta",
-        header: "derived",
-        relativePath: "results/derived.fasta",
-      }),
-    ).resolves.toMatchObject({
-      transactionId: "host-transaction-1",
-      state: "published",
-    });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/export",
-        payload: expect.objectContaining({
-          relativePath: "results/derived.fasta",
-          collisionPolicy: "fail",
-          artifactKind: "sequence-fasta",
-        }),
-      }),
-    );
-    expect(JSON.stringify(request.mock.calls)).not.toContain(
-      "destinationGrantId",
-    );
-  });
-
-  it("refuses path traversal before requesting a scientific artifact grant", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await expect(
-      client.exportDerivedCopy({
-        recordNumber: 1,
-        idempotencyKey: "unsafe-export-1",
-        memberName: "derived.fasta",
-        format: "fasta",
-        header: "derived",
-        relativePath: "../derived.fasta",
-      }),
-    ).rejects.toThrow(/destination/u);
-    expect(request).not.toHaveBeenCalled();
-  });
-
-  it.each([
-    "C:/Windows/derived.fasta",
-    "C:\\Windows\\derived.fasta",
-    "\\\\server\\share\\derived.fasta",
-    "\\\\?\\C:\\Windows\\derived.fasta",
-    "results/derived.fasta:hidden",
-    "results/CON.fasta",
-    "results/derived.fasta ",
-  ])(
-    "rejects the platform-unsafe derived destination before native dispatch: %s",
-    async (relativePath) => {
-      const request = vi.fn<SequenceScientificDataTransport["request"]>();
-      const client = new ScientificSequenceDataClient({ request }, session);
-      await expect(
-        client.exportDerivedCopy({
-          recordNumber: 1,
-          idempotencyKey: "unsafe-windows-export-1",
-          memberName: "derived.fasta",
-          format: "fasta",
-          header: "derived",
-          relativePath,
-        }),
-      ).rejects.toThrow(/destination/u);
-      expect(request).not.toHaveBeenCalled();
-    },
-  );
-
-  it.each(["CON", "AUX.fasta", "COM1.fastq", "LPT9.fa", "result.fasta "])(
-    "rejects the Windows-reserved artifact member before requesting a grant: %s",
-    async (memberName) => {
-      const request = vi.fn<SequenceScientificDataTransport["request"]>();
-      const client = new ScientificSequenceDataClient({ request }, session);
-      await expect(
-        client.beginArtifactExport({
-          artifactKind: "sequence-fasta",
-          collisionPolicy: "fail",
-          idempotencyKey: "unsafe-windows-member-1",
-          memberName,
-          relativePath: "results/derived.fasta",
-        }),
-      ).rejects.toThrow(/safe/u);
-      expect(request).not.toHaveBeenCalled();
-    },
-  );
-
-  it("pages original record metadata over the generation-scoped host bridge", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          cursor: "0",
-          nextCursor: "1",
-          sourceRevision: session.sourceRevision,
-          complete: false,
-          records: [
-            {
-              id: "late-record",
-              description: "Late record",
-              sequenceLength: 7,
-            },
-          ],
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(client.listRecords({ limit: 1 })).resolves.toMatchObject({
-      nextCursor: "1",
-      records: [{ id: "late-record" }],
-    });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        family: "sequence",
-        logicalSessionId: session.logicalSessionId,
-        backendInstanceId: session.backendInstanceId,
-        backendGeneration: 4,
-        sourceRevision: session.sourceRevision,
-        operation: "ui/scientific/sequence/records",
-        payload: { cursor: "0", limit: 1 },
-      }),
-    );
-  });
-
-  it("preserves exact source-matched FASTQ qualities", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          sequence: "ACGT",
-          quality: "1234",
-          start1: 1,
-          end1: 4,
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    expect(
-      await client.readResidueWindow({
-        recordNumber: 100_001,
-        start1Decimal: "100000001",
-        end1Decimal: "100000004",
-        includeQuality: true,
-      }),
-    ).toMatchObject({ sequence: "ACGT", quality: "1234" });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/window",
-        payload: expect.objectContaining({
-          recordNumber: 100_001,
-          start1Decimal: "100000001",
-          includeQuality: true,
-        }),
-      }),
-    );
-  });
-
-  it.each([
-    { name: "missing", sourceRevision: undefined },
-    { name: "stale", sourceRevision: "changed-source" },
-  ])(
-    "refuses a $name source revision on a residue window",
-    async ({ sourceRevision }) => {
-      const request: SequenceScientificDataTransport["request"] = async () => ({
-        structuredContent: {
-          ...(sourceRevision == null ? {} : { sourceRevision }),
-          sequence: "ACGT",
-          quality: "1234",
-          start1: 1,
-          end1: 4,
-        },
-      });
-      const client = new ScientificSequenceDataClient({ request }, session);
-
-      await expect(
-        client.readResidueWindow({
-          recordNumber: 1,
-          start1Decimal: "1",
-          end1Decimal: "4",
-          includeQuality: true,
-        }),
-      ).rejects.toThrow(/sourceRevision|revision/u);
-    },
-  );
-
-  it("rejects stale source results instead of silently loading the whole file", async () => {
-    const request: SequenceScientificDataTransport["request"] = async () => ({
-      structuredContent: {
-        cursor: "0",
-        nextCursor: null,
-        sourceRevision: "changed-source",
-        complete: true,
-        records: [],
-      },
-    });
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await expect(client.listRecords({ limit: 1 })).rejects.toThrow(/revision/u);
-  });
-
-  it("refuses a partial or substituted FASTQ quality string", async () => {
-    const request: SequenceScientificDataTransport["request"] = async () => ({
-      structuredContent: {
-        sourceRevision: session.sourceRevision,
-        sequence: "ACGT",
-        quality: "12",
-      },
-    });
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await expect(
-      client.readResidueWindow({
-        recordNumber: 1,
-        start1Decimal: "1",
-        end1Decimal: "4",
-        includeQuality: true,
-      }),
-    ).rejects.toThrow(/qualities/u);
-  });
-
-  it("reads distant alignment tiles without constructing a dense matrix", async () => {
-    const request: SequenceScientificDataTransport["request"] = async () => ({
-      structuredContent: {
-        sourceRevision: session.sourceRevision,
-        rowStart1: 100_001,
-        rowEnd1: 100_001,
-        columnStart1: 100_000_001,
-        columnEnd1: 100_000_004,
-        rows: [{ id: "late-row", row1: 100_001, aligned: "A-CG" }],
-      },
-    });
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await expect(
-      client.readAlignmentTile({
-        rowStart1: 100_001,
-        rowEnd1: 100_001,
-        columnStart1: 100_000_001,
-        columnEnd1: 100_000_004,
-      }),
-    ).resolves.toMatchObject({ rows: [{ aligned: "A-CG" }] });
-  });
-
-  it.each([
-    { name: "missing", sourceRevision: undefined },
-    { name: "stale", sourceRevision: "changed-source" },
-  ])(
-    "refuses a $name source revision on an alignment tile",
-    async ({ sourceRevision }) => {
-      const request: SequenceScientificDataTransport["request"] = async () => ({
-        structuredContent: {
-          ...(sourceRevision == null ? {} : { sourceRevision }),
-          rowStart1: 1,
-          rowEnd1: 1,
-          columnStart1: 1,
-          columnEnd1: 4,
-          rows: [{ id: "row-1", row1: 1, aligned: "A-CG" }],
-        },
-      });
-      const client = new ScientificSequenceDataClient({ request }, session);
-
-      await expect(
-        client.readAlignmentTile({
-          rowStart1: 1,
-          rowEnd1: 1,
-          columnStart1: 1,
-          columnEnd1: 4,
-        }),
-      ).rejects.toThrow(/sourceRevision|revision/u);
-    },
-  );
-
-  it("refuses another family's session or oversized pages", async () => {
-    const request: SequenceScientificDataTransport["request"] = async () => ({
-      structuredContent: {},
-    });
-    const client = new ScientificSequenceDataClient({ request }, session);
-    await expect(client.listRecords({ limit: 257 })).rejects.toThrow(
-      /bounded/u,
-    );
-  });
-
-  it("requests revision-fenced sequence composition from the isolated backend", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          alphabet: "dna",
-          ambiguousBases: 0,
-          canonicalBases: 4,
-          counts: [
-            { symbol: "A", count: 1 },
-            { symbol: "C", count: 1 },
-            { symbol: "G", count: 1 },
-            { symbol: "T", count: 1 },
-          ],
-          gaps: 0,
-          gcExpectedFraction: 0.5,
-          gcFraction: 0.5,
-          length: 4,
-          recordNumber: 1,
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.analyzeComposition({
-        recordNumber: 1,
-        start1Decimal: "1",
-        end1Decimal: "4",
-      }),
-    ).resolves.toMatchObject({ canonicalBases: 4, gcFraction: 0.5 });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/analysis/composition",
-        sourceRevision: session.sourceRevision,
-        payload: {
-          recordNumber: 1,
-          start1Decimal: "1",
-          end1Decimal: "4",
-          alphabet: "dna",
-        },
-      }),
-    );
-  });
-
-  it("validates bounded reverse-complement and exact genetic-code translation", async () => {
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValueOnce({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          alphabet: "dna",
-          length: 9,
-          recordNumber: 1,
-          sequence: "TTACGGCAT",
-        },
-      })
-      .mockResolvedValueOnce({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          ambiguousCodons: 0,
-          codonsTranslated: 3,
-          frame: 0,
-          geneticCode: 1,
-          partialBases: 0,
-          protein: "MP*",
-          recordNumber: 1,
-          resolvedAmbiguousCodons: 0,
-          stopCount: 1,
-          strand: "+",
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-    const window = { recordNumber: 1, start1Decimal: "1", end1Decimal: "9" };
-
-    await expect(client.reverseComplement(window)).resolves.toMatchObject({
-      sequence: "TTACGGCAT",
-    });
-    await expect(client.translate(window)).resolves.toMatchObject({
-      protein: "MP*",
-    });
-    expect(request.mock.calls.map(([input]) => input.operation)).toEqual([
-      "ui/scientific/sequence/analysis/reverse-complement",
-      "ui/scientific/sequence/analysis/translate",
-    ]);
-    await expect(
-      client.translate({ ...window, geneticCode: 7 }),
-    ).rejects.toThrow(/genetic code/u);
-    expect(request).toHaveBeenCalledTimes(2);
-  });
-
-  it("forwards ORF bounds using the actual production worker parameter", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          complete: true,
-          orfs: [
-            {
-              complete: true,
-              end1: 9,
-              frame: 0,
-              protein: "MK",
-              start1: 1,
-              startCodon: "ATG",
-              stopCodon: "TAA",
-              strand: "+",
-            },
-          ],
-          recordNumber: 1,
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.findOpenReadingFrames({
-        recordNumber: 1,
-        start1Decimal: "1",
-        end1Decimal: "9",
-        minCodons: 2,
-      }),
-    ).resolves.toMatchObject({ orfs: [{ protein: "MK" }] });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/analysis/orfs",
-        payload: expect.objectContaining({ minAminoAcids: 2, maxOrfs: 1024 }),
-      }),
-    );
-  });
-
-  it("searches source-backed motifs within the production comparison budget", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          bins: [{ count: 2, start1: 1, end1: 8 }],
-          comparisons: 8,
-          complete: true,
-          hits: [
-            {
-              distance: 0,
-              end1: 3,
-              patternId: "motif-1",
-              start1: 1,
-              strand: "+",
-              wrapsOrigin: false,
-            },
-          ],
-          interpretation: "exact-sequence-match-not-functional-validation",
-          patterns: [{ id: "motif-1", mode: "literal" }],
-          recordNumber: 1,
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.searchAdvanced({
-        recordNumber: 1,
-        start1Decimal: "1",
-        end1Decimal: "8",
-        patterns: [{ id: "motif-1", mode: "literal", pattern: "ACG" }],
-      }),
-    ).resolves.toMatchObject({ hits: [{ start1: 1, end1: 3 }] });
-    expect(request).toHaveBeenCalledWith(
-      expect.objectContaining({
-        operation: "ui/scientific/sequence/search/advanced",
-      }),
-    );
-  });
-
-  it("reads authenticated quality-control and evidence-tile operations", async () => {
-    const request = vi
-      .fn<SequenceScientificDataTransport["request"]>()
-      .mockResolvedValueOnce({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          complete: true,
-          completenessReasons: [],
-          cycles: [],
-          format: "fastq",
-          method: "exact",
-          populationRecords: 2,
-          qualityEncoding: "phred+33",
-          recordsAnalyzed: 2,
-          sourceEtag: session.sourceRevision,
-          totals: { bases: 8 },
-        },
-      })
-      .mockResolvedValueOnce({
-        structuredContent: {
-          sourceRevision: session.sourceRevision,
-          complete: true,
-          reference: "chr1",
-          start1: 1,
-          end1: 8,
-          items: [{ reference: "chr1", start1: 2, end1: 4, id: "variant-1" }],
-        },
-      });
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.qualityControl({ maxRecords: 2 }),
-    ).resolves.toMatchObject({
-      recordsAnalyzed: 2,
-      qualityEncoding: "phred+33",
-    });
-    await expect(
-      client.readEvidenceTile({
-        records: [{ reference: "chr1", start1: 2, end1: 4, id: "variant-1" }],
-        reference: "chr1",
-        start1: 1,
-        end1: 8,
-      }),
-    ).resolves.toMatchObject({ items: [{ id: "variant-1" }] });
-    expect(request.mock.calls.map(([input]) => input.operation)).toEqual([
-      "ui/scientific/sequence/qc",
-      "ui/scientific/sequence/evidence/tile",
-    ]);
-  });
-
-  it("rejects stale advanced results and unsafe window or track budgets before use", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>(
-      async () => ({
-        structuredContent: {
-          sourceRevision: "stale-source-revision",
-          alphabet: "dna",
-          length: 4,
-          recordNumber: 1,
-          sequence: "ACGT",
-        },
-      }),
-    );
-    const client = new ScientificSequenceDataClient({ request }, session);
-
-    await expect(
-      client.reverseComplement({
-        recordNumber: 1,
-        start1Decimal: "1",
-        end1Decimal: "4",
-      }),
-    ).rejects.toThrow(/revision/u);
-    await expect(
-      client.analyzeComposition({
-        recordNumber: 1,
-        start1Decimal: "1",
-        end1Decimal: "1048577",
-      }),
-    ).rejects.toThrow(/bounded/u);
-    await expect(
-      client.readTrackTile({
-        records: [{ reference: "chr1", start1: 5, end1: 2 }],
-        reference: "chr1",
-        start1: 1,
-        end1: 8,
-      }),
-    ).rejects.toThrow(/coordinates/u);
-    expect(request).toHaveBeenCalledTimes(1);
-  });
-
-  it("propagates user cancellation before issuing a source request", async () => {
-    const request = vi.fn<SequenceScientificDataTransport["request"]>();
-    const client = new ScientificSequenceDataClient({ request }, session);
-    const controller = new AbortController();
-    controller.abort();
-
-    await expect(
-      client.listRecords({ limit: 1, signal: controller.signal }),
-    ).rejects.toThrow();
-    expect(request).not.toHaveBeenCalled();
-  });
-});
-
-function sequenceHostContext(
-  options: {
-    backendGeneration?: number;
-    backendInstanceId?: string;
-    canEditApprovedSource?: boolean;
-    channelId?: string;
-    expiresAtMs?: number;
-    frameId?: string;
-    logicalSessionId?: string;
-    sourceRevision?: string;
-  } = {},
-): { scientificViewers: Record<string, unknown> } {
-  const nextSession = {
-    ...session,
-    backendGeneration: options.backendGeneration ?? session.backendGeneration,
-    backendInstanceId: options.backendInstanceId ?? session.backendInstanceId,
-    canEditApprovedSource:
-      options.canEditApprovedSource ?? session.canEditApprovedSource,
-    logicalSessionId: options.logicalSessionId ?? session.logicalSessionId,
-    sourceRevision: options.sourceRevision ?? session.sourceRevision,
-  };
-  return {
-    scientificViewers: {
-      attachment: {
-        backendGeneration: nextSession.backendGeneration,
-        backendInstanceId: nextSession.backendInstanceId,
-        channelId: options.channelId ?? "sequence-channel-1",
-        expiresAtMs: options.expiresAtMs ?? Date.now() + 120_000,
-        family: nextSession.family,
-        frameId: options.frameId ?? "sequence-frame-1",
-        logicalSessionId: nextSession.logicalSessionId,
-      },
-      binaryTransfer: "bounded-process-ipc",
-      effectiveCapabilities: { ...nextSession, canReadRanges: true },
-      familyScopedChannels: true,
-      processIsolation: "family-process",
-      protocolVersion: 1,
-      transportSupportsRangeReads: true,
-    },
-  };
-}

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removed `/files/src~1sequence~1pinned-inspector.tsx`

BEFORE

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AFTER

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removed `/files/src~1sequence~1preview.test.tsx`

BEFORE

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AFTER

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removed `/files/src~1sequence~1quality-track.tsx`

BEFORE

{
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AFTER

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removed `/files/src~1sequence~1quality.ts`

BEFORE

{
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AFTER

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removed `/files/src~1sequence~1read-pileup.test.ts`

BEFORE

{
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AFTER

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removed `/files/src~1sequence~1read-pileup.ts`

BEFORE

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AFTER

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BEFORE

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AFTER

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removed `/files/src~1sequence~1search-panel.tsx`

BEFORE

{
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AFTER

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removed `/files/src~1sequence~1search.test.ts`

BEFORE

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AFTER

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removed `/files/src~1sequence~1search.ts`

BEFORE

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AFTER

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removed `/files/src~1sequence~1selection.test.ts`

BEFORE

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AFTER

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BEFORE

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AFTER

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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removed `/files/src~1sequence~1sequence-overview.test.ts`

BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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AFTER

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AFTER

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BEFORE

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AFTER

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AFTER

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BEFORE

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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BEFORE

{
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AFTER

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AFTER

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BEFORE

{
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AFTER

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{
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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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AFTER

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BEFORE

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AFTER

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BEFORE

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AFTER

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AFTER

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AFTER

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AFTER

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BEFORE

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AFTER

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{
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AFTER

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BEFORE

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AFTER

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AFTER

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AFTER

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AFTER

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SHA-256 of public snapshot: 3d0564840f9fe2a4607dcfa3ac18b6f38a1415ca67c6b3f49ff495736b42f386

Update to Biological Sequence & Alignment Viewer

Package or technical metadata updated

Package file

Package file

Package file

Package file

Compare saved observations

Changed files

src/persistent/scientific-data-client.test.ts

changed /files/.codex-plugin~1plugin.json/sha256

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removed /files/e2e~1plugin-runtime-root.mjs

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removed /files/e2e~1public-starter-failure-evidence.spec.ts

removed /files/e2e~1sequence-viewer.spec.ts

added /files/integrity.json

added /files/launch_node

added /files/launch_node.cmd

removed /files/lsc-109-qualification.json

removed /files/package.json

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removed /files/pnpm-lock.yaml

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removed `/files/e2e~1persistent-native-recovery.spec.ts`

removed `/files/e2e~1plugin-runtime-root.mjs`

removed `/files/e2e~1public-starter-evidence.spec.ts`

removed `/files/e2e~1public-starter-failure-evidence.spec.ts`

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added `/files/integrity.json`

added `/files/launch_node`

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changed `/files/skills~1biological-sequence-viewer~1SKILL.md/sha256`

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