diff --git a/src/domain/apple/appleApplication.test.ts b/src/domain/apple/appleApplication.test.ts
index 0fedfde02b..72fcb1509f 100644
--- a/src/domain/apple/appleApplication.test.ts
+++ b/src/domain/apple/appleApplication.test.ts
@@ -685,7 +685,7 @@ describe("Apple application bridge candidates", () => {
       ),
     );
     const result = project(
-      inventoryEvidence("zip", "Fixture.zip", [...scripts, ...native]),
+      inventoryEvidence("ipa", "Fixture.ipa", [...scripts, ...native]),
     );
 
     expect(result.components.javascript).toHaveLength(129);
@@ -970,3 +970,41 @@ it("preserves observed unavailable bundle metadata and signing paths without inv
   expect(result.platforms).toEqual(["ios"]);
   expect(result.unavailable_components).toHaveLength(3);
 });
+
+it.each(["zip", "directory", "dmg"] as const)(
+  "does not apply IPA roots to a %s inventory",
+  (format) => {
+    const result = project(
+      inventoryEvidence(format, `Sample.${format}`, [
+        { path: "Payload/App.app/Info.plist", format: "plist" },
+        { path: "Extras/Other.app/Info.plist", format: "plist" },
+      ]),
+    );
+    expect(result.root_format).toBe(format);
+    expect(result.application_roots).toEqual([]);
+    expect(result.platforms).toEqual([]);
+    expect(result.bundles).toEqual([]);
+  },
+);
+
+it.each(["ipa", "zip", "directory", "dmg"] as const)(
+  "uses only the %s root convention in a mixed inventory",
+  (format) => {
+    const source = inventoryEvidence(format, `Mixed.${format}`, [
+      { path: "Payload/App.app/Info.plist", format: "plist" },
+      { path: "Extras/Other.app/Contents/Info.plist", format: "plist" },
+      macho("Extras/Other.app/Contents/MacOS/Other"),
+      {
+        path: "Extras/Other.app/Contents/Resources/app.js",
+        format: "javascript-bundle",
+      },
+    ]);
+    const result = project(source);
+    expect(result.application_roots).toEqual([
+      format === "ipa" ? "Payload/App.app" : "Extras/Other.app",
+    ]);
+    expect(result.platforms).toEqual([format === "ipa" ? "ios" : "macos"]);
+    expect(result.components.javascript).toHaveLength(1);
+    expect(result.components.executables).toHaveLength(1);
+  },
+);
diff --git a/src/domain/apple/appleBundleAnatomy.ts b/src/domain/apple/appleBundleAnatomy.ts
index 2265938f0d..6be7696292 100644
--- a/src/domain/apple/appleBundleAnatomy.ts
+++ b/src/domain/apple/appleBundleAnatomy.ts
@@ -123,12 +123,13 @@ const applicationRoots = (
   for (const path of directoryPaths(tree)) {
     const segments = path.split("/");
     const app = segments[1];
-    if (
-      anatomyNameIs(segments[0] ?? "", "Payload") &&
-      app !== undefined &&
-      /\.app$/iu.test(app)
-    ) {
-      found.add(`${segments[0]}/${app}`);
+    if (subject.format === "ipa") {
+      if (
+        anatomyNameIs(segments[0] ?? "", "Payload") &&
+        app !== undefined &&
+        /\.app$/iu.test(app)
+      )
+        found.add(`${segments[0]}/${app}`);
       continue;
     }
     const index = segments.findIndex(
diff --git a/tests/boundary/cli/appleContainerRootCli.test.ts b/tests/boundary/cli/appleContainerRootCli.test.ts
new file mode 100644
index 0000000000..1426745b8c
--- /dev/null
+++ b/tests/boundary/cli/appleContainerRootCli.test.ts
@@ -0,0 +1,114 @@
+import { readFile, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+import {
+  TextReader,
+  Uint8ArrayReader,
+  Uint8ArrayWriter,
+  ZipWriter,
+} from "@zip.js/zip.js";
+import { expect } from "vitest";
+import { appleApplicationProjectionResultSchema } from "../../../src/domain/apple/appleApplication.js";
+import { parseEvidence } from "../../../src/domain/evidence.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+import { cliTest } from "../../support/cli/cliFixture.js";
+
+cliTest.for([
+  {
+    name: "flat ZIP",
+    extension: "zip",
+    payload: true,
+    deep: false,
+    roots: [],
+    platforms: [],
+  },
+  {
+    name: "flat IPA",
+    extension: "ipa",
+    payload: true,
+    deep: false,
+    roots: ["Payload/Main.app"],
+    platforms: ["ios"],
+  },
+  {
+    name: "deep ZIP",
+    extension: "zip",
+    payload: false,
+    deep: true,
+    roots: ["Extras/Helper.app"],
+    platforms: ["macos"],
+  },
+  {
+    name: "IPA with unrooted deep helper",
+    extension: "ipa",
+    payload: true,
+    deep: true,
+    roots: ["Payload/Main.app"],
+    platforms: ["ios"],
+  },
+])(
+  "keeps format-specific Apple roots through CLI and MCP ($name)",
+  async (fixture, { cli }) => {
+    const root = await createTestTempDirectory("rea-apple-root-format-");
+    const path = join(root, `Sample.${fixture.extension}`);
+    const writer = new ZipWriter(new Uint8ArrayWriter());
+    if (fixture.payload)
+      await writer.add(
+        "Payload/Main.app/Info.plist",
+        new TextReader("<plist><dict/></plist>"),
+      );
+    await writer.add(
+      "Extras/Other.app/Info.plist",
+      new TextReader("<plist><dict/></plist>"),
+    );
+    if (fixture.deep) {
+      await writer.add(
+        "Extras/Helper.app/Contents/Info.plist",
+        new TextReader("<plist><dict/></plist>"),
+      );
+      const macho = Buffer.concat([
+        Buffer.from("cffaedfe070000010300008002000000", "hex"),
+        Buffer.alloc(40),
+      ]);
+      await writer.add(
+        "Extras/Helper.app/Contents/MacOS/Helper",
+        new Uint8ArrayReader(macho),
+      );
+      await writer.add("Shared/other.js", new TextReader("console.log(2)"));
+    }
+    const bytes = await writer.close();
+    await writeFile(path, bytes);
+    const inspected = await cli.run({
+      arguments: ["inspect-artifact", path, "--json"],
+    });
+    expect(inspected.exitCode, inspected.stderr).toBe(0);
+    const source = parseEvidence(inspected.json);
+    const input = { inventory_evidence: [source] };
+    const request = join(root, "request.json");
+    await writeFile(request, JSON.stringify(input));
+    const projected = await cli.run({
+      arguments: ["project-apple-application-graph", request, "--json"],
+    });
+    expect(projected.exitCode, projected.stderr).toBe(0);
+    const cliGraph = appleApplicationProjectionResultSchema.parse(
+      parseEvidence(projected.json).normalized_result,
+    );
+    expect(cliGraph.root_format).toBe(fixture.extension);
+    expect(cliGraph.application_roots).toEqual(fixture.roots);
+    expect(cliGraph.platforms).toEqual(fixture.platforms);
+    if (fixture.deep && fixture.extension === "ipa")
+      expect(cliGraph.bridge_candidates).toContainEqual({
+        source_path: "Shared/other.js",
+        native_path: "Extras/Helper.app/Contents/MacOS/Helper",
+        basis: "javascript-and-native-content",
+      });
+    const call = await cli.sharedMcpCall?.();
+    if (call === undefined) throw new Error("Missing production MCP session");
+    const reply = await call("project_apple_application_graph", input);
+    expect(reply.isError, JSON.stringify(reply)).not.toBe(true);
+    const mcpGraph = appleApplicationProjectionResultSchema.parse(
+      parseEvidence(reply.structuredContent).normalized_result,
+    );
+    expect(mcpGraph).toEqual(cliGraph);
+    expect(Buffer.compare(await readFile(path), Buffer.from(bytes))).toBe(0);
+  },
+);