diff --git a/docs/javascript-artifact-reconstruction.md b/docs/javascript-artifact-reconstruction.md
index 02373d6257..da5dca64bd 100644
--- a/docs/javascript-artifact-reconstruction.md
+++ b/docs/javascript-artifact-reconstruction.md
@@ -60,6 +60,12 @@ manifest and graph commitments, JavaScript Application Graph, static
 Electron summary, reconstruction statistics, and explicit limitations. It does
 not require a live Hopper, Ghidra, browser, or Electron process.
 
+The application graph selects the shallowest `package.json` outside
+`node_modules` as its package root, breaking equal-depth ties by Unicode
+code-point order. Dependency manifests remain package observations but do not
+declare Electron main or renderer entries. If only dependency manifests are
+present, the inventory artifact remains the graph root.
+
 ## ASAR integrity
 
 ASAR inventory checks Electron integrity metadata for embedded archive entries
diff --git a/src/application/javascript/JavaScriptArtifactGraphStructure.ts b/src/application/javascript/JavaScriptArtifactGraphStructure.ts
index 112a5f8b62..971c569613 100644
--- a/src/application/javascript/JavaScriptArtifactGraphStructure.ts
+++ b/src/application/javascript/JavaScriptArtifactGraphStructure.ts
@@ -26,6 +26,7 @@ import {
   staticInferenceEvidence,
 } from "./JavaScriptArtifactGraphEvidence.js";
 import { resolveArtifactPathByContext } from "./JavaScriptArtifactPathResolution.js";
+import { compareUnicodeCodePoints } from "../../domain/unicodeCodePointOrder.js";
 
 interface PackageRoleInput {
   readonly packageNode: ApplicationNode;
@@ -281,6 +282,7 @@ export const addJavaScriptPackageNodes = (
   context: JavaScriptArtifactGraphContext,
 ): ApplicationNode[] => {
   const roots: ApplicationNode[] = [];
+  const rootPath = applicationManifestPath(context);
   for (const packageValue of context.analysis.packages) {
     const file = context.filesByPath.get(packageValue.path);
     if (file === undefined) continue;
@@ -309,7 +311,7 @@ export const addJavaScriptPackageNodes = (
         },
       ],
     });
-    if (roots.length === 0) {
+    if (file.path === rootPath) {
       roots.push(node);
       context.accumulator.addEdge({
         source_node_id: node.node_id,
@@ -330,6 +332,7 @@ export const addJavaScriptPackageNodes = (
         file,
         operation: "inventory-package",
       });
+    if (dependencyManifest(file.path)) continue;
     addPackageRole(context, {
       packageNode: node,
       packageFile: file,
@@ -346,6 +349,24 @@ export const addJavaScriptPackageNodes = (
   return roots;
 };
 
+/** Dependency-only artifacts retain their inventory root. */
+const applicationManifestPath = (
+  context: JavaScriptArtifactGraphContext,
+): string | undefined =>
+  context.analysis.packages
+    .map(({ path }) => path)
+    .filter(
+      (path) => context.filesByPath.has(path) && !dependencyManifest(path),
+    )
+    .sort(
+      (left, right) =>
+        left.split("/").length - right.split("/").length ||
+        compareUnicodeCodePoints(left, right),
+    )[0];
+
+const dependencyManifest = (path: string): boolean =>
+  path.split("/").slice(0, -1).includes("node_modules");
+
 const createFileTarget = (
   context: JavaScriptArtifactGraphContext,
   file: JavaScriptArtifactFile,
diff --git a/tests/acceptance/applications/applicationManifestRoots.test.ts b/tests/acceptance/applications/applicationManifestRoots.test.ts
new file mode 100644
index 0000000000..8e3dcab102
--- /dev/null
+++ b/tests/acceptance/applications/applicationManifestRoots.test.ts
@@ -0,0 +1,120 @@
+import { mkdir, writeFile } from "node:fs/promises";
+import { join } from "node:path";
+
+import { expect } from "vitest";
+import { z } from "zod";
+
+import { javascriptApplicationAnalysisResultSchema } from "../../../src/domain/javascript/javascriptApplicationAnalysis.js";
+import { connectLocalToolsMcp } from "../../fixtures/localToolsMcp.js";
+import { createTestTempDirectory } from "../../fixtures/temporaryDirectory.js";
+import { cliTest } from "../../support/cli/cliFixture.js";
+
+cliTest.for(["CLI", "stdio MCP"] as const)(
+  "keeps dependency manifests out of application roots and Electron entries through %s",
+  async (surface, { cli }) => {
+    const root = await createTestTempDirectory("rea-application-manifest-");
+    const dependency = join(root, "node_modules", "dep");
+    const nested = join(root, "a");
+    await Promise.all([mkdir(dependency, { recursive: true }), mkdir(nested)]);
+    await Promise.all([
+      writeFile(
+        join(nested, "package.json"),
+        JSON.stringify({ name: "nested" }),
+      ),
+      writeFile(
+        join(root, "package.json"),
+        JSON.stringify({ name: "app", main: "main.js" }),
+      ),
+      writeFile(
+        join(root, "main.js"),
+        "throw new Error('source must remain inert');",
+      ),
+      writeFile(
+        join(dependency, "package.json"),
+        JSON.stringify({
+          name: "dep",
+          main: "index.js",
+          browser: "browser.js",
+        }),
+      ),
+      writeFile(join(dependency, "index.js"), "module.exports = {};"),
+      writeFile(join(dependency, "browser.js"), "export const browser = true;"),
+    ]);
+
+    let document: unknown;
+    if (surface === "CLI") {
+      const response = await cli.run({
+        arguments: ["analyze-javascript-application", root, "--json"],
+      });
+      expect(response.exitCode).toBe(0);
+      document = response.json;
+    } else {
+      const { call } = await connectLocalToolsMcp();
+      const response = await call("analyze_javascript_application", {
+        input_path: root,
+      });
+      expect(response.isError, JSON.stringify(response)).not.toBe(true);
+      document = response.structuredContent;
+    }
+    const { graph } = z
+      .object({ normalized_result: javascriptApplicationAnalysisResultSchema })
+      .parse(document).normalized_result;
+    expect(
+      graph.nodes
+        .filter(({ node_id }) => graph.root_node_ids.includes(node_id))
+        .flatMap(({ observations }) => observations.map(({ label }) => label)),
+    ).toEqual(["app"]);
+    expect(
+      graph.nodes
+        .filter(({ kind }) => kind === "electron-main")
+        .flatMap(({ observations }) =>
+          observations.map(({ properties }) => properties.declared_path),
+        ),
+    ).toEqual(["main.js"]);
+    expect(
+      graph.nodes.filter(({ kind }) => kind === "electron-renderer"),
+    ).toEqual([]);
+    expect(
+      graph.nodes
+        .filter(({ kind }) => kind === "package")
+        .flatMap(({ observations }) => observations.map(({ label }) => label))
+        .sort(),
+    ).toEqual(["app", "dep", "nested"]);
+  },
+);
+
+cliTest(
+  "keeps the artifact root when only dependency manifests are present",
+  async ({ cli }) => {
+    const root = await createTestTempDirectory("rea-dependency-only-");
+    const dependency = join(root, "node_modules", "dep");
+    await mkdir(dependency, { recursive: true });
+    await writeFile(
+      join(dependency, "package.json"),
+      JSON.stringify({ name: "dep", main: "index.js" }),
+    );
+    await writeFile(join(dependency, "index.js"), "module.exports = {};");
+    const response = await cli.run({
+      arguments: ["analyze-javascript-application", root, "--json"],
+    });
+    expect(response.exitCode, response.stderr).toBe(0);
+    const { graph } = z
+      .object({ normalized_result: javascriptApplicationAnalysisResultSchema })
+      .parse(response.json).normalized_result;
+    expect(
+      graph.nodes
+        .filter(({ node_id }) => graph.root_node_ids.includes(node_id))
+        .map(({ kind }) => kind),
+    ).toEqual(["artifact"]);
+    expect(
+      graph.nodes
+        .filter(({ kind }) => kind === "package")
+        .flatMap(({ observations }) => observations.map(({ label }) => label)),
+    ).toEqual(["dep"]);
+    expect(
+      graph.nodes.some(
+        ({ kind }) => kind === "electron-main" || kind === "electron-renderer",
+      ),
+    ).toBe(false);
+  },
+);