fix(javascript): keep dependency manifests out of application roots

Select the shallowest inventoried nondependency manifest and retain dependency package evidence without assigning Electron entry roles. Keep the artifact root when no application manifest is observed.

Adapted from PR #1392, with compiled CLI and stdio MCP regressions for root selection and dependency-only inputs.

Co-authored-by: Marnix Pluim <marnixpluim@users.noreply.github.com>

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>

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,