fix(install): skip linking into .bit_roots when rootComponents is disabled

scopes/workspace/modules/node-modules-linker/node-modules-linker.ts

@@ -70,13 +70,20 @@ export default class NodeModuleLinker {
       this.workspace.clearAllComponentsCache();
     }
 
-    await linkPkgsToRootComponents(
-      {
-        rootComponentsPath: this.workspace.rootComponentsPath,
-        workspacePath,
-      },
-      this.components.map((comp) => componentIdToPackageName(comp.state._consumer))
-    );
+    // Only update `.bit_roots` when root components are actually in use. Otherwise
+    // we'd be hard-linking into a stale tree left over from a previous install where
+    // rootComponents was enabled — pnpm no longer manages that subtree, so its layout
+    // can be inconsistent and `mkdir` may throw ENOTDIR/ENOENT through a broken
+    // ancestor inside `.bit_roots/<env>/node_modules/...`.
+    if (this.workspace.hasRootComponents()) {
+      await linkPkgsToRootComponents(
+        {
+          rootComponentsPath: this.workspace.rootComponentsPath,
+          workspacePath,
+        },
+        this.components.map((comp) => componentIdToPackageName(comp.state._consumer))
+      );
+    }
     return linksResults;
   }
   async getLinks(): Promise<DataToPersist> {

scopes/workspace/workspace/workspace.ts

@@ -309,6 +309,14 @@ export class Workspace implements ComponentFactory {
     return path.join(baseDir, BIT_ROOTS_DIR);
   }
 
+  /**
+   * Whether the workspace is configured to use root components (the `.bit_roots`
+   * per-env install layout under `node_modules`).
+   */
+  hasRootComponents(): boolean {
+    return this.dependencyResolver.hasRootComponents();
+  }
+
   /** get the `node_modules` folder of this workspace */
   private get modulesPath() {
     return path.join(this.path, 'node_modules');