Normalized paths for pnpm

src/mutators/builtIn/fixIncompleteTypes/fixIncompleteInterfaceOrTypeLiteralGenerics/collectGenericNodeReferences.ts

@@ -268,7 +268,7 @@ const expressionRefersToOriginalType = (
 	// This can go wrong easily: e.g. with multiple type arguments that have intermixed usages
 	if (
 		isTypeArgumentsType(expressionNodeType) &&
-		expressionNodeType.typeArguments?.includes(originalType)
+		expressionNodeType.typeArguments.includes(originalType)
 	) {
 		return true;
 	}

src/shared/references.ts

@@ -75,11 +75,7 @@ const findRelevantNodeReferences = (
 	node: ts.Node,
 ): ts.ReferenceEntry[] | undefined => {
 	// Find all locations the node is referenced
-	const nodeSourceFile = node.getSourceFile();
-	const referencedSymbols = services.languageService.findReferences(
-		nodeSourceFile.fileName,
-		node.getStart(nodeSourceFile),
-	);
+	const referencedSymbols = findReferencesForNormalizedFileName(services, node);
 	if (referencedSymbols === undefined) {
 		return undefined;
 	}
@@ -104,3 +100,25 @@ const findRelevantNodeReferences = (
 
 	return Array.from(references);
 };
+
+function findReferencesForNormalizedFileName(
+	services: LanguageServices,
+	node: ts.Node,
+) {
+	const nodeSourceFile = node.getSourceFile();
+	try {
+		return services.languageService.findReferences(
+			// TypeScript stores pnpm-resolved node_modules under non-pnpm paths.
+			nodeSourceFile.fileName.replace(
+				/node_modules\/\.pnpm\/.+\/node_modules/,
+				"node_modules",
+			),
+			node.getStart(nodeSourceFile),
+		);
+	} catch {
+		return services.languageService.findReferences(
+			nodeSourceFile.fileName,
+			node.getStart(nodeSourceFile),
+		);
+	}
+}