diff --git a/src/servicesHost.ts b/src/servicesHost.ts
index f54e9d71c..91fa9faf0 100644
--- a/src/servicesHost.ts
+++ b/src/servicesHost.ts
@@ -96,8 +96,7 @@ export function makeServicesHost(
 
     getProjectReferences: () => projectReferences,
 
-    getScriptFileNames: () =>
-      [...files.keys()].filter(filePath => filePath.match(scriptRegex)),
+    getScriptFileNames: () => Array.from(instance.rootFileNames),
 
     getScriptVersion: (fileName: string) => {
       fileName = path.normalize(fileName);
@@ -351,7 +350,7 @@ export function makeWatchHost(
   return watchHost;
 
   function getRootFileNames() {
-    return [...files.keys()].filter(filePath => filePath.match(scriptRegex));
+    return Array.from(instance.rootFileNames);
   }
 
   function readFileWithCachingText(fileName: string, encoding?: string) {
diff --git a/src/utils.ts b/src/utils.ts
index b81409ebe..391913a83 100644
--- a/src/utils.ts
+++ b/src/utils.ts
@@ -259,7 +259,11 @@ export function isRootFileOrExempt(
   fileName: string,
   instance: TSInstance
 ): boolean {
-  if (instance.rootFileNames.has(fileName)) {
+  // node_modules checking handled separately, later
+  if (
+    instance.rootFileNames.has(fileName) ||
+    fileName.indexOf('node_modules') > -1
+  ) {
     return true;
   }
 
diff --git a/test/comparison-tests/appendSuffixTo/tsconfig.json b/test/comparison-tests/appendSuffixTo/tsconfig.json
index 1db219bc0..b71270932 100644
--- a/test/comparison-tests/appendSuffixTo/tsconfig.json
+++ b/test/comparison-tests/appendSuffixTo/tsconfig.json
@@ -1,7 +1,4 @@
 {
 	"compilerOptions": {
-	},
-    "files": [
-        "index.vue.ts"
-    ]
+	}
 }
diff --git a/test/comparison-tests/nodeModulesMeaningfulErrorWhenImportingTs/tsconfig.json b/test/comparison-tests/nodeModulesMeaningfulErrorWhenImportingTs/tsconfig.json
index 0fa41fd51..0967ef424 100644
--- a/test/comparison-tests/nodeModulesMeaningfulErrorWhenImportingTs/tsconfig.json
+++ b/test/comparison-tests/nodeModulesMeaningfulErrorWhenImportingTs/tsconfig.json
@@ -1,8 +1 @@
-{
-	"compilerOptions": {
-	    "include": [
-            "node_modules",
-            "app.ts"
-        ]
-	}
-}
+{}