Update based on feedback

src/compiler/core.ts

@@ -2736,7 +2736,7 @@ namespace ts {
         function fileExists(fileName: string): boolean {
             const path = toPath(fileName);
             const result = getCachedFileSystemEntriesForBaseDir(path);
-            return (result && hasEntry(result.files, getBaseNameOfFileName(fileName))) ||
+            return result && hasEntry(result.files, getBaseNameOfFileName(fileName)) ||
                 host.fileExists(fileName);
         }
 

src/compiler/sys.ts

@@ -30,6 +30,9 @@ namespace ts {
         mtime?: Date;
     }
 
+    /**
+     * Partial interface of the System thats needed to support the caching of directory structure
+     */
     export interface PartialSystem {
         writeFile(path: string, data: string, writeByteOrderMark?: boolean): void;
         fileExists(path: string): boolean;

src/harness/unittests/programMissingFiles.ts

@@ -3,7 +3,7 @@
 namespace ts {
     function verifyMissingFilePaths(missingPaths: ReadonlyArray<Path>, expected: ReadonlyArray<string>) {
         assert.isDefined(missingPaths);
-        const map = arrayToMap(expected, k => k, _v => true);
+        const map = arrayToSet(expected) as Map<boolean>;
         for (const missing of missingPaths) {
             const value = map.get(missing);
             assert.isTrue(value, `${missing} to be ${value === undefined ? "not present" : "present only once"}, in actual: ${missingPaths} expected: ${expected}`);