fix(reference): never resolve a directory to an extensionless index (#3789)

resolveInternalSpecifier offered posix.join(dir, "index") as the
second candidate, ahead of every extension. With both dep.js and an
extensionless dep/index present, require("./dep") therefore resolved to
dep/index, a file that neither Node nor TypeScript ever selects.

Directory candidates now carry an extension. File and index ordering is
otherwise unchanged, so Node-validated cases such as dep/index.js
winning over dep.cjs keep their meaning.

Fixes #3381

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

src/application/ReferenceSourceImportEntries.ts

@@ -110,9 +110,11 @@ const resolveInternalSpecifier = (
   const directoryReference =
     specifier.endsWith("/") || [".", ".."].includes(posix.basename(specifier));
   const suffixes = ["", ".ts", ".js", ".mjs", ".cjs", ".tsx", ".jsx"];
+  // A directory resolves only to an index with an extension; neither Node nor
+  // TypeScript selects an extensionless `index` file.
   const candidates = suffixes.flatMap((suffix) => [
     ...(directoryReference ? [] : [`${normalized}${suffix}`]),
-    posix.join(normalized, `index${suffix}`),
+    ...(suffix === "" ? [] : [posix.join(normalized, `index${suffix}`)]),
   ]);
   // Retain present runtime files first; substitute only a missing counterpart.
   // Counterparts cover explicit filenames, not directory/index resolution.

tests/boundary/cli/referenceSourceDirectoryImports.test.ts

@@ -29,11 +29,13 @@ describe.skipIf(process.platform === "win32")(
           ["direct.cjs", "./lib.js", "lib.js"],
           ["fallback.cjs", "./fallback", "fallback/index.js"],
           ["legacy-order.cjs", "./dep", "dep/index.js"],
+          ["bare-index.cjs", "./bare", "bare.js"],
         ] as const;
         const unresolved = [
           ["missing.cjs", "./missing/", "missing/"],
           ["escape.cjs", "../outside/", "../outside/"],
           ["main.ts", "./folder.js/.", "folder.js"],
+          ["only-bare.cjs", "./only/", "only/"],
         ] as const;
         const files = new Map<string, string>([
           ["index.js", 'module.exports = "root index";\n'],
@@ -48,6 +50,9 @@ describe.skipIf(process.platform === "win32")(
             'export const value = "emitted filename counterpart";\n',
           ],
           ["missing.js", 'module.exports = "not a directory";\n'],
+          ["bare.js", 'module.exports = "file before directory";\n'],
+          ["bare/index", 'module.exports = "extensionless index";\n'],
+          ["only/index", 'module.exports = "extensionless index";\n'],
           ...[...imports, ...unresolved].map(
             ([path, specifier]) =>
               [path, `require(${JSON.stringify(specifier)});\n`] as const,
@@ -75,6 +80,9 @@ describe.skipIf(process.platform === "win32")(
         expect(() =>
           createRequire(join(root, "main.ts")).resolve("./folder.js/."),
         ).toThrow();
+        expect(() =>
+          createRequire(join(root, "only-bare.cjs")).resolve("./only/"),
+        ).toThrow();
         expect(
           createRequire(join(root, "escape.cjs")).resolve("../outside/"),
         ).toBe(outside);