Override the config source with the local one as it should be

src/Composer/Factory.php

@@ -286,7 +286,9 @@ class Factory
         $config->merge($localConfig);
         if (isset($composerFile)) {
             $io->writeError('Loading config file ' . $composerFile, true, IOInterface::DEBUG);
-            $localAuthFile = new JsonFile(dirname(realpath($composerFile)) . '/auth.json');
+            $config->setConfigSource(new JsonConfigSource(new JsonFile(realpath($composerFile), null, $io)));
+
+            $localAuthFile = new JsonFile(dirname(realpath($composerFile)) . '/auth.json', null, $io);
             if ($localAuthFile->exists()) {
                 $io->writeError('Loading config file ' . $localAuthFile->getPath(), true, IOInterface::DEBUG);
                 $config->merge(array('config' => $localAuthFile->read()));