diff --git a/cli/run/index.ts b/cli/run/index.ts
index 190ff1efd21..dc6616ce064 100644
--- a/cli/run/index.ts
+++ b/cli/run/index.ts
@@ -16,7 +16,7 @@ export default function runRollup(command: any) {
 		if (command.input) {
 			handleError({
 				code: 'DUPLICATE_IMPORT_OPTIONS',
-				message: 'use --input, or pass input path as argument'
+				message: 'Either use --input, or pass input path as argument'
 			});
 		}
 		inputSource = command._;
diff --git a/src/utils/parseOptions.ts b/src/utils/parseOptions.ts
index 69af1fafb97..c683f06a325 100644
--- a/src/utils/parseOptions.ts
+++ b/src/utils/parseOptions.ts
@@ -43,7 +43,7 @@ const getObjectOption = (
 	const commandOption = normalizeObjectOptionValue(overrides[name]);
 	const configOption = normalizeObjectOptionValue(config[name]);
 	if (commandOption !== undefined) {
-		return commandOption && configOption ? { ...configOption, ...commandOption } : commandOption;
+		return commandOption && { ...configOption, ...commandOption };
 	}
 	return configOption;
 };
diff --git a/test/cli/node_modules/rollup-config-foo/lib/config.js b/test/cli/node_modules/rollup-config-foo/lib/config.js
deleted file mode 100644
index db00f465db4..00000000000
--- a/test/cli/node_modules/rollup-config-foo/lib/config.js
+++ /dev/null
@@ -1,11 +0,0 @@
-var replace = require( 'rollup-plugin-replace' );
-
-module.exports = {
-	input: 'main.js',
-	output: {
-		format: 'cjs'
-	},
-	plugins: [
-		replace( { 'ANSWER': 42 } )
-	]
-};
diff --git a/test/cli/node_modules/rollup-config-foo/package.json b/test/cli/node_modules/rollup-config-foo/package.json
deleted file mode 100644
index fbd490130d0..00000000000
--- a/test/cli/node_modules/rollup-config-foo/package.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-	"main": "lib/config.js"
-}
diff --git a/test/cli/node_modules/foo/lib/config.js b/test/cli/node_modules_rename_me/bar/lib/config.js
similarity index 100%
rename from test/cli/node_modules/foo/lib/config.js
rename to test/cli/node_modules_rename_me/bar/lib/config.js
diff --git a/test/cli/node_modules/foo/package.json b/test/cli/node_modules_rename_me/bar/package.json
similarity index 100%
rename from test/cli/node_modules/foo/package.json
rename to test/cli/node_modules_rename_me/bar/package.json
diff --git a/test/cli/node_modules_rename_me/foo/lib/config.js b/test/cli/node_modules_rename_me/foo/lib/config.js
deleted file mode 100644
index db00f465db4..00000000000
--- a/test/cli/node_modules_rename_me/foo/lib/config.js
+++ /dev/null
@@ -1,11 +0,0 @@
-var replace = require( 'rollup-plugin-replace' );
-
-module.exports = {
-	input: 'main.js',
-	output: {
-		format: 'cjs'
-	},
-	plugins: [
-		replace( { 'ANSWER': 42 } )
-	]
-};
diff --git a/test/cli/node_modules_rename_me/foo/package.json b/test/cli/node_modules_rename_me/foo/package.json
deleted file mode 100644
index fbd490130d0..00000000000
--- a/test/cli/node_modules_rename_me/foo/package.json
+++ /dev/null
@@ -1,3 +0,0 @@
-{
-	"main": "lib/config.js"
-}
diff --git a/test/cli/samples/duplicate-import-options/_config.js b/test/cli/samples/duplicate-import-options/_config.js
new file mode 100644
index 00000000000..00eded60316
--- /dev/null
+++ b/test/cli/samples/duplicate-import-options/_config.js
@@ -0,0 +1,10 @@
+const { assertStderrIncludes } = require('../../../utils.js');
+
+module.exports = {
+	description: 'throws if different types of entries are combined',
+	command: 'rollup main.js --format es --input main.js',
+	error: () => true,
+	stderr(stderr) {
+		assertStderrIncludes(stderr, '[!] Either use --input, or pass input path as argument');
+	}
+};
diff --git a/test/cli/samples/duplicate-import-options/main.js b/test/cli/samples/duplicate-import-options/main.js
new file mode 100644
index 00000000000..17eee8f1f7e
--- /dev/null
+++ b/test/cli/samples/duplicate-import-options/main.js
@@ -0,0 +1 @@
+assert.equal( 1 + 1, 2 );
diff --git a/test/cli/samples/external-modules-auto-global/_config.js b/test/cli/samples/external-modules-auto-global/_config.js
index 9f3e784156f..8163c5ad414 100644
--- a/test/cli/samples/external-modules-auto-global/_config.js
+++ b/test/cli/samples/external-modules-auto-global/_config.js
@@ -1,5 +1,11 @@
+const assert = require('assert');
+
 module.exports = {
 	description: 'populates options.external with --global keys',
-	command: 'rollup main.js --format iife --globals mathematics:Math',
-	execute: true
+	command:
+		'rollup main.js --format iife --globals mathematics:Math,promises:Promise --external promises',
+	execute: true,
+	stderr(stderr) {
+		assert.strictEqual(stderr.indexOf('(!)'), -1);
+	}
 };
diff --git a/test/cli/samples/external-modules-auto-global/main.js b/test/cli/samples/external-modules-auto-global/main.js
index dcd8569f77f..ad436c33986 100644
--- a/test/cli/samples/external-modules-auto-global/main.js
+++ b/test/cli/samples/external-modules-auto-global/main.js
@@ -1,3 +1,5 @@
 import { max } from 'mathematics';
+import { resolve } from 'promises';
 
 assert.equal( max( 1, 2, 3 ), 3 );
+assert.ok( resolve().then );
diff --git a/test/cli/samples/external-modules/_config.js b/test/cli/samples/external-modules/_config.js
index 8117a61be71..dbae8e93f67 100644
--- a/test/cli/samples/external-modules/_config.js
+++ b/test/cli/samples/external-modules/_config.js
@@ -1,5 +1,10 @@
+const assert = require('assert');
+
 module.exports = {
 	description: 'allows external modules to be specified with --external=foo,bar,baz',
-	command: 'rollup main.js --format cjs --external path,util',
-	execute: true
+	command: 'rollup main.js --format cjs --external=path,util',
+	execute: true,
+	stderr(stderr) {
+		assert.strictEqual(stderr.indexOf('(!)'), -1);
+	}
 };
diff --git a/test/cli/samples/node-config-auto-prefix/_config.js b/test/cli/samples/node-config-auto-prefix/_config.js
index 88b1368e750..084ade901da 100644
--- a/test/cli/samples/node-config-auto-prefix/_config.js
+++ b/test/cli/samples/node-config-auto-prefix/_config.js
@@ -1,5 +1,5 @@
 module.exports = {
-	description: 'uses config file installed from npm',
+	description: 'uses config file installed from npm, automatically adding a rollup-config- prefix',
 	command: 'rollup --config node:foo',
 	execute: true
 };
diff --git a/test/cli/samples/node-config-not-found/_config.js b/test/cli/samples/node-config-not-found/_config.js
new file mode 100644
index 00000000000..cf53bf19d71
--- /dev/null
+++ b/test/cli/samples/node-config-not-found/_config.js
@@ -0,0 +1,10 @@
+const { assertStderrIncludes } = require('../../../utils.js');
+
+module.exports = {
+	description: 'throws if a config in node_modules cannot be found',
+	command: 'rollup --config node:baz',
+	error: () => true,
+	stderr(stderr) {
+		assertStderrIncludes(stderr, '[!] Could not resolve config file node:baz');
+	}
+};
diff --git a/test/cli/samples/node-config-not-found/_expected.js b/test/cli/samples/node-config-not-found/_expected.js
new file mode 100644
index 00000000000..b5aa08a6ad6
--- /dev/null
+++ b/test/cli/samples/node-config-not-found/_expected.js
@@ -0,0 +1,11 @@
+(function (global, factory) {
+	typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() :
+	typeof define === 'function' && define.amd ? define(factory) :
+	global.myBundle = factory();
+}(this, function () { 'use strict';
+
+	var main = 42;
+
+	return main;
+
+}));
diff --git a/test/cli/samples/node-config-not-found/main.js b/test/cli/samples/node-config-not-found/main.js
new file mode 100644
index 00000000000..df16c1b06b9
--- /dev/null
+++ b/test/cli/samples/node-config-not-found/main.js
@@ -0,0 +1 @@
+assert.equal( ANSWER, 42 );
diff --git a/test/cli/samples/node-config/_config.js b/test/cli/samples/node-config/_config.js
index c17da4b1e3a..fdd13b0cc98 100644
--- a/test/cli/samples/node-config/_config.js
+++ b/test/cli/samples/node-config/_config.js
@@ -1,6 +1,6 @@
 module.exports = {
 	description: 'uses config file installed from npm',
-	command: 'rollup --config node:foo',
+	command: 'rollup --config node:bar',
 	cwd: __dirname,
 	execute: true
 };