diff --git a/sphinx/config.py b/sphinx/config.py
index cb9955efe..9ea2226e5 100644
--- a/sphinx/config.py
+++ b/sphinx/config.py
@@ -214,8 +214,11 @@ class Config(object):
         self.overrides = overrides
         self.values = Config.config_values.copy()
         config = {}
-        if "extensions" in overrides:
-            config["extensions"] = overrides["extensions"]
+        if 'extensions' in overrides:
+            if isinstance(overrides['extensions'], (str, unicode)):
+                config['extensions'] = overrides.pop('extensions').split(',')
+            else:
+                config['extensions'] = overrides.pop('extensions')
         if dirname is not None:
             config_file = path.join(dirname, filename)
             config['__file__'] = config_file
@@ -259,22 +262,25 @@ class Config(object):
                 warn('unknown config value %r in override, ignoring' % valname)
                 continue
             defvalue = self.values[valname][0]
-            if isinstance(defvalue, dict):
-                warn('cannot override dictionary config setting %r, '
-                     'ignoring (use %r to set individual elements)' %
-                     (valname, valname + '.key=value'))
-                continue
-            elif isinstance(defvalue, list):
-                config[valname] = value.split(',')
-            elif isinstance(defvalue, (int, long)):
-                try:
-                    config[valname] = int(value)
-                except ValueError:
-                    warn('invalid number %r for config value %r, ignoring'
-                         % (value, valname))
-            elif not isinstance(defvalue, (str, unicode)):
-                warn('cannot override config setting %r with unsupported type, '
-                     'ignoring' % valname)
+            if isinstance(value, (str, unicode)):
+                if isinstance(defvalue, dict):
+                    warn('cannot override dictionary config setting %r, '
+                         'ignoring (use %r to set individual elements)' %
+                         (valname, valname + '.key=value'))
+                    continue
+                elif isinstance(defvalue, list):
+                    config[valname] = value.split(',')
+                elif isinstance(defvalue, (int, long)):
+                    try:
+                        config[valname] = int(value)
+                    except ValueError:
+                        warn('invalid number %r for config value %r, ignoring'
+                             % (value, valname))
+                elif defvalue is not None and not isinstance(defvalue, (str, unicode)):
+                    warn('cannot override config setting %r with unsupported type, '
+                         'ignoring' % valname)
+                else:
+                    config[valname] = value
             else:
                 config[valname] = value
         for name in config:
diff --git a/tests/test_config.py b/tests/test_config.py
index 4d3d51b09..ea6f3ba4e 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -19,7 +19,8 @@ from sphinx.util.pycompat import b
 
 
 @with_app(confoverrides={'master_doc': 'master', 'nonexisting_value': 'True',
-                         'latex_elements.docclass': 'scrartcl'})
+                         'latex_elements.docclass': 'scrartcl',
+                         'modindex_common_prefix': 'path1,path2'})
 def test_core_config(app):
     cfg = app.config
 
@@ -31,6 +32,7 @@ def test_core_config(app):
     # overrides
     assert cfg.master_doc == 'master'
     assert cfg.latex_elements['docclass'] == 'scrartcl'
+    assert cfg.modindex_common_prefix == ['path1', 'path2']
 
     # simple default values
     assert 'locale_dirs' not in cfg.__dict__
@@ -92,7 +94,7 @@ def test_errors_warnings(dir):
     write_file(dir / 'conf.py', u'# -*- coding: utf-8\n\n'
                u'project = u"Jägermeister"\n', 'utf-8')
     cfg = Config(dir, 'conf.py', {}, None)
-    cfg.init_values()
+    cfg.init_values(lambda warning: 1/0)
     assert cfg.project == u'Jägermeister'
 
     # test the warning for bytestrings with non-ascii content
@@ -122,5 +124,5 @@ def test_config_eol(tmpdir):
     for eol in ('\n', '\r\n'):
         configfile.write_bytes(b('project = "spam"' + eol))
         cfg = Config(tmpdir, 'conf.py', {}, None)
-        cfg.init_values()
+        cfg.init_values(lambda warning: 1/0)
         assert cfg.project == u'spam'
diff --git a/tests/test_intersphinx.py b/tests/test_intersphinx.py
index a8679e7e2..8ce02cc18 100644
--- a/tests/test_intersphinx.py
+++ b/tests/test_intersphinx.py
@@ -81,7 +81,7 @@ def test_read_inventory_v2():
            '/util/glossary.html#term-a-term'
 
 
-@with_app(confoverrides={'extensions': 'sphinx.ext.intersphinx'})
+@with_app()
 @with_tempdir
 def test_missing_reference(tempdir, app):
     inv_file = tempdir / 'inventory'
@@ -157,7 +157,7 @@ def test_missing_reference(tempdir, app):
     assert contnode[0].astext() == 'py3k:unknown'
 
 
-@with_app(confoverrides={'extensions': 'sphinx.ext.intersphinx'})
+@with_app()
 @with_tempdir
 def test_load_mappings_warnings(tempdir, app):
     """