diff --git a/CHANGES b/CHANGES
index 03ee55b47..893827869 100644
--- a/CHANGES
+++ b/CHANGES
@@ -89,6 +89,13 @@ Release 1.0 (in development)
 Release 0.6.5 (in development)
 ==============================
 
+* #345: Fix cropping of sidebar scroll bar with ``stickysidebar``
+  option of the default theme.
+
+* #341: Always generate UNIX newlines in the quickstart Makefile.
+
+* #338: Fix running with ``-C`` under Windows.
+
 * In autodoc, allow customizing the signature of an object where
   the built-in mechanism fails.
 
diff --git a/sphinx/application.py b/sphinx/application.py
index f21aa60d7..636d436cd 100644
--- a/sphinx/application.py
+++ b/sphinx/application.py
@@ -95,6 +95,11 @@ class Sphinx(object):
         self.config = Config(confdir, CONFIG_FILENAME, confoverrides, self.tags)
         self.config.check_unicode(self.warn)
 
+        # set confdir to srcdir if -C given (!= no confdir); a few pieces
+        # of code expect a confdir to be set
+        if self.confdir is None:
+            self.confdir = self.srcdir
+
         # load all extension modules
         for extension in self.config.extensions:
             self.setup_extension(extension)
diff --git a/sphinx/environment.py b/sphinx/environment.py
index 0c83bb4f6..dddcd4369 100644
--- a/sphinx/environment.py
+++ b/sphinx/environment.py
@@ -618,7 +618,7 @@ class BuildEnvironment:
         self.note_citations_from(docname, doctree)
         self.build_toc_from(docname, doctree)
 
-        # store time of reading, used to find outdated files
+        # store time of build, for outdated files detection
         self.all_docs[docname] = time.time()
 
         if app:
diff --git a/sphinx/quickstart.py b/sphinx/quickstart.py
index f38d653ae..7e261e4bb 100644
--- a/sphinx/quickstart.py
+++ b/sphinx/quickstart.py
@@ -787,7 +787,8 @@ directly.'''
     if d['makefile']:
         d['rsrcdir'] = d['sep'] and 'source' or '.'
         d['rbuilddir'] = d['sep'] and 'build' or d['dot'] + 'build'
-        f = open(path.join(d['path'], 'Makefile'), 'w')
+        # use binary mode, to avoid writing \r\n on Windows
+        f = open(path.join(d['path'], 'Makefile'), 'wb')
         f.write((MAKEFILE % d).encode('utf-8'))
         f.close()
 
diff --git a/sphinx/themes/default/static/default.css_t b/sphinx/themes/default/static/default.css_t
index 495cccdb9..42fc377f8 100644
--- a/sphinx/themes/default/static/default.css_t
+++ b/sphinx/themes/default/static/default.css_t
@@ -73,10 +73,11 @@ div.related a {
 div.sphinxsidebar {
     {%- if theme_stickysidebar|tobool %}
     top: 30px;
+    bottom: 0;
     margin: 0;
     position: fixed;
     overflow: auto;
-    height: 100%;
+    height: auto;
     {%- endif %}
     {%- if theme_rightsidebar|tobool %}
     float: right;