some minor changes in Jekyll options and CSS:

1. ignore by-products from Jekyll;
2. set the baseurl (for Github), and use shorter permanent links;
3. do not show the horizontal scroll bar for <pre> when not necessary;
4. add a horizontal line above the footnotes section;

.gitignore

@@ -1,3 +1,5 @@
 .Rproj.user
 .Rhistory
 .RData
+_site/
+.sass-cache/

_config.yml

@@ -5,10 +5,11 @@ description: > # this means to ignore newlines until "baseurl:"
   Write an awesome description for your new site here. You can edit this
   line in _config.yml. It will appear in your document head meta (for
   Google search results) and in your feed.xml site description.
-baseurl: "" # the subpath of your site, e.g. /blog/
+baseurl: "/knitr-jekyll" # the subpath of your site, e.g. /blog/
 url: "http://yourdomain.com" # the base hostname & protocol for your site
 twitter_username: jekyllrb
 github_username:  jekyll
+permalink: /:year/:month/:title.html
 
 # Build settings
 markdown: kramdown

_sass/_base.scss

@@ -139,7 +139,7 @@ code {
 
 pre {
     padding: 8px 12px;
-    overflow-x: scroll;
+    overflow-x: auto;
 
     > code {
         border: 0;

_sass/_layout.scss

@@ -234,3 +234,8 @@
         }
     }
 }
+
+.footnotes {
+    border-top: darkgray 1px solid;
+    padding-top: 1em;
+}