Change default config to use pathPrefix: "/" and then use --pathprefix="/eleventy-base-blog/ for GitHub deploy command. Requires Eleventy v0.2.11

.eleventy.js

@@ -44,8 +44,11 @@ module.exports = function(eleventyConfig) {
       "css"
     ],
 
-    // if your site lives in a subdirectory, change this
-    pathPrefix: "/eleventy-base-blog/",
+    // If your site lives in a different subdirectory, change this.
+    // Leading or trailing slashes are all normalized away, so don’t worry about it.
+    // If you don’t have a subdirectory, use "" or "/" (they do the same thing)
+    // This is only used for URLs (it does not affect your file structure)
+    pathPrefix: "/",
 
     markdownTemplateEngine: "liquid",
     htmlTemplateEngine: "njk",