diff --git a/docs/js/docurium.js b/docs/js/docurium.js
index 4365f5b5d..466c63d0d 100644
--- a/docs/js/docurium.js
+++ b/docs/js/docurium.js
@@ -39,7 +39,7 @@ $(function() {
       content = $('.content')
       content.empty()
 
-      content.append($('<h1>').append("API Docs"))
+      content.append($('<h1>').append("Public API Functions"))
 
       // Function Groups
       for (var i in data['groups']) {
diff --git a/lib/docurium.rb b/lib/docurium.rb
index 508aeb821..ab7248e3e 100644
--- a/lib/docurium.rb
+++ b/lib/docurium.rb
@@ -5,24 +5,27 @@
 class Docurium
   Version = VERSION = '0.0.1'
 
-  attr_accessor :header_dir, :branch, :output_dir, :valid, :data
+  attr_accessor :header_dir, :branch, :output_dir, :data
 
-  def initialize(dir)
-    @valid = false
+  def initialize(config_file)
     @data = {:files => [], :functions => {}, :globals => {}, :types => {}, :prefix => ''}
-    if !dir
-      puts "You need to specify a directory"
-    else
-      @valid = true
-      @data[:prefix] = "include/git2"
-      @header_dir = File.expand_path(dir)
-    end
+    raise "You need to specify a config file" if !config_file
+    raise "You need to specify a valid config file" if !valid_config(config_file)
   end
 
-  def set_function_filter(prefix)
-    @prefix_filter = prefix
+  def valid_config(file)
+    return false if !File.file?(file)
+    fpath = File.expand_path(file)
+    @project_dir = File.dirname(fpath)
+    @config_file = File.basename(fpath)
+    @options = JSON.parse(File.read(fpath))
+    @data[:prefix] = @options['input'] || ''
+    @header_dir = File.join(@project_dir, @data[:prefix])
+    raise "Not an input directory" if !File.directory?(@header_dir)
+    true
   end
 
+
   def set_branch(branch)
     @branch = branch
   end
@@ -57,7 +60,11 @@ def parse_headers
   def group_functions
     func = {}
     @data[:functions].each_pair do |key, value|
-      k = key.gsub(@prefix_filter, '') if @prefix_filter
+      if @options['prefix']
+        k = key.gsub(@options['prefix'], '')
+      else
+        k = key
+      end
       group, rest = k.split('_', 2)
       next if group.empty?
       if !rest
diff --git a/lib/docurium/cli.rb b/lib/docurium/cli.rb
index 1cbf10553..f0366d941 100644
--- a/lib/docurium/cli.rb
+++ b/lib/docurium/cli.rb
@@ -3,15 +3,7 @@ class CLI
 
     def self.doc(idir, options)
       doc = Docurium.new(idir)
-      if doc.valid
-        doc.set_function_filter(options[:f]) if options[:f]
-        if options[:b]
-          doc.set_branch(options[:b])
-        elsif options[:o]
-          doc.set_output_dir(options[:o])
-        end
-        doc.generate_docs
-      end
+      doc.generate_docs
     end
 
   end