diff --git a/middleman-core/lib/middleman-core/application.rb b/middleman-core/lib/middleman-core/application.rb
index ea98a17d..38ba9ed2 100644
--- a/middleman-core/lib/middleman-core/application.rb
+++ b/middleman-core/lib/middleman-core/application.rb
@@ -29,26 +29,25 @@ module Middleman
     # Ready (all loading and parsing of extensions complete) hook
     define_hook :ready
 
-    class << self
-
-      # Mix-in helper methods. Accepts either a list of Modules
-      # and/or a block to be evaluated
-      # @return [void]
-      def helpers(*extensions, &block)
-        class_eval(&block)   if block_given?
-        include(*extensions) if extensions.any?
-      end
+    # Mix-in helper methods. Accepts either a list of Modules
+    # and/or a block to be evaluated
+    # @return [void]
+    def self.helpers(*extensions, &block)
+      class_eval(&block)   if block_given?
+      include(*extensions) if extensions.any?
     end
-
     delegate :helpers, :to => :"self.class"
 
     # Root project directory (overwritten in middleman build/server)
     # @return [String]
-    config.define_setting :root, (ENV["MM_ROOT"] || Dir.pwd), 'Root project directory'
+    def self.root
+      ENV["MM_ROOT"] || Dir.pwd
+    end
+    delegate :root, :to => :"self.class"
 
     # Pathname-addressed root
     def self.root_path
-      Pathname(config[:root])
+      Pathname(root)
     end
     delegate :root_path, :to => :"self.class"
 
@@ -96,14 +95,6 @@ module Middleman
     # @return [String]
     config.define_setting :http_prefix, "/", 'Default prefix for building paths'
 
-    # Default string encoding for templates and output.
-    # @return [String]
-    config.define_setting :encoding,    "utf-8", 'Default string encoding for templates and output'
-
-    # Whether to catch and display exceptions
-    # @return [Boolean]
-    config.define_setting :show_exceptions, true, 'Whether to catch and display exceptions'
-
     # Default layout name
     # @return [String, Symbold]
     config.define_setting :layout, :_auto_layout, 'Default layout name'
@@ -182,7 +173,7 @@ module Middleman
     #
     # @return [String]
     def source_dir
-      File.join(config[:root], config[:source])
+      File.join(root, config[:source])
     end
 
     delegate :logger, :instrument, :to => ::Middleman::Util
diff --git a/middleman-core/lib/middleman-core/cli/build.rb b/middleman-core/lib/middleman-core/cli/build.rb
index 861c6458..6b9dcb5a 100644
--- a/middleman-core/lib/middleman-core/cli/build.rb
+++ b/middleman-core/lib/middleman-core/cli/build.rb
@@ -114,7 +114,7 @@ module Middleman::Cli
       # @param [Middleman::Sitemap::Resource] resource
       # @return [String] The full path of the file that was written
       def render_to_file(resource)
-        build_dir = self.class.shared_instance.build_dir
+        build_dir = self.class.shared_instance.config[:build_dir]
         output_file = File.join(build_dir, resource.destination_path)
 
         begin
diff --git a/middleman-core/lib/middleman-core/core_extensions/external_helpers.rb b/middleman-core/lib/middleman-core/core_extensions/external_helpers.rb
index 3e4716b0..6907740b 100644
--- a/middleman-core/lib/middleman-core/core_extensions/external_helpers.rb
+++ b/middleman-core/lib/middleman-core/core_extensions/external_helpers.rb
@@ -18,7 +18,7 @@ module Middleman
 
           # After config
           app.after_configuration do
-            helpers_path = File.expand_path(config[:helpers_dir], config[:root])
+            helpers_path = File.join(root, config[:helpers_dir])
             next unless File.exists?(helpers_path)
 
             Dir[File.join(helpers_path, config[:helpers_filename_glob])].each do |filename|
diff --git a/middleman-core/lib/middleman-core/core_extensions/file_watcher.rb b/middleman-core/lib/middleman-core/core_extensions/file_watcher.rb
index 1883b57b..a55471d9 100644
--- a/middleman-core/lib/middleman-core/core_extensions/file_watcher.rb
+++ b/middleman-core/lib/middleman-core/core_extensions/file_watcher.rb
@@ -29,7 +29,7 @@ module Middleman
 
           # Before parsing config, load the data/ directory
           app.before_configuration do
-            files.reload_path(data_dir)
+            files.reload_path(config[:data_dir])
           end
 
           # After config, load everything else
diff --git a/middleman-core/lib/middleman-core/core_extensions/front_matter.rb b/middleman-core/lib/middleman-core/core_extensions/front_matter.rb
index 9f55c60e..6fd3047d 100644
--- a/middleman-core/lib/middleman-core/core_extensions/front_matter.rb
+++ b/middleman-core/lib/middleman-core/core_extensions/front_matter.rb
@@ -62,7 +62,7 @@ module Middleman::CoreExtensions
       def clear_data(file)
         # Copied from Sitemap::Store#file_to_path, but without
         # removing the file extension
-        file = File.expand_path(file, @app.root)
+        file = File.join(@app.root, file)
         prefix = @app.source_dir.sub(/\/$/, "") + "/"
         return unless file.include?(prefix)
         path = file.sub(prefix, "")
diff --git a/middleman-core/lib/middleman-core/core_extensions/rendering.rb b/middleman-core/lib/middleman-core/core_extensions/rendering.rb
index 3e040564..2836a105 100644
--- a/middleman-core/lib/middleman-core/core_extensions/rendering.rb
+++ b/middleman-core/lib/middleman-core/core_extensions/rendering.rb
@@ -272,7 +272,7 @@ module Middleman
         # @return [String]
         def fetch_layout(engine, opts)
           # The layout name comes from either the system default or the options
-          local_layout = opts.has_key?(:layout) ? opts[:layout] : layout
+          local_layout = opts.has_key?(:layout) ? opts[:layout] : config[:layout]
           return false unless local_layout
 
           # Look for engine-specific options
diff --git a/middleman-core/lib/middleman-core/core_extensions/routing.rb b/middleman-core/lib/middleman-core/core_extensions/routing.rb
index 0416fec1..7b427acb 100644
--- a/middleman-core/lib/middleman-core/core_extensions/routing.rb
+++ b/middleman-core/lib/middleman-core/core_extensions/routing.rb
@@ -28,7 +28,7 @@ module Middleman
         # @param [String, Symbol] layout_name
         # @return [void]
         def with_layout(layout_name, &block)
-          old_layout = layout
+          old_layout = config[:layout]
 
           config[:layout] = layout_name
           instance_exec(&block) if block_given?
@@ -50,7 +50,7 @@ module Middleman
           blocks << block if block_given?
 
           # Default layout
-          opts[:layout] = layout if opts[:layout].nil?
+          opts[:layout] = config[:layout] if opts[:layout].nil?
 
           # If the url is a regexp
           if url.is_a?(Regexp) || url.include?("*")
@@ -66,7 +66,7 @@ module Middleman
           # Normalized path
           url = '/' + Middleman::Util.normalize_path(url)
           if url.end_with?('/') || File.directory?(File.join(source_dir, url))
-            url = File.join(url, index_file)
+            url = File.join(url, config[:index_file])
           end
 
           # Setup proxy
diff --git a/middleman-core/lib/middleman-core/core_extensions/ruby_encoding.rb b/middleman-core/lib/middleman-core/core_extensions/ruby_encoding.rb
index e9168386..3ff70b13 100644
--- a/middleman-core/lib/middleman-core/core_extensions/ruby_encoding.rb
+++ b/middleman-core/lib/middleman-core/core_extensions/ruby_encoding.rb
@@ -6,6 +6,10 @@ module Middleman::CoreExtensions::RubyEncoding
 
     # Once registerd
     def registered(app)
+      # Default string encoding for templates and output.
+      # @return [String]
+      app.config.define_setting :encoding,    "utf-8", 'Default string encoding for templates and output'
+
       app.send :include, InstanceMethods
     end
 
@@ -15,8 +19,8 @@ module Middleman::CoreExtensions::RubyEncoding
   module InstanceMethods
     def initialize
       if Object.const_defined?(:Encoding)
-        Encoding.default_internal = encoding
-        Encoding.default_external = encoding
+        Encoding.default_internal = config[:encoding]
+        Encoding.default_external = config[:encoding]
       end
 
       super
diff --git a/middleman-core/lib/middleman-core/core_extensions/show_exceptions.rb b/middleman-core/lib/middleman-core/core_extensions/show_exceptions.rb
index 9dd27fb8..8c34612a 100644
--- a/middleman-core/lib/middleman-core/core_extensions/show_exceptions.rb
+++ b/middleman-core/lib/middleman-core/core_extensions/show_exceptions.rb
@@ -11,10 +11,14 @@ module Middleman
 
         # Once registered
         def registered(app)
+          # Whether to catch and display exceptions
+          # @return [Boolean]
+          app.config.define_setting :show_exceptions, true, 'Whether to catch and display exceptions'
+
           # When in dev
           app.configure :development do
             # Include middlemare
-            if show_exceptions
+            if config[:show_exceptions]
               use ::Middleman::CoreExtensions::ShowExceptions::Middleware
             end
           end
diff --git a/middleman-core/lib/middleman-core/renderers/less.rb b/middleman-core/lib/middleman-core/renderers/less.rb
index 5f789980..6784e54c 100644
--- a/middleman-core/lib/middleman-core/renderers/less.rb
+++ b/middleman-core/lib/middleman-core/renderers/less.rb
@@ -19,7 +19,7 @@ module Middleman
           end
 
           app.after_configuration do
-            ::Less.paths << File.expand_path(css_dir, source_dir)
+            ::Less.paths << File.join(source_dir, config[:css_dir])
           end
 
           # Tell Tilt to use it as well (for inline sass blocks)
diff --git a/middleman-core/lib/middleman-core/sitemap/extensions/on_disk.rb b/middleman-core/lib/middleman-core/sitemap/extensions/on_disk.rb
index 52600ed7..d311973d 100644
--- a/middleman-core/lib/middleman-core/sitemap/extensions/on_disk.rb
+++ b/middleman-core/lib/middleman-core/sitemap/extensions/on_disk.rb
@@ -45,7 +45,7 @@ module Middleman
           path = @sitemap.file_to_path(file)
           return false unless path
 
-          ignored = @app.ignored_sitemap_matchers.any? do |name, callback|
+          ignored = @app.config[:ignored_sitemap_matchers].any? do |name, callback|
             callback.call(file)
           end
 
@@ -85,7 +85,7 @@ module Middleman
             ::Middleman::Sitemap::Resource.new(
               @sitemap,
               @sitemap.file_to_path(file),
-              File.expand_path(file, @app.root)
+              File.join(@app.root, file)
             )
           end
         end
diff --git a/middleman-core/lib/middleman-core/sitemap/store.rb b/middleman-core/lib/middleman-core/sitemap/store.rb
index 0b4a1f71..cf3779b2 100644
--- a/middleman-core/lib/middleman-core/sitemap/store.rb
+++ b/middleman-core/lib/middleman-core/sitemap/store.rb
@@ -164,7 +164,7 @@ module Middleman
       # @param [String] file
       # @return [String]
       def file_to_path(file)
-        file = File.expand_path(file, @app.root)
+        file = File.join(@app.root, file)
 
         prefix = @app.source_dir.sub(/\/$/, "") + "/"
         return false unless file.start_with?(prefix)
@@ -172,8 +172,8 @@ module Middleman
         path = file.sub(prefix, "")
 
         # Replace a file name containing automatic_directory_matcher with a folder
-        unless @app.automatic_directory_matcher.nil?
-          path = path.gsub(@app.automatic_directory_matcher, "/")
+        unless @app.config[:automatic_directory_matcher].nil?
+          path = path.gsub(@app.config[:automatic_directory_matcher], "/")
         end
 
         extensionless_path(path)
diff --git a/middleman-core/lib/middleman-core/step_definitions/builder_steps.rb b/middleman-core/lib/middleman-core/step_definitions/builder_steps.rb
index be1bb082..e119568d 100644
--- a/middleman-core/lib/middleman-core/step_definitions/builder_steps.rb
+++ b/middleman-core/lib/middleman-core/step_definitions/builder_steps.rb
@@ -10,9 +10,12 @@ end
 Given /^an empty app$/ do
   step %Q{a directory named "empty_app"}
   step %Q{I cd to "empty_app"}
+  ENV["MM_ROOT"] = nil
 end
 
 Given /^a fixture app "([^\"]*)"$/ do |path|
+  ENV["MM_ROOT"] = nil
+
   # This step can be reentered from several places but we don't want
   # to keep re-copying and re-cd-ing into ever-deeper directories
   next if File.basename(current_dir) == path
diff --git a/middleman-core/lib/middleman-core/step_definitions/server_steps.rb b/middleman-core/lib/middleman-core/step_definitions/server_steps.rb
index 8a0997f5..ac0a7c3c 100644
--- a/middleman-core/lib/middleman-core/step_definitions/server_steps.rb
+++ b/middleman-core/lib/middleman-core/step_definitions/server_steps.rb
@@ -40,9 +40,10 @@ Given /^the Server is running$/ do
     ENV["MM_SOURCE"] = ""
   end
 
+  ENV["MM_ROOT"] = root_dir
+
   initialize_commands = @initialize_commands || []
   initialize_commands.unshift lambda {
-    set :root, root_dir
     set :environment, @current_env || :development
     set :show_exceptions, false
   }