diff --git a/CHANGELOG b/CHANGELOG
index 0fa72041..98a83d98 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,7 @@
+2.0.13
+====
+middleman build --clean keeps the build directory clean of leftover files
+
 2.0.12
 ====
 Sinatra 1.3.1 and Padrino 0.10.4
diff --git a/features/clean_build.feature b/features/clean_build.feature
new file mode 100644
index 00000000..9298c4bd
--- /dev/null
+++ b/features/clean_build.feature
@@ -0,0 +1,10 @@
+Feature: Build Clean
+  Scenario: Build and Clean an app
+    Given app "clean-app" is using config "empty"
+    And a built app at "clean-app"
+    And app "clean-app" is using config "complications"
+    And a built app at "clean-app" with flags "--clean"
+    Then "should_be_ignored.html" should not exist at "clean-app"
+    And "should_be_ignored2.html" should not exist at "clean-app"
+    And "should_be_ignored3.html" should not exist at "clean-app"
+    And cleanup built app at "clean-app"
\ No newline at end of file
diff --git a/features/step_definitions/builder_steps.rb b/features/step_definitions/builder_steps.rb
index 2050627b..69bc3d8e 100644
--- a/features/step_definitions/builder_steps.rb
+++ b/features/step_definitions/builder_steps.rb
@@ -1,5 +1,13 @@
 require 'fileutils'
 
+Given /^app "([^"]*)" is using config "([^"]*)"$/ do |path, config_name|
+  root = File.dirname(File.dirname(File.dirname(__FILE__)))
+  target = File.join(root, "fixtures", path)
+  config_path = File.join(target, "config-#{config_name}.rb")
+  config_dest = File.join(target, "config.rb")
+  FileUtils.cp(config_path, config_dest)
+end
+
 Given /^a built app at "([^"]*)"$/ do |path|
   root = File.dirname(File.dirname(File.dirname(__FILE__)))
   target = File.join(root, "fixtures", path)
diff --git a/fixtures/clean-app/config-complications.rb b/fixtures/clean-app/config-complications.rb
new file mode 100644
index 00000000..828aa09f
--- /dev/null
+++ b/fixtures/clean-app/config-complications.rb
@@ -0,0 +1,11 @@
+page "/fake.html", :proxy => "/real.html", :layout => false
+
+ignore "/should_be_ignored.html"
+page "/should_be_ignored2.html", :ignore => true
+page "/target_ignore.html", :proxy => "/should_be_ignored3.html", :ignore => true
+
+%w(one two).each do |num|
+  page "/fake/#{num}.html", :proxy => "/real/index.html" do
+    @num = num
+  end
+end
\ No newline at end of file
diff --git a/fixtures/clean-app/config-empty.rb b/fixtures/clean-app/config-empty.rb
new file mode 100644
index 00000000..e69de29b
diff --git a/fixtures/clean-app/config.rb b/fixtures/clean-app/config.rb
new file mode 100644
index 00000000..828aa09f
--- /dev/null
+++ b/fixtures/clean-app/config.rb
@@ -0,0 +1,11 @@
+page "/fake.html", :proxy => "/real.html", :layout => false
+
+ignore "/should_be_ignored.html"
+page "/should_be_ignored2.html", :ignore => true
+page "/target_ignore.html", :proxy => "/should_be_ignored3.html", :ignore => true
+
+%w(one two).each do |num|
+  page "/fake/#{num}.html", :proxy => "/real/index.html" do
+    @num = num
+  end
+end
\ No newline at end of file
diff --git a/fixtures/clean-app/source/index.html.haml b/fixtures/clean-app/source/index.html.haml
new file mode 100755
index 00000000..6ef080c6
--- /dev/null
+++ b/fixtures/clean-app/source/index.html.haml
@@ -0,0 +1,6 @@
+%h1 Welcome
+
+:markdown
+  ## H2
+  
+  Paragraph
\ No newline at end of file
diff --git a/fixtures/clean-app/source/layout.haml b/fixtures/clean-app/source/layout.haml
new file mode 100644
index 00000000..e5a7a094
--- /dev/null
+++ b/fixtures/clean-app/source/layout.haml
@@ -0,0 +1,6 @@
+%html
+  %head
+    %title My Sample Site
+    / Comment in layout
+  %body
+    = yield
\ No newline at end of file
diff --git a/fixtures/clean-app/source/layouts/custom.haml b/fixtures/clean-app/source/layouts/custom.haml
new file mode 100755
index 00000000..87de0ed3
--- /dev/null
+++ b/fixtures/clean-app/source/layouts/custom.haml
@@ -0,0 +1,5 @@
+%html
+  %head
+    %title Custom Layout
+  %body
+    = yield
\ No newline at end of file
diff --git a/fixtures/clean-app/source/real.html b/fixtures/clean-app/source/real.html
new file mode 100644
index 00000000..cb312952
--- /dev/null
+++ b/fixtures/clean-app/source/real.html
@@ -0,0 +1 @@
+I am real
\ No newline at end of file
diff --git a/fixtures/clean-app/source/real/index.html.erb b/fixtures/clean-app/source/real/index.html.erb
new file mode 100644
index 00000000..190d84ec
--- /dev/null
+++ b/fixtures/clean-app/source/real/index.html.erb
@@ -0,0 +1,5 @@
+---
+layout: false
+---
+
+I am real: <%= @num %>
\ No newline at end of file
diff --git a/fixtures/clean-app/source/should_be_ignored.html b/fixtures/clean-app/source/should_be_ignored.html
new file mode 100644
index 00000000..fb81d5c0
--- /dev/null
+++ b/fixtures/clean-app/source/should_be_ignored.html
@@ -0,0 +1 @@
+<h1>Ignore me!</h1>
\ No newline at end of file
diff --git a/fixtures/clean-app/source/should_be_ignored2.html b/fixtures/clean-app/source/should_be_ignored2.html
new file mode 100644
index 00000000..0940fd7c
--- /dev/null
+++ b/fixtures/clean-app/source/should_be_ignored2.html
@@ -0,0 +1 @@
+<h1>Ignore me! 2</h1>
\ No newline at end of file
diff --git a/fixtures/clean-app/source/should_be_ignored3.html b/fixtures/clean-app/source/should_be_ignored3.html
new file mode 100644
index 00000000..98007c81
--- /dev/null
+++ b/fixtures/clean-app/source/should_be_ignored3.html
@@ -0,0 +1 @@
+<h1>Ignore me! 3</h1>
\ No newline at end of file
diff --git a/fixtures/clean-app/source/static.html b/fixtures/clean-app/source/static.html
new file mode 100755
index 00000000..7e50df4e
--- /dev/null
+++ b/fixtures/clean-app/source/static.html
@@ -0,0 +1 @@
+Static, no code!
\ No newline at end of file
diff --git a/lib/middleman/builder.rb b/lib/middleman/builder.rb
index ea79d53e..d6f6e4d8 100644
--- a/lib/middleman/builder.rb
+++ b/lib/middleman/builder.rb
@@ -211,7 +211,7 @@ module Middleman
 
       files.each { |f| base.remove_file f, config }
 
-      directories.sort_by! {|d| d.length }.reverse!
+      directories = directories.sort_by {|d| d.length }.reverse!
 
       directories.each do |d|
         base.remove_file(d, config) if directory_empty? d 
diff --git a/lib/middleman/version.rb b/lib/middleman/version.rb
index 81ca3880..8522387a 100644
--- a/lib/middleman/version.rb
+++ b/lib/middleman/version.rb
@@ -1,3 +1,3 @@
 module Middleman
-  VERSION = "2.0.12"
+  VERSION = "2.0.13"
 end