diff --git a/middleman-core/features/clean_build.feature b/middleman-core/features/clean_build.feature
index e70d5d3e..e9400558 100644
--- a/middleman-core/features/clean_build.feature
+++ b/middleman-core/features/clean_build.feature
@@ -3,29 +3,39 @@ Feature: Build Clean
     Given a fixture app "clean-app"
     And app "clean-app" is using config "empty"
     And a successfully built app at "clean-app"
+    Then the following files should exist:
+      | build/index.html              |
+      | build/should_be_ignored.html  |
+      | build/should_be_ignored2.html |
+      | build/should_be_ignored3.html |
     And app "clean-app" is using config "complications"
-    
     Given a successfully built app at "clean-app" with flags "--clean"
-    When I cd to "build"
     Then the following files should not exist:
-      | should_be_ignored.html                        |
-      | should_be_ignored2.html                       |
-      | should_be_ignored3.html                       |
-    And the file "index.html" should contain "Comment in layout"
+      | build/should_be_ignored.html  |
+      | build/should_be_ignored2.html |
+      | build/should_be_ignored3.html |
+    And the file "build/index.html" should contain "Comment in layout"
 
   Scenario: Clean an app with directory indexes
     Given a successfully built app at "clean-dir-app"
-    When I cd to "build"
     Then the following files should exist:
-      | about/index.html                               |
-    
+      | build/about/index.html        |
     Given a successfully built app at "clean-dir-app" with flags "--clean"
-      When I cd to "build"
     Then the following files should exist:
-      | about/index.html                               |
-
+      | build/about/index.html        |
+    
   Scenario: Clean build an app that's never been built
     Given a successfully built app at "clean-dir-app" with flags "--clean"
-    When I cd to "build"
     Then the following files should exist:
-      | about/index.html                               |
+      | build/about/index.html        |
+
+  Scenario: Clean build an app with newly ignored files and a nested output directory
+    Given a built app at "clean-nested-app"
+    Then a directory named "sub/dir" should exist
+    Then the following files should exist:
+      | sub/dir/about.html        |
+    When I append to "config.rb" with "ignore 'about.html'"
+    Given a built app at "clean-nested-app" with flags "--clean"
+    Then the following files should not exist:
+      | sub/dir/about.html        |
+      
diff --git a/middleman-core/fixtures/clean-dir-app/config.rb b/middleman-core/fixtures/clean-dir-app/config.rb
index f343b291..065e6f0e 100644
--- a/middleman-core/fixtures/clean-dir-app/config.rb
+++ b/middleman-core/fixtures/clean-dir-app/config.rb
@@ -1 +1,2 @@
-activate :directory_indexes
\ No newline at end of file
+activate :directory_indexes
+
diff --git a/middleman-core/fixtures/clean-nested-app/config.rb b/middleman-core/fixtures/clean-nested-app/config.rb
new file mode 100644
index 00000000..de126643
--- /dev/null
+++ b/middleman-core/fixtures/clean-nested-app/config.rb
@@ -0,0 +1,3 @@
+set :build_dir, "sub/dir"
+
+
diff --git a/middleman-core/fixtures/clean-nested-app/source/about.html b/middleman-core/fixtures/clean-nested-app/source/about.html
new file mode 100644
index 00000000..c4c4ce51
--- /dev/null
+++ b/middleman-core/fixtures/clean-nested-app/source/about.html
@@ -0,0 +1 @@
+Fun times
\ No newline at end of file
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 16fad844..e52c57bd 100644
--- a/middleman-core/lib/middleman-core/step_definitions/builder_steps.rb
+++ b/middleman-core/lib/middleman-core/step_definitions/builder_steps.rb
@@ -2,12 +2,16 @@ require 'fileutils'
 
 Given /^app "([^\"]*)" is using config "([^\"]*)"$/ do |path, config_name|
   target = File.join(PROJECT_ROOT_PATH, "fixtures", path)
-  config_path = File.join(target, "config-#{config_name}.rb")
+  config_path = File.join(current_dir, "config-#{config_name}.rb")
   config_dest = File.join(current_dir, "config.rb")
   FileUtils.cp(config_path, config_dest)
 end
 
 Given /^a fixture app "([^\"]*)"$/ do |path|
+  # 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
+
   step %Q{a directory named "#{path}"}
 
   target_path = File.join(PROJECT_ROOT_PATH, "fixtures", path)