Homagah it all renders I think.

features/collections.feature

@@ -7,7 +7,7 @@ Feature: Collections
     Given I have an "index.html" page that contains "Collections: {{ site.collections }}"
     And I have fixture collections
     And I have a configuration file with "collections" set to "['methods']"
-    When I debug jekyll
+    When I run jekyll
     Then the _site directory should exist
     And I should see "Collections: {\"methods\"=>#<Jekyll::Collection @label=methods docs=\[#<Jekyll::Document _methods/configuration.md collection=methods>, #<Jekyll::Document _methods/sanitized_path.md collection=methods>, #<Jekyll::Document _methods/site/generate.md collection=methods>, #<Jekyll::Document _methods/site/initialize.md collection=methods>, #<Jekyll::Document _methods/um_hi.md collection=methods>\]>}" in "_site/index.html"
 
@@ -21,4 +21,18 @@ Feature: Collections
     When I run jekyll
     Then the _site directory should exist
     And I should see "Collections: methods" in "_site/index.html"
-    And I should see "Whatever: foo.bar" in "_site/methods/configuration.html"
+    And I should see "<p>Whatever: foo.bar</p>" in "_site/methods/configuration.html"
+
+  Scenario: Rendered document in a layout
+    Given I have an "index.html" page that contains "Collections: {{ site.collections.methods.label }}"
+    And I have a default layout that contains "<div class='title'>Tom Preston-Werner</div> {{content}}"
+    And I have fixture collections
+    And I have a configuration file with:
+      | key         | value       |
+      | collections | ['methods'] |
+      | render      | ['methods'] |
+    When I run jekyll
+    Then the _site directory should exist
+    And I should see "Collections: methods" in "_site/index.html"
+    And I should see "<p>Run your generators! default</p>" in "_site/methods/site/generate.html"
+    And I should see "<div class='title'>Tom Preston-Werner</div>" in "_site/methods/site/generate.html"

lib/jekyll/renderer.rb

@@ -31,6 +31,7 @@ module Jekyll
       payload = Utils.deep_merge_hashes({
         "page" => document.to_liquid
       }, site.site_payload)
+
       info    = {
         filters:   [Jekyll::Filters],
         registers: { :site => site, :page => payload['page'] }
@@ -117,7 +118,7 @@ module Jekyll
           File.join(site.config['layouts'], layout.name)
         )
 
-        if layout = layouts[layout.data["layout"]]
+        if layout = site.layouts[layout.data["layout"]]
           if used.include?(layout)
             layout = nil # avoid recursive chain
           else

lib/jekyll/site.rb

@@ -92,7 +92,7 @@ module Jekyll
       end
     end
 
-    def render
+    def to_render
       config['render'] || Array.new
     end
 
@@ -197,9 +197,7 @@ module Jekyll
     #
     # Returns nothing.
     def read_collections
-      if collections
-        collections.each { |_, collection| collection.read }
-      end
+      collections.each { |_, collection| collection.read }
     end
 
     # Run each of the Generators.
@@ -217,11 +215,9 @@ module Jekyll
     def render
       relative_permalinks_deprecation_method
 
-      if collections
-        collections.each do |label, collection|
-          collection.docs.each do |document|
-            document.output = Jekyll::Renderer.new(self, document).run
-          end
+      collections.each do |label, collection|
+        collection.docs.each do |document|
+          document.output = Jekyll::Renderer.new(self, document).run
         end
       end
 
@@ -389,11 +385,9 @@ module Jekyll
 
     def documents
       docs = Set.new
-      if collections
-        collections.each do |label, coll|
-          if render.include?(label)
-            docs = docs.merge(coll.docs)
-          end
+      collections.each do |label, coll|
+        if to_render.include?(label)
+          docs = docs.merge(coll.docs)
         end
       end
       docs

test/source/_methods/site/generate.md

@@ -1,5 +1,6 @@
 ---
 title: "Site#generate"
+layout: default
 ---
 
-Run your generators!
+Run your generators! {{ page.layout }}

test/test_collections.rb

@@ -12,7 +12,7 @@ class TestCollections < Test::Unit::TestCase
     end
 
     should "not contain any collections" do
-      assert_nil @site.collections
+      assert_equal @site.collections, Hash.new
     end
   end
 

test/test_document.rb

@@ -2,7 +2,7 @@ require 'helper'
 
 class TestDocument < Test::Unit::TestCase
 
-  context "" do
+  context "a document in a collection" do
     setup do
       @site = Site.new(Jekyll.configuration({
         "collections" => ["methods"],
@@ -42,4 +42,7 @@ class TestDocument < Test::Unit::TestCase
 
   end
 
+  context " a document part of a rendered collection" do
+  end
+
 end