diff --git a/features/permalinks.feature b/features/permalinks.feature
index e462627e..86c2c94e 100644
--- a/features/permalinks.feature
+++ b/features/permalinks.feature
@@ -143,14 +143,40 @@ Feature: Fancy permalinks
     And I should see "I am PHP" in "_site/2016/i-am-php.php"
     And I should see "I am also PHP" in "_site/i-am-also-php.php"
 
-  Scenario: Use the same permalink twice
+  Scenario: Using the same permalink twice
     Given I have a "cool.md" page with permalink "/amazing.html" that contains "I am cool"
     And I have an "awesome.md" page with permalink "/amazing.html" that contains "I am also awesome"
+    And I have an "amazing.html" file with content:
+      """
+      Hello World
+      I'm a static file
+      """
+    And I have a "_config.yml" file with content:
+      """
+      collections:
+        puppies:
+          output: true
+          permalink: /:collection/:year/:month/:day/:title:output_ext
+      """
+    And I have a _puppies directory
+    And I have the following documents under the puppies collection:
+      | title  | date       | content             |
+      | Rover  | 2009-03-27 | content for Rover.  |
+    And I have a _posts directory
+    And I have the following post:
+      | title     | date       | layout | category  | content                 |
+      | Rover     | 2009-03-27 | none   | puppies   | Luke, I am your father. |
     When I run jekyll build
     Then I should get a zero exit status
     And the _site directory should exist
-    And I should see "Conflict: The URL '" in the build output
-    And I should see "amazing.html' is the destination for the following pages: awesome.md, cool.md" in the build output
+    And I should see "Conflict: The following destination is shared by multiple files." in the build output
+    And I should see "_site/amazing.html" in the build output
+    And I should see "awesome.md" in the build output
+    And I should see "cool.md" in the build output
+    And I should see "amazing.html" in the build output
+    And I should see "_site/puppies/2009/03/27/rover.html" in the build output
+    And I should see "_posts/2009-03-27-rover.markdown" in the build output
+    And I should see "_puppies/rover.md" in the build output
 
   Scenario: Redirecting from an existing permalink
     Given I have a configuration file with "plugins" set to "[jekyll-redirect-from]"
@@ -166,5 +192,7 @@ Feature: Fancy permalinks
     When I run jekyll build
     Then I should get a zero exit status
     And the _site directory should exist
-    And I should not see "Conflict: The URL '" in the build output
-    And I should not see "offers/index.html' is the destination for the following pages: offers.html, redirect.html" in the build output
+    And I should not see "Conflict: The following destination is shared by multiple files." in the build output
+    And I should not see "_site/offers/index.html" in the build output
+    And I should not see "offers.html" in the build output
+    And I should not see "redirect.html" in the build output
diff --git a/lib/jekyll/commands/doctor.rb b/lib/jekyll/commands/doctor.rb
index 736f3616..aa99b66c 100644
--- a/lib/jekyll/commands/doctor.rb
+++ b/lib/jekyll/commands/doctor.rb
@@ -67,15 +67,16 @@ module Jekyll
 
         def conflicting_urls(site)
           conflicting_urls = false
-          urls = {}
-          urls = collect_urls(urls, site.pages, site.dest)
-          urls = collect_urls(urls, site.posts.docs, site.dest)
-          urls.each do |url, paths|
+          destination_map(site).each do |dest, paths|
             next unless paths.size > 1
 
             conflicting_urls = true
-            Jekyll.logger.warn "Conflict:", "The URL '#{url}' is the destination" \
-              " for the following pages: #{paths.join(", ")}"
+            Jekyll.logger.warn "Conflict:",
+                               "The following destination is shared by multiple files."
+            Jekyll.logger.warn "", "The written file may end up with unexpected contents."
+            Jekyll.logger.warn "", dest.to_s.cyan
+            paths.each { |path| Jekyll.logger.warn "", " - #{path}" }
+            Jekyll.logger.warn ""
           end
           conflicting_urls
         end
@@ -122,18 +123,15 @@ module Jekyll
 
         private
 
-        def collect_urls(urls, things, destination)
-          things.each do |thing|
-            next if allow_used_permalink?(thing)
+        def destination_map(site)
+          {}.tap do |result|
+            site.each_site_file do |thing|
+              next if allow_used_permalink?(thing)
 
-            dest = thing.destination(destination)
-            if urls[dest]
-              urls[dest] << thing.path
-            else
-              urls[dest] = [thing.path]
+              dest_path = thing.destination(site.dest)
+              (result[dest_path] ||= []) << thing.path
             end
           end
-          urls
         end
 
         def allow_used_permalink?(item)