diff --git a/bin/jekyll b/bin/jekyll
index 6d3767e6..2e631bbb 100755
--- a/bin/jekyll
+++ b/bin/jekyll
@@ -86,6 +86,20 @@ command :serve do |c|
 end
 alias_command :server, :serve
 
+command :doctor do |c|
+  c.syntax = 'jekyll doctor'
+  c.description = 'Search site and print specific deprecation warnings'
+
+  c.option '--config CONFIG_FILE[,CONFIG_FILE2,...]', Array, 'Custom configuration file'
+
+  c.action do |args, options|
+    options = normalize_options(options.__hash__)
+    options = Jekyll.configuration(options)
+    Jekyll::Commands::Doctor.process(options)
+  end
+end
+alias_command :hyde, :doctor
+
 command :import do |c|
   c.syntax = 'jekyll import <platform> [options]'
   c.description = 'Import your old blog to Jekyll'
diff --git a/lib/jekyll/commands/doctor.rb b/lib/jekyll/commands/doctor.rb
new file mode 100644
index 00000000..1819e0c7
--- /dev/null
+++ b/lib/jekyll/commands/doctor.rb
@@ -0,0 +1,29 @@
+module Jekyll
+  module Commands
+    class Doctor < Command
+      class << self
+        def process(options)
+          site = Jekyll::Site.new(options)
+          site.read
+
+          unless deprecated_relative_permalinks(site)
+            Jekyll::Logger.info "Your test results", "are in. Everything looks fine."
+          end
+        end
+
+        def deprecated_relative_permalinks(site)
+          contains_deprecated_pages = false
+          site.pages.each do |page|
+            if page.uses_relative_permalinks
+              Jekyll::Logger.warn "Deprecation:", "'#{page.path}' uses relative" +
+                                  " permalinks which will be deprecated in" +
+                                  " Jekyll v1.1 and beyond."
+              contains_deprecated_pages = true
+            end
+          end
+          contains_deprecated_pages
+        end
+      end
+    end
+  end
+end
diff --git a/lib/jekyll/configuration.rb b/lib/jekyll/configuration.rb
index 50dca537..0db188d3 100644
--- a/lib/jekyll/configuration.rb
+++ b/lib/jekyll/configuration.rb
@@ -19,7 +19,10 @@ module Jekyll
       'limit_posts'   => 0,
       'lsi'           => false,
       'future'        => true,           # remove and make true just default
-      'pygments'      => true,           # remove and make true just default
+      'pygments'      => true,
+
+      'relative_permalinks' => true,     # backwards-compatibility with < 1.0
+                                         # will be set to false once 1.1 hits
 
       'markdown'      => 'maruku',
       'permalink'     => 'date',
diff --git a/lib/jekyll/page.rb b/lib/jekyll/page.rb
index 730af13f..ef7c4d3a 100644
--- a/lib/jekyll/page.rb
+++ b/lib/jekyll/page.rb
@@ -64,7 +64,11 @@ module Jekyll
       return @url if @url
 
       url = if permalink
-        permalink
+        if site.config['relative_permalinks']
+          File.join(@dir, permalink)
+        else
+          permalink
+        end
       else
         {
           "path"       => @dir,
@@ -114,7 +118,14 @@ module Jekyll
       self.data.deep_merge({
         "url"        => self.url,
         "content"    => self.content,
-        "path"       => self.data['path'] || File.join(@dir, @name).sub(/\A\//, '') })
+        "path"       => self.data['path'] || path })
+    end
+
+    # The path to the source file
+    #
+    # Returns the path to the source file
+    def path
+      File.join(@dir, @name).sub(/\A\//, '')
     end
 
     # Obtain destination path.
@@ -144,5 +155,9 @@ module Jekyll
     def index?
       basename == 'index'
     end
+
+    def uses_relative_permalinks
+      permalink && @dir != "" && site.config['relative_permalinks']
+    end
   end
 end
diff --git a/lib/jekyll/site.rb b/lib/jekyll/site.rb
index d8a36e1b..16ccd7e9 100644
--- a/lib/jekyll/site.rb
+++ b/lib/jekyll/site.rb
@@ -231,6 +231,7 @@ module Jekyll
       end
 
       self.pages.each do |page|
+        relative_permalinks_deprecation_method if page.uses_relative_permalinks
         page.render(self.layouts, payload)
       end
 
@@ -418,5 +419,18 @@ module Jekyll
       post.categories.each { |c| self.categories[c] << post }
       post.tags.each { |c| self.tags[c] << post }
     end
+
+    def relative_permalinks_deprecation_method
+      if config['relative_permalinks'] && !@deprecated_relative_permalinks
+        $stderr.puts # Places newline after "Generating..."
+        Jekyll::Logger.warn "Deprecation:", "Starting in 1.1, permalinks for pages" +
+                                            " in subfolders must be relative to the" +
+                                            " site source directory, not the parent" +
+                                            " directory. Check http://jekyllrb.com/docs/upgrading/"+
+                                            " for more info."
+        $stderr.print Jekyll::Logger.formatted_topic("") + "..." # for "done."
+        @deprecated_relative_permalinks = true
+      end
+    end
   end
 end