Addressed comments from @irrationalfab:

- simplified collection of unique prefix_header_contents
- reduced sub specs in spec from 4 to 2
Removed inline documentation and added @notes and @todos.
Added entry to Changelog.

CHANGELOG.md

@@ -8,6 +8,11 @@ To install or update CocoaPods see this [guide](http://docs.cocoapods.org/guides
 
 ##### Enhancements
 
+* Generated prefix header file will now have unique prefix_header_contents for
+  Pods with subspecs.
+  [Luis de la Rosa](https://github.com/luisdelarosa)
+  [#1449](https://github.com/CocoaPods/CocoaPods/issues/1449)
+  
 * Add version to output of `pod list`
   [Stefan Damm](https://github.com/StefanDamm)
   [Robert Zuber](https://github.com/z00b)

lib/cocoapods/generator/prefix_header.rb

@@ -40,9 +40,12 @@ module Pod
       #         added to the top of the prefix header. For OS X `Cocoa/Cocoa.h`
       #         is imported.
       #
+      # @note   Only unique prefix_header_contents are added to the prefix header.
+      #
       # @return [String]
       #
       # @todo   Subspecs can specify prefix header information too.
+      # @todo   Check to see if we have a similar duplication issue with file_accessor.prefix_header.
       #
       def generate
         result =  "#ifdef __OBJC__\n"
@@ -53,23 +56,17 @@ module Pod
           result << %|\n#import "#{import}"|
         end
 
-        # collect all the prefix_header_contents and only get the unique contents so that we don't have duplicates
-        all_prefix_header_contents = file_accessors.collect do |file_accessor|
+        unique_prefix_header_contents = file_accessors.collect do |file_accessor|
           file_accessor.spec_consumer.prefix_header_contents
-        end
-        unique_and_non_nil_prefix_header_contents = all_prefix_header_contents.compact.uniq
-
-        # newline to separate prefix_headers and prefix_header_contents from the imports
+        end.compact.uniq
+        
         result << "\n"
         
-        # output those unique prefix_header_contents
-        unique_and_non_nil_prefix_header_contents.each do |prefix_header_contents|
+        unique_prefix_header_contents.each do |prefix_header_contents|
           result << prefix_header_contents
           result << "\n"
         end
         
-        # output the prefix_headers
-        # todo check to see if we have a similar duplicating issue with these
         file_accessors.each do |file_accessor|
           if prefix_header = file_accessor.prefix_header
             result << Pathname(prefix_header).read

spec/unit/generator/prefix_header_spec.rb

@@ -21,10 +21,10 @@ module Pod
       EOS
     end
 
+    # @note Declaring a subspec was found in issue #1449 to generate duplicates of the prefix_header_contents
     it "does not duplicate the contents of the specification's prefix header when a subspec is declared" do
       @spec.prefix_header_contents = '#import "BlocksKit.h"'
       @spec.prefix_header_file = nil
-      # Declaring a subspec was found in issue #1449 to generate duplicates of the prefix_header_contents
       @spec.subspec 'UI' do |subspec|
         subspec.source_files = 'Source/UI/*.{h,m}'
       end
@@ -37,10 +37,10 @@ module Pod
       EOS
     end
 
+    # @note Declaring a subspec was found in issue #1449 to generate duplicates of the prefix_header_contents
     it "does not duplicate the contents of the specification's prefix header when a subspec is declared multiple times" do
       @spec.prefix_header_contents = '#import "BlocksKit.h"'
       @spec.prefix_header_file = nil
-      # Declaring a subspec was found in issue #1449 to generate duplicates of the prefix_header_contents
       @spec.subspec 'UI' do |su|
           su.source_files = 'Source/UI/*.{h,m}'
       end
@@ -48,15 +48,7 @@ module Pod
       @spec.subspec 'Helpers' do |sh|
           sh.source_files = 'Source/Helpers/*.{h,m}'
       end
-    
-      @spec.subspec 'Additions' do |sa|
-          sa.source_files = 'Source/Additions/*.{h,m}'
-      end
-    
-      @spec.subspec 'Dashboard' do |sd|
-          sd.source_files = 'Source/Dashboard/*.{h,m}'
-          sd.resources    = 'Source/Dashboard/*.{xib}'
-      end
+
       @gen.generate.should == <<-EOS.strip_heredoc
       #ifdef __OBJC__
       #import <UIKit/UIKit.h>