[UserInterface] Print warnings at the end of the execution

- This also fixes and issue where the order of the warnings was not in
  sync with STDOUT.

lib/cocoapods/command.rb

@@ -34,6 +34,7 @@ module Pod
         exit!(0)
       end
       super(argv)
+      UI.print_warnings
     end
 
     def self.report_error(error)

lib/cocoapods/installer.rb

@@ -84,7 +84,6 @@ module Pod
       resolve_dependencies
       download_dependencies
       generate_pods_project
-
       integrate_user_project if config.integrate_targets?
     end
 

lib/cocoapods/user_interface.rb

@@ -13,12 +13,15 @@ module Pod
     @title_level       =  0
     @indentation_level =  2
     @treat_titles_as_messages = false
+    @warnings = []
 
     class << self
 
       include Config::Mixin
 
-      attr_accessor :indentation_level, :title_level
+      attr_accessor :indentation_level
+      attr_accessor :title_level
+      attr_accessor :warnings
 
       # Prints a title taking an optional verbose prefix and
       # a relative indentation valid for the UI action in the passed
@@ -133,8 +136,8 @@ module Pod
         puts("\n[!] #{message}".green)
       end
 
-      # Prints an important warning to the user optionally followed by actions
-      # that the user should take.
+      # Stores important warning to the user optionally followed by actions
+      # that the user should take. To print them use #{print_warnings}
       #
       # @param [String]  message The message to print.
       # @param [Array]   actions The actions that the user should take.
@@ -142,11 +145,23 @@ module Pod
       # return [void]
       #
       def warn(message, actions = [], verbose_only = false)
+        warnings << { :message => message, :actions => actions }
+      end
+
+      # Prints the stored warnings. This method is intended to be called at the
+      # end of the execution of the binary.
+      #
+      # @return [void]
+      #
+      def print_warnings
         return if config.silent? && verbose_only
-        STDERR.puts("\n[!] #{message}".yellow)
-        actions.each do |action|
-          indented = wrap_string(action, "    - ")
-          puts(indented)
+        STDOUT.flush
+        warnings.each do |warning|
+          STDERR.puts("\n[!] #{warning[:message]}".yellow)
+          warning[:actions].each do |action|
+            indented = wrap_string(action, "    - ")
+            puts(indented)
+          end
         end
       end
 

spec/integration/install_podfile_callbacks/after/execution_output.txt

@@ -32,8 +32,6 @@ Downloading dependencies
 
 Generating Pods project
   - Creating Pods project
-
-[!] Podfile#config is deprecated. The config is accessible from the parameter passed to the hooks
   - Running pre install hooks
     - Podfile
   - Adding source files to Pods project
@@ -60,3 +58,5 @@ Integrating client projects
 [!] From now on use `SampleApp.xcworkspace`.
 
 Integrating `libPods.a` into target `SampleApp` of project `SampleApp.xcodeproj`.
+
+[!] Podfile#config is deprecated. The config is accessible from the parameter passed to the hooks