[XCConfigIntegrator] Assign xcconfigs to all targets being integrated.

Fixes #2752.

CHANGELOG.md

@@ -81,6 +81,12 @@ To install or update CocoaPods see this [guide](http://docs.cocoapods.org/guides
 
 ##### Bug Fixes
 
+* `XCConfigIntegrator` Fixes an issue where not all targets that need
+  integration where being integrated, but were getting incorrect warnings about
+  the user having specified a custom base configuration.  
+  [Eloy Durán](https://github.com/alloy)
+  [2752](https://github.com/CocoaPods/CocoaPods/issues/2752)
+
 * Do not try to clone spec-repos in `/`.  
   [Eloy Durán](https://github.com/alloy)
   [#2723](https://github.com/CocoaPods/CocoaPods/issues/2723)

lib/cocoapods/installer/user_project_integrator/target_integrator/xcconfig_integrator.rb

@@ -83,22 +83,26 @@ module Pod
           # @param  [Xcodeproj::XCBuildConfiguration] config
           #         The build configuration.
           #
+          # @return [Boolean] Indicates whether or not any changes were made.
+          #
           def self.set_target_xcconfig(pod_bundle, target, config)
             path = pod_bundle.xcconfig_relative_path(config.name)
             group = config.project['Pods'] || config.project.new_group('Pods')
             file_ref = group.files.find { |f| f.path == path }
-            if config.base_configuration_reference != file_ref
+            if config.base_configuration_reference &&
+                config.base_configuration_reference != file_ref
               UI.warn 'CocoaPods did not set the base configuration of your ' \
               'project because your project already has a custom ' \
               'config set. In order for CocoaPods integration to work at ' \
               'all, please either set the base configurations of the target ' \
               "`#{target.name}` to `#{path}` or include the `#{path}` in your " \
               'build configuration.'
-              false
-            elsif !file_ref
+            elsif config.base_configuration_reference.nil? || file_ref.nil?
               file_ref ||= group.new_file(path)
               config.base_configuration_reference = file_ref
+              return true
             end
+            false
           end
 
           private

spec/unit/installer/user_project_integrator/target_integrator/xcconfig_integrator_spec.rb

@@ -62,5 +62,15 @@ module Pod
       UI.warnings.should.match /not set.*base configuration/
     end
 
+    it 'sets the Pods xcconfig as the base config on other targets if no base has been set yet' do
+      target = @project.targets[1]
+      XCConfigIntegrator.integrate(@pod_bundle, [@target, target])
+      target.build_configurations.each do |config|
+        config.base_configuration_reference.path.should.include 'Pods'
+      end
+
+      UI.warnings.should.not.match /not set.*base configuration/
+    end
+
   end
 end