[Install/Update] Forgot to stage two files :-).

lib/cocoapods/command/update.rb

@@ -35,10 +35,10 @@ def run
           raise Informative, "No `Podfile.lock' found in the current working directory, run `pod install'."
         end
 
-        # if @update_repo
-        #   print_title 'Updating Spec Repositories', true
-        #   Repo.new(ARGV.new(["update"])).run
-        # end
+        if @update_repo
+          print_title 'Updating Spec Repositories', true
+          Repo.new(ARGV.new(["update"])).run
+        end
 
         sandbox = Sandbox.new(config.project_pods_root)
         resolver = Resolver.new(podfile, lockfile, sandbox)

lib/cocoapods/resolver.rb

@@ -68,10 +68,13 @@ def resolve
         end
       end
 
-      lock_dependencies_version unless update_mode
       @cached_specs = {}
       @targets_and_specs = {}
       @external_pods = []
+      @dependencies_podfile_incompatible = []
+      @removed_pods = []
+
+      lock_dependencies_version unless update_mode
 
       @podfile.target_definitions.values.each do |target_definition|
         puts "\nResolving dependencies for target `#{target_definition.name}' (#{target_definition.platform}):".green if config.verbose?
@@ -161,8 +164,6 @@ def removed_pods
     #
     def lock_dependencies_version
       return unless lockfile
-      @dependencies_podfile_incompatible = []
-      @removed_pods = []
 
       puts "\nFinding updated or removed pods:".green if config.verbose?
       podfile_deps_names = podfile_dependencies.map(&:name)