--- a/Support/app/controllers/branch_controller.rb
+++ b/Support/app/controllers/branch_controller.rb
@@ -75,14 +75,13 @@ class BranchController < ApplicationController
     end
     
     puts "<h2>Merging #{@merge_from_branch} into #{@c_branch}</h2>"
-    flush
     
     with_submodule_cacheing do
       @result = git.merge(@merge_from_branch)
       render "merge"
-      true
     end
     rescan_project
+    true
   end
     
   protected

--- a/Support/app/helpers/submodule_helper.rb
+++ b/Support/app/helpers/submodule_helper.rb
@@ -1,5 +1,6 @@
 module SubmoduleHelper
   module Update
+    flush
     def with_submodule_cacheing(&block)
       git.submodule.all.each { |m| m.cache }
       begin

--- a/Support/lib/commands/submodule.rb
+++ b/Support/lib/commands/submodule.rb
@@ -68,7 +68,8 @@ class SCM::Git::Submodule < SCM::Git::CommandProxyBase
     end
     
     def restore
-      if ! File.exist?(abs_path) && File.exist?(abs_cache_path)
+      if File.exist?(abs_cache_path) && ! Dir.has_a_file?(abs_path)
+        FileUtils.rm_rf(abs_path)
         FileUtils.mkdir_p(File.dirname(abs_path))
         FileUtils.mv(abs_cache_path, abs_path, :force => true)
       end
@@ -76,3 +77,8 @@ class SCM::Git::Submodule < SCM::Git::CommandProxyBase
   end
 end
 
+class Dir
+  def self.has_a_file?(abs_path)
+    Dir[abs_path + "/**/*"].any? {|f| File.file?(f) }
+  end
+end
\ No newline at end of file

--- a/Support/lib/git.rb
+++ b/Support/lib/git.rb
@@ -341,6 +341,13 @@ module SCM
       end
     end
     
+    def logger
+      @logger ||= 
+        begin
+          require 'logger'
+          Logger.new(ROOT + "/git.log")
+        end
+    end
     
     protected
       def get_range_arg(options, keys = [:revisions, :branches, :tags])

--- a/Support/spec/lib/commands/submodule_spec.rb
+++ b/Support/spec/lib/commands/submodule_spec.rb
@@ -66,7 +66,7 @@ EOF
     end
     
     it "should restore when submodule isn't in working copy" do
-      File.should_receive(:exist?).with(@submodule.abs_path).and_return(false)
+      Dir.should_receive(:has_a_file?).with(@submodule.abs_path).and_return(false)
       File.should_receive(:exist?).with(@submodule.abs_cache_path).and_return(true)
       FileUtils.should_receive(:mkdir_p).with(File.dirname(@submodule.abs_path))
       FileUtils.should_receive(:mv).with(@submodule.abs_cache_path, @submodule.abs_path, :force => true)