diff --git a/lib/homesick.rb b/lib/homesick.rb
index b90de36..6b28ef5 100644
--- a/lib/homesick.rb
+++ b/lib/homesick.rb
@@ -153,33 +153,18 @@ class Homesick < Thor
 
     # Are we already tracking this or anything inside it?
     target = Pathname.new(castle_path.join(file.basename))
-
     if target.exist?
-
       if absolute_path.directory?
-        child_files = absolute_path.children
-        child_files.each do |child|
-
-          if target.join(child.basename).exist?
-            next
-          end
-
-          mv child, target
-        end
+        move_dir_contents(target, absolute_path)
         absolute_path.rmtree
-        manifest = Pathname.new(repos_dir.join(castle, '.manifest'))
-        if manifest.exist?
-          lines = IO.readlines(manifest).delete_if { |line| line == "#{relative_dir + file.basename}\n" }
-          File.open(manifest, 'w') { |manfile| manfile.puts lines }
-        end
+        manifest_remove(castle, relative_dir + file.basename)
 
-      elsif absolute_path.mtime > target.mtime && !absolute_path.symlink?
+      elsif more_recent? absolute_path, target
         target.delete
         mv absolute_path, castle_path
       else
-        shell.say_status(:track, "#{target} already exists, and is more recent than #{file}. Run 'homesick SYMLINK CASTLE' to create symlinks.")
+        shell.say_status(:track, "#{target} already exists, and is more recent than #{file}. Run 'homesick SYMLINK CASTLE' to create symlinks.", :blue) unless options[:quiet]
       end
-
     else
       mv absolute_path, castle_path
     end
@@ -194,14 +179,10 @@ class Homesick < Thor
       git_add absolute_path
     end
 
-    # are we tracking something nested? Add the parent dir to the manifest unless its already listed
+    # are we tracking something nested? Add the parent dir to the manifest
     unless relative_dir.eql?(Pathname.new('.'))
-      manifest_path = Pathname.new(repos_dir.join(castle, '.manifest'))
-      File.open(manifest_path, 'a+') do |manifest|
-        manifest.puts relative_dir unless manifest.readlines.inject(false) { |memo, line| line.eql?("#{relative_dir.to_s}\n") || memo }
-      end
+      manifest_add(castle, relative_dir)
     end
-
   end
 
   desc "list", "List cloned castles"
@@ -310,4 +291,54 @@ class Homesick < Thor
       git_push
     end
   end
+
+  def manifest(castle)
+    Pathname.new(repos_dir.join(castle, '.manifest'))
+  end
+
+  def manifest_add(castle, path)
+    manifest_path = manifest(castle)
+    File.open(manifest_path, 'a+') do |manifest|
+      manifest.puts path unless manifest.readlines.inject(false) { |memo, line| line.eql?("#{path.to_s}\n") || memo }
+    end
+
+    inside castle_dir(castle) do
+      git_add manifest_path
+    end
+  end
+
+  def manifest_remove(castle, path)
+    manifest_file = manifest(castle)
+    if manifest_file.exist?
+      lines = IO.readlines(manifest_file).delete_if { |line| line == "#{path}\n" }
+      File.open(manifest_file, 'w') { |manfile| manfile.puts lines }
+    end
+
+    inside castle_dir(castle) do
+      git_add manifest_file
+    end
+  end
+
+  def move_dir_contents(target, dir_path)
+    child_files = dir_path.children
+    child_files.each do |child|
+
+      target_path = target.join(child.basename)
+      if target_path.exist?
+        if more_recent?(child, target_path) && target.file?
+          target_path.delete
+          mv child, target
+        end
+        next
+      end
+
+      mv child, target
+    end
+  end
+
+  def more_recent?(first, second)
+    first_p = Pathname.new(first)
+    second_p = Pathname.new(second)
+    first_p.mtime > second_p.mtime && !first_p.symlink?
+  end
 end