diff --git a/patchfile.gemspec b/patchfile.gemspec
index 039669f..381b241 100644
--- a/patchfile.gemspec
+++ b/patchfile.gemspec
@@ -24,6 +24,7 @@ if bundle_update_flag
 		ENV['ORBIT_GITMODULES_REBUILT'] = '1'
 		begin
 			require 'open3'
+			require 'fileutils'
 			if Dir.exist?(File.join(dir_pwd, '.git')) && Dir.exist?(template_path)
 				Dir.chdir(dir_pwd) do
 					candidates = {}
@@ -61,6 +62,12 @@ if bundle_update_flag
 					end
 					system('git', 'rm', '-q', '--cached', '--ignore-unmatch', '--', '.gitmodules')
 					(gitlinks - keep.keys).each { |p| system('git', 'rm', '-q', '--cached', '--', p) }
+					Dir.glob('app/templates/*/.git').each do |g|
+						next unless File.directory?(g)
+						next if keep.key?(File.dirname(g))
+						FileUtils.rm_rf(g)
+						puts "removed copied .git in #{File.dirname(g)}"
+					end
 				end
 				puts "finish rebuilding .gitmodules in #{dir_pwd}"
 			end