diff --git a/lib/backup/repository.rb b/lib/backup/repository.rb
index 62a510f2acc..c5e3d049fd7 100644
--- a/lib/backup/repository.rb
+++ b/lib/backup/repository.rb
@@ -71,7 +71,7 @@ module Backup
 
       print 'Put GitLab hooks in repositories dirs'.yellow
       gitlab_shell_user_home = File.expand_path("~#{Gitlab.config.gitlab_shell.ssh_user}")
-      if system("#{gitlab_shell_user_home}/gitlab-shell/support/rewrite-hooks.sh")
+      if system("#{gitlab_shell_user_home}/gitlab-shell/support/rewrite-hooks.sh #{Gitlab.config.gitlab_shell.repos_path}")
         puts " [DONE]".green
       else
         puts " [FAILED]".red
diff --git a/lib/tasks/gitlab/backup.rake b/lib/tasks/gitlab/backup.rake
index 65d99d1aea3..920d29a444e 100644
--- a/lib/tasks/gitlab/backup.rake
+++ b/lib/tasks/gitlab/backup.rake
@@ -90,6 +90,9 @@ namespace :gitlab do
       settings = YAML.load_file("backup_information.yml")
       ENV["VERSION"] = "#{settings[:db_version]}" if settings[:db_version].to_i > 0
 
+      # backups directory is not always sub of Rails root and able to execute the git rev-parse below
+      Dir.chdir(Rails.root)
+
       # restoring mismatching backups can lead to unexpected problems
       if settings[:gitlab_version] != %x{git rev-parse HEAD}.gsub(/\n/,"")
         puts "GitLab version mismatch:".red
diff --git a/lib/tasks/gitlab/shell.rake b/lib/tasks/gitlab/shell.rake
index ec5451dd47c..11d4eacaa69 100644
--- a/lib/tasks/gitlab/shell.rake
+++ b/lib/tasks/gitlab/shell.rake
@@ -26,10 +26,12 @@ namespace :gitlab do
     warn_user_is_not_gitlab
 
     gitlab_shell_authorized_keys = File.join(File.expand_path("~#{Gitlab.config.gitlab_shell.ssh_user}"),'.ssh/authorized_keys')
-    puts "This will rebuild an authorized_keys file."
-    puts "You will lose any data stored in #{gitlab_shell_authorized_keys}."
-    ask_to_continue
-    puts ""
+    unless ENV['force'] == 'yes'
+      puts "This will rebuild an authorized_keys file."
+      puts "You will lose any data stored in #{gitlab_shell_authorized_keys}."
+      ask_to_continue
+      puts ""
+    end
 
     system("echo '# Managed by gitlab-shell' > #{gitlab_shell_authorized_keys}")