diff --git a/debian/gitlab.links b/debian/gitlab.links
index a459f4fb82..1e97355d3e 100644
--- a/debian/gitlab.links
+++ b/debian/gitlab.links
@@ -2,10 +2,7 @@ var/lib/gitlab/uploads usr/share/gitlab/public/uploads
 var/log/gitlab usr/share/gitlab/log
 run/gitlab usr/share/gitlab/tmp/pids
 run/gitlab usr/share/gitlab/tmp/sockets
-etc/gitlab/unicorn.rb usr/share/gitlab/config/unicorn.rb
-etc/gitlab/database.yml usr/share/gitlab/config/database.yml
-etc/gitlab/gitlab.yml usr/share/gitlab/config/gitlab.yml
-etc/gitlab/resque.yml usr/share/gitlab/config/resque.yml
+etc/gitlab usr/share/gitlab/config
 usr/share/javascript/jquery-history/jquery.history.min.js usr/share/gitlab/vendor/assets/javascripts/jquery.history.js
 usr/share/javascript/jquery-cookie/jquery.cookie.min.js usr/share/gitlab/vendor/assets/javascripts/jquery.cookie.js
 usr/share/javascript/jquery-nicescroll/jquery.nicescroll.min.js usr/share/gitlab/vendor/assets/javascripts/jquery.nicescroll.min.js
diff --git a/debian/install b/debian/install
index 28c5f1080a..2fcdef99cb 100644
--- a/debian/install
+++ b/debian/install
@@ -6,7 +6,7 @@ debian/conf/resque.yml etc/gitlab
 debian/conf/gitlab-debian.conf etc/gitlab
 debian/conf/*.target lib/systemd/system
 debian/conf/*.service lib/systemd/system
-debian/conf/smtp_settings.rb usr/share/gitlab/config/initializers
+debian/conf/smtp_settings.rb etc/gitlab/initializers
 debian/conf/tmpfiles.d/gitlab.conf usr/lib/tmpfiles.d
 debian/adduser.sh usr/lib/gitlab/scripts
 debian/grantpriv.sh usr/lib/gitlab/scripts
@@ -14,7 +14,7 @@ debian/rake-tasks.sh usr/lib/gitlab/scripts
 app usr/share/gitlab
 bin usr/share/gitlab
 CHANGELOG usr/share/gitlab
-config usr/share/gitlab
+config/* etc/gitlab
 config.ru usr/share/gitlab
 CONTRIBUTING.md usr/share/gitlab
 db usr/share/gitlab
@@ -27,7 +27,6 @@ Gemfile usr/share/gitlab
 GITLAB_SHELL_VERSION usr/share/gitlab
 GITLAB_WORKHORSE_VERSION usr/share/gitlab
 lib usr/share/gitlab
-log usr/share/gitlab
 MAINTENANCE.md usr/share/gitlab
 PROCESS.md usr/share/gitlab
 Procfile usr/share/gitlab
diff --git a/debian/rules b/debian/rules
index 87103d5c88..21b31613fd 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,6 +13,7 @@ override_dh_install:
 	dh_systemd_start gitlab.target
 	# Make sure we are installing all required files in debian/install
 	sh debian/upstream-file-count-check.sh
+	rm -rf debian/gitlab/usr/share/gitlab/tmp/*
 
 override_dh_installinit:
 	dh_installinit --no-start
diff --git a/debian/upstream-file-count-check.sh b/debian/upstream-file-count-check.sh
index ccd31f2faa..e0a03aa88a 100644
--- a/debian/upstream-file-count-check.sh
+++ b/debian/upstream-file-count-check.sh
@@ -1,9 +1,9 @@
 ucount=$(ls -1 | wc -l)
 dcount=$(cat debian/install |cut -d' ' -f1|grep -v debian |wc -l)
-ignored=5
+ignored=6
 if ! [ $(echo "$ucount" - "$dcount"|bc) -eq $ignored ]; then
   echo "Found new files added by upstream and not added to debian/install"
-  echo "Add them to debian/install or adjust 'ignored=5'"
+  echo "Add them to debian/install or adjust 'ignored=${ignored}'"
   echo "in debian/upstream-file-count-check.sh as required"
   exit 1
 fi