diff --git a/data/hooks/backup/05-conf_ldap b/data/hooks/backup/05-conf_ldap
old mode 100755
new mode 100644
diff --git a/data/hooks/backup/08-conf_ssh b/data/hooks/backup/08-conf_ssh
deleted file mode 100755
index ee976080c..000000000
--- a/data/hooks/backup/08-conf_ssh
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/bin/bash
-
-# Exit hook on subcommand error or unset variable
-set -eu
-
-# Source YNH helpers
-source /usr/share/yunohost/helpers
-
-# Backup destination
-backup_dir="${1}/conf/ssh"
-
-# Backup the configuration
-if [ -d /etc/ssh/ ]; then
-    ynh_backup "/etc/ssh" "$backup_dir"
-else
-    echo "SSH is not installed"
-fi
diff --git a/data/hooks/backup/14-conf_ssowat b/data/hooks/backup/14-conf_ssowat
deleted file mode 100755
index d4db72493..000000000
--- a/data/hooks/backup/14-conf_ssowat
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-# Exit hook on subcommand error or unset variable
-set -eu
-
-# Source YNH helpers
-source /usr/share/yunohost/helpers
-
-# Backup destination
-backup_dir="${1}/conf/ssowat"
-
-# Backup the configuration
-ynh_backup "/etc/ssowat" "$backup_dir"
diff --git a/data/hooks/backup/17-data_home b/data/hooks/backup/17-data_home
old mode 100755
new mode 100644
diff --git a/data/hooks/backup/20-conf_ynh_firewall b/data/hooks/backup/20-conf_ynh_firewall
deleted file mode 100755
index 98be3eb09..000000000
--- a/data/hooks/backup/20-conf_ynh_firewall
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-# Exit hook on subcommand error or unset variable
-set -eu
-
-# Source YNH helpers
-source /usr/share/yunohost/helpers
-
-# Backup destination
-backup_dir="${1}/conf/ynh/firewall"
-
-# Backup the configuration
-ynh_backup "/etc/yunohost/firewall.yml" "${backup_dir}/firewall.yml"
diff --git a/data/hooks/backup/21-conf_ynh_certs b/data/hooks/backup/21-conf_ynh_certs
old mode 100755
new mode 100644
diff --git a/data/hooks/backup/22-conf_mail b/data/hooks/backup/22-conf_mail
deleted file mode 100644
index b604d8aa8..000000000
--- a/data/hooks/backup/22-conf_mail
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-source /usr/share/yunohost/helpers
-ynh_abort_if_errors
-YNH_CWD="${YNH_BACKUP_DIR%/}/conf/dkim"
-mkdir -p "$YNH_CWD"
-cd "$YNH_CWD"
-
-ynh_backup --src_path="/etc/dkim"
diff --git a/data/hooks/backup/23-data_mail b/data/hooks/backup/23-data_mail
old mode 100755
new mode 100644
diff --git a/data/hooks/backup/26-conf_xmpp b/data/hooks/backup/26-conf_xmpp
deleted file mode 100755
index b55ad2bfc..000000000
--- a/data/hooks/backup/26-conf_xmpp
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/bash
-
-# Exit hook on subcommand error or unset variable
-set -eu
-
-# Source YNH helpers
-source /usr/share/yunohost/helpers
-
-# Backup destination
-backup_dir="${1}/conf/xmpp"
-
-# Backup the configuration
-ynh_backup /etc/metronome "${backup_dir}/etc"
-ynh_backup /var/lib/metronome "${backup_dir}/var"
diff --git a/data/hooks/backup/27-data_xmpp b/data/hooks/backup/27-data_xmpp
new file mode 100644
index 000000000..2cd93e02b
--- /dev/null
+++ b/data/hooks/backup/27-data_xmpp
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+# Exit hook on subcommand error or unset variable
+set -eu
+
+# Source YNH helpers
+source /usr/share/yunohost/helpers
+
+# Backup destination
+backup_dir="${1}/data/xmpp"
+
+ynh_backup /var/lib/metronome "${backup_dir}/var_lib_metronome"
+ynh_backup /var/xmpp-upload/ "${backup_dir}/var_xmpp-upload"
diff --git a/data/hooks/backup/29-conf_nginx b/data/hooks/backup/29-conf_nginx
deleted file mode 100755
index 81e145e24..000000000
--- a/data/hooks/backup/29-conf_nginx
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-# Exit hook on subcommand error or unset variable
-set -eu
-
-# Source YNH helpers
-source /usr/share/yunohost/helpers
-
-# Backup destination
-backup_dir="${1}/conf/nginx"
-
-# Backup the configuration
-ynh_backup "/etc/nginx/conf.d" "$backup_dir"
diff --git a/data/hooks/backup/40-conf_ynh_currenthost b/data/hooks/backup/40-conf_ynh_currenthost
deleted file mode 100755
index 6a98fd0d2..000000000
--- a/data/hooks/backup/40-conf_ynh_currenthost
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-# Exit hook on subcommand error or unset variable
-set -eu
-
-# Source YNH helpers
-source /usr/share/yunohost/helpers
-
-# Backup destination
-backup_dir="${1}/conf/ynh"
-
-# Backup the configuration
-ynh_backup "/etc/yunohost/current_host" "${backup_dir}/current_host"
diff --git a/data/hooks/backup/40-conf_ynh_settings b/data/hooks/backup/40-conf_ynh_settings
new file mode 100644
index 000000000..77148c4d9
--- /dev/null
+++ b/data/hooks/backup/40-conf_ynh_settings
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+# Exit hook on subcommand error or unset variable
+set -eu
+
+# Source YNH helpers
+source /usr/share/yunohost/helpers
+
+# Backup destination
+backup_dir="${1}/conf/ynh"
+
+# Backup the configuration
+ynh_backup "/etc/yunohost/firewall.yml" "${backup_dir}/firewall.yml"
+ynh_backup "/etc/yunohost/current_host" "${backup_dir}/current_host"
+[ ! -e "/etc/yunohost/settings.json" ] || ynh_backup "/etc/yunohost/settings.json" "${backup_dir}/settings.json"
+[ ! -d "/etc/yunohost/dyndns" ] || ynh_backup "/etc/yunohost/dyndns" "${backup_dir}/dyndns"
+[ ! -d "/etc/dkim" ] || ynh_backup "/etc/dkim" "${backup_dir}/dkim"
diff --git a/data/hooks/backup/42-conf_ynh_dyndns b/data/hooks/backup/42-conf_ynh_dyndns
deleted file mode 100644
index 6343f9086..000000000
--- a/data/hooks/backup/42-conf_ynh_dyndns
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/bin/bash
-
-source /usr/share/yunohost/helpers
-ynh_abort_if_errors
-YNH_CWD="${YNH_BACKUP_DIR%/}/conf/ynh/dyndns"
-mkdir -p $YNH_CWD
-cd "$YNH_CWD"
-
-# Backup the configuration
-ynh_exec_warn_less ynh_backup --src_path="/etc/yunohost/dyndns" --not_mandatory
diff --git a/data/hooks/backup/50-conf_manually_modified_files b/data/hooks/backup/50-conf_manually_modified_files
new file mode 100644
index 000000000..685fb56a8
--- /dev/null
+++ b/data/hooks/backup/50-conf_manually_modified_files
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+source /usr/share/yunohost/helpers
+ynh_abort_if_errors
+YNH_CWD="${YNH_BACKUP_DIR%/}/conf/manually_modified_files"
+mkdir -p "$YNH_CWD"
+cd "$YNH_CWD"
+
+yunohost tools shell -c "from yunohost.regenconf import manually_modified_files; print('\n'.join(manually_modified_files()))" > ./manually_modified_files_list
+
+ynh_backup --src_path="./manually_modified_files_list"
+
+for file in $(cat ./manually_modified_files_list)
+do
+    ynh_backup --src_path="$file"
+done
+    
+ynh_backup --src_path="/etc/ssowat/conf.json.persistent"
diff --git a/data/hooks/restore/05-conf_ldap b/data/hooks/restore/05-conf_ldap
index bdc1ebcdf..8dc511695 100644
--- a/data/hooks/restore/05-conf_ldap
+++ b/data/hooks/restore/05-conf_ldap
@@ -1,61 +1,54 @@
+#!/bin/bash
+
 backup_dir="${1}/conf/ldap"
 
-if [[ $EUID -ne 0 ]]; then
+systemctl stop slapd
 
-    # We need to execute this script as root, since the ldap
-    # service will be shut down during the operation (and sudo
-    # won't be available)
-    /bin/bash $(readlink -f $0) $1
+# Create a directory for backup
+TMPDIR="/tmp/$(date +%s)"
+mkdir -p "$TMPDIR"
 
-else
+die() {
+    state=$1
+    error=$2
 
-    service slapd stop || true
+    # Restore saved configuration and database
+    [[ $state -ge 1 ]] \
+      && (rm -rf /etc/ldap/slapd.d &&
+          mv "${TMPDIR}/slapd.d" /etc/ldap/slapd.d)
+    [[ $state -ge 2 ]] \
+      && (rm -rf /var/lib/ldap &&
+          mv "${TMPDIR}/ldap" /var/lib/ldap)
+    chown -R openldap: /etc/ldap/slapd.d /var/lib/ldap
 
-    # Create a directory for backup
-    TMPDIR="/tmp/$(date +%s)"
-    mkdir -p "$TMPDIR"
-
-    die() {
-        state=$1
-        error=$2
-
-        # Restore saved configuration and database
-        [[ $state -ge 1 ]] \
-          && (rm -rf /etc/ldap/slapd.d &&
-              mv "${TMPDIR}/slapd.d" /etc/ldap/slapd.d)
-        [[ $state -ge 2 ]] \
-          && (rm -rf /var/lib/ldap &&
-              mv "${TMPDIR}/ldap" /var/lib/ldap)
-        chown -R openldap: /etc/ldap/slapd.d /var/lib/ldap
-
-        service slapd start
-        rm -rf "$TMPDIR"
-
-        # Print an error message and exit
-        printf "%s" "$error" 1>&2
-        exit 1
-    }
-
-    # Restore the configuration
-    mv /etc/ldap/slapd.d "$TMPDIR"
-    mkdir -p /etc/ldap/slapd.d
-    cp -a "${backup_dir}/ldap.conf" /etc/ldap/ldap.conf
-    cp -a "${backup_dir}/slapd.ldif" /etc/ldap/slapd.ldif
-    # Legacy thing but we need it to force the regen-conf in case of it exist
-    cp -a "${backup_dir}/slapd.conf" /etc/ldap/slapd.conf
-    slapadd -F /etc/ldap/slapd.d -b cn=config \
-        -l "${backup_dir}/cn=config.master.ldif" \
-      || die 1 "Unable to restore LDAP configuration"
-    chown -R openldap: /etc/ldap/slapd.d
-
-    # Restore the database
-    mv /var/lib/ldap "$TMPDIR"
-    mkdir -p /var/lib/ldap
-    slapadd -F /etc/ldap/slapd.d -b dc=yunohost,dc=org \
-        -l "${backup_dir}/dc=yunohost-dc=org.ldif" \
-      || die 2 "Unable to restore LDAP database"
-    chown -R openldap: /var/lib/ldap
-
-    service slapd start
+    systemctl start slapd
     rm -rf "$TMPDIR"
-fi
+
+    # Print an error message and exit
+    printf "%s" "$error" 1>&2
+    exit 1
+}
+
+# Restore the configuration
+mv /etc/ldap/slapd.d "$TMPDIR"
+mkdir -p /etc/ldap/slapd.d
+cp -a "${backup_dir}/ldap.conf" /etc/ldap/ldap.conf
+cp -a "${backup_dir}/slapd.ldif" /etc/ldap/slapd.ldif
+# Legacy thing but we need it to force the regen-conf in case of it exist
+[ ! -e "${backup_dir}/slapd.conf" ] \
+    || cp -a "${backup_dir}/slapd.conf" /etc/ldap/slapd.conf
+slapadd -F /etc/ldap/slapd.d -b cn=config \
+    -l "${backup_dir}/cn=config.master.ldif" \
+  || die 1 "Unable to restore LDAP configuration"
+chown -R openldap: /etc/ldap/slapd.d
+
+# Restore the database
+mv /var/lib/ldap "$TMPDIR"
+mkdir -p /var/lib/ldap
+slapadd -F /etc/ldap/slapd.d -b dc=yunohost,dc=org \
+    -l "${backup_dir}/dc=yunohost-dc=org.ldif" \
+  || die 2 "Unable to restore LDAP database"
+chown -R openldap: /var/lib/ldap
+
+systemctl start slapd
+rm -rf "$TMPDIR"
diff --git a/data/hooks/restore/08-conf_ssh b/data/hooks/restore/08-conf_ssh
deleted file mode 100644
index 4b69d1696..000000000
--- a/data/hooks/restore/08-conf_ssh
+++ /dev/null
@@ -1,9 +0,0 @@
-backup_dir="$1/conf/ssh"
-
-if [ -d /etc/ssh/ ]; then
-    cp -a $backup_dir/. /etc/ssh
-    service ssh restart
-else
-    echo "SSH is not installed"
-fi
-
diff --git a/data/hooks/restore/14-conf_ssowat b/data/hooks/restore/14-conf_ssowat
deleted file mode 100644
index 71a011488..000000000
--- a/data/hooks/restore/14-conf_ssowat
+++ /dev/null
@@ -1,3 +0,0 @@
-backup_dir="$1/conf/ssowat"
-
-cp -a $backup_dir/. /etc/ssowat
diff --git a/data/hooks/restore/20-conf_ynh_firewall b/data/hooks/restore/20-conf_ynh_firewall
deleted file mode 100644
index 1789aed1e..000000000
--- a/data/hooks/restore/20-conf_ynh_firewall
+++ /dev/null
@@ -1,4 +0,0 @@
-backup_dir="$1/conf/ynh/firewall"
-
-cp -a $backup_dir/. /etc/yunohost
-yunohost firewall reload
diff --git a/data/hooks/restore/21-conf_ynh_certs b/data/hooks/restore/21-conf_ynh_certs
index 983bfb5a1..a6b45efeb 100644
--- a/data/hooks/restore/21-conf_ynh_certs
+++ b/data/hooks/restore/21-conf_ynh_certs
@@ -3,5 +3,3 @@ backup_dir="$1/conf/ynh/certs"
 mkdir -p /etc/yunohost/certs/
 
 cp -a $backup_dir/. /etc/yunohost/certs/
-service nginx reload
-service metronome reload
diff --git a/data/hooks/restore/22-conf_mail b/data/hooks/restore/22-conf_mail
deleted file mode 100644
index 77e0a4d42..000000000
--- a/data/hooks/restore/22-conf_mail
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-backup_dir="$1/conf/dkim"
-
-cp -a $backup_dir/etc/dkim/. /etc/dkim
-
-chown -R root:root /etc/dkim
-chown _rspamd:root /etc/dkim
-chown _rspamd:root /etc/dkim/*.mail.key
diff --git a/data/hooks/restore/23-data_mail b/data/hooks/restore/23-data_mail
index f9fd6e699..b3946f341 100644
--- a/data/hooks/restore/23-data_mail
+++ b/data/hooks/restore/23-data_mail
@@ -2,7 +2,3 @@ backup_dir="$1/data/mail"
 
 cp -a $backup_dir/. /var/mail/ || echo 'No mail found'
 chown -R vmail:mail /var/mail/
-
-# Restart services to use migrated certs
-service postfix restart
-service dovecot restart
diff --git a/data/hooks/restore/26-conf_xmpp b/data/hooks/restore/26-conf_xmpp
deleted file mode 100644
index a300a7268..000000000
--- a/data/hooks/restore/26-conf_xmpp
+++ /dev/null
@@ -1,7 +0,0 @@
-backup_dir="$1/conf/xmpp"
-
-cp -a $backup_dir/etc/. /etc/metronome
-cp -a $backup_dir/var/. /var/lib/metronome
-
-# Restart to apply new conf and certs
-service metronome restart
diff --git a/data/hooks/restore/27-data_xmpp b/data/hooks/restore/27-data_xmpp
new file mode 100644
index 000000000..02a4c6703
--- /dev/null
+++ b/data/hooks/restore/27-data_xmpp
@@ -0,0 +1,4 @@
+backup_dir="$1/data/xmpp"
+
+cp -a $backup_dir/var_lib_metronome/. /var/lib/metronome
+cp -a $backup_dir/var_xmpp-upload/. /var/xmpp-upload
diff --git a/data/hooks/restore/29-conf_nginx b/data/hooks/restore/29-conf_nginx
deleted file mode 100644
index 7288f52f3..000000000
--- a/data/hooks/restore/29-conf_nginx
+++ /dev/null
@@ -1,7 +0,0 @@
-backup_dir="$1/conf/nginx"
-
-# Copy all conf except apps specific conf located in DOMAIN.d
-find $backup_dir/ -mindepth 1 -maxdepth 1 -name '*.d' -or -exec cp -a {} /etc/nginx/conf.d/ \;
-
-# Restart to use new conf and certs
-service nginx restart
diff --git a/data/hooks/restore/40-conf_ynh_currenthost b/data/hooks/restore/40-conf_ynh_currenthost
deleted file mode 100644
index 700e806b4..000000000
--- a/data/hooks/restore/40-conf_ynh_currenthost
+++ /dev/null
@@ -1,3 +0,0 @@
-backup_dir="$1/conf/ynh"
-
-cp -a "${backup_dir}/current_host" /etc/yunohost/current_host
diff --git a/data/hooks/restore/40-conf_ynh_settings b/data/hooks/restore/40-conf_ynh_settings
new file mode 100644
index 000000000..4de29a4aa
--- /dev/null
+++ b/data/hooks/restore/40-conf_ynh_settings
@@ -0,0 +1,7 @@
+backup_dir="$1/conf/ynh"
+
+cp -a "${backup_dir}/current_host" /etc/yunohost/current_host
+cp -a "${backup_dir}/firewall.yml" /etc/yunohost/firewall.yml
+[ ! -e "${backup_dir}/settings.json" ] || cp -a "${backup_dir}/settings.json" "/etc/yunohost/settings.json"
+[ ! -d "${backup_dir}/dyndns" ] || cp -raT "${backup_dir}/dyndns" "/etc/yunohost/dyndns"
+[ ! -d "${backup_dir}/dkim" ] || cp -raT "${backup_dir}/dkim" "/etc/dkim"
diff --git a/data/hooks/restore/42-conf_ynh_dyndns b/data/hooks/restore/42-conf_ynh_dyndns
deleted file mode 100644
index 8ed4941ef..000000000
--- a/data/hooks/restore/42-conf_ynh_dyndns
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/bash
-
-source /usr/share/yunohost/helpers
-ynh_abort_if_errors
-YNH_CWD="${YNH_BACKUP_DIR%/}/conf/ynh/dyndns"
-cd "$YNH_CWD"
-
-# Restore file if exists
-ynh_restore_file --origin_path="/etc/yunohost/dyndns" --not_mandatory
diff --git a/data/hooks/restore/50-conf_manually_modified_files b/data/hooks/restore/50-conf_manually_modified_files
new file mode 100644
index 000000000..2d0943043
--- /dev/null
+++ b/data/hooks/restore/50-conf_manually_modified_files
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+source /usr/share/yunohost/helpers
+ynh_abort_if_errors
+YNH_CWD="${YNH_BACKUP_DIR%/}/conf/manually_modified_files"
+cd "$YNH_CWD"
+
+for file in $(cat ./manually_modified_files_list)
+do
+    ynh_restore_file --origin_path="$file" --not_mandatory
+done
+
+ynh_restore_file --origin_path="/etc/ssowat/conf.json.persistent" --not_mandatory
diff --git a/src/yunohost/tests/test_backuprestore.py b/src/yunohost/tests/test_backuprestore.py
index 7a2a64756..30204fa86 100644
--- a/src/yunohost/tests/test_backuprestore.py
+++ b/src/yunohost/tests/test_backuprestore.py
@@ -413,7 +413,7 @@ def test_backup_with_different_output_directory(mocker):
     # Create the backup
     with message(mocker, "backup_created"):
         backup_create(
-            system=["conf_ssh"],
+            system=["conf_ynh_settings"],
             apps=None,
             output_directory="/opt/test_backup_output_directory",
             name="backup",
@@ -427,7 +427,7 @@ def test_backup_with_different_output_directory(mocker):
     archives_info = backup_info(archives[0], with_details=True)
     assert archives_info["apps"] == {}
     assert len(archives_info["system"].keys()) == 1
-    assert "conf_ssh" in archives_info["system"].keys()
+    assert "conf_ynh_settings" in archives_info["system"].keys()
 
 
 @pytest.mark.clean_opt_dir
@@ -436,7 +436,7 @@ def test_backup_using_copy_method(mocker):
     # Create the backup
     with message(mocker, "backup_created"):
         backup_create(
-            system=["conf_nginx"],
+            system=["conf_ynh_settings"],
             apps=None,
             output_directory="/opt/test_backup_output_directory",
             methods=["copy"],
@@ -675,9 +675,9 @@ def test_backup_binds_are_readonly(mocker, monkeypatch):
     def custom_mount_and_backup(self):
         self._organize_files()
 
-        confssh = os.path.join(self.work_dir, "conf/ssh")
+        conf = os.path.join(self.work_dir, "conf/ynh/dkim")
         output = subprocess.check_output(
-            "touch %s/test 2>&1 || true" % confssh,
+            "touch %s/test 2>&1 || true" % conf,
             shell=True,
             env={"LANG": "en_US.UTF-8"},
         )