diff --git a/.gitignore b/.gitignore
index 3ed2386..09e69f3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -221,3 +221,4 @@ pip-log.txt
 *-swp
 
 auto_update_config.sh
+*.sw[op]
diff --git a/conf/gunicorn.conf.py b/conf/gunicorn.conf.py
index 533a73e..bcbdb4c 100644
--- a/conf/gunicorn.conf.py
+++ b/conf/gunicorn.conf.py
@@ -1,3 +1,5 @@
+# WARNING: Don't edit this file. All change will be removed after each app upgrade
+
 import os
 
 daemon = True
diff --git a/conf/seafevents.conf b/conf/seafevents.conf
index 8cfa634..484984f 100644
--- a/conf/seafevents.conf
+++ b/conf/seafevents.conf
@@ -1,3 +1,5 @@
+# WARNING: Don't edit this file. All change will be removed after each app upgrade
+
 [DATABASE]
 type = mysql
 host = 127.0.0.1
diff --git a/conf/seafile.conf b/conf/seafile.conf
index a684aa8..38730e5 100644
--- a/conf/seafile.conf
+++ b/conf/seafile.conf
@@ -1,3 +1,5 @@
+# WARNING: Don't edit this file. All change will be removed after each app upgrade
+
 [fileserver]
 port = __PORT_FILESERVER__
 
diff --git a/conf/seahub_settings.py b/conf/seahub_settings.py
index 4c72450..7f054a4 100644
--- a/conf/seahub_settings.py
+++ b/conf/seahub_settings.py
@@ -1,5 +1,7 @@
 # -*- coding: utf-8 -*-
 
+# WARNING: Don't edit this file. All change will be removed after each app upgrade
+
 SECRET_KEY = "{{ seahub_secret_key }}"
 
 DATABASES = {
diff --git a/manifest.toml b/manifest.toml
index 482853d..779ea70 100644
--- a/manifest.toml
+++ b/manifest.toml
@@ -18,7 +18,8 @@ code = "https://github.com/haiwen/seafile-server"
 cpe = "cpe:2.3:a:seafile:seafile"
 
 [integration]
-yunohost = ">= 11.2.13"
+yunohost = ">= 11.2.30"
+helpers_version = "2.1"
 architectures = ["amd64", "arm64"]
 multi_instance = false
 ldap = true
@@ -62,12 +63,10 @@ ram.runtime = "500M"
 [resources]
     [resources.system_user]
     allow_email = true
-    home = "/opt/yunohost/__APP__"
 
     [resources.install_dir]
-    dir = "/opt/yunohost/__APP__"
     owner = "__APP__:rwx"
-    group = "www-data:rx"
+    group = "www-data:r-x"
 
     [resources.data_dir]
     dir = "/home/yunohost.app/__APP__"
diff --git a/scripts/_common.sh b/scripts/_common.sh
index f65469b..67d58c2 100644
--- a/scripts/_common.sh
+++ b/scripts/_common.sh
@@ -31,7 +31,7 @@ fi
 #=================================================
 
 run_seafile_cmd() {
-    ynh_exec_warn_less systemd-run --wait --uid="$app" --gid="$app" \
+    ynh_hide_warnings systemd-run --wait --uid="$app" --gid="$app" \
         --property=RootDirectory="$install_dir"/seafile_image \
         --property="BindPaths=$systemd_seafile_bind_mount" \
         $@
@@ -47,8 +47,10 @@ install_source() {
 }
 
 set_permission() {
+    chown "$app:$app" "$install_dir"
+    chmod u=rwx,g=rx,o= "$install_dir"
     chown -R "$app:$app" "$install_dir"/{conf,ccnet}
-    chmod -R u+rwX,g-w,o= "$install_dir"/{conf,ccnet}
+    chmod -R u+rwX,g+rX-w,o= "$install_dir"/{conf,ccnet}
     chown -R "$app:$app" "$install_dir"/seafile_image/opt/seafile
     chmod -R u+rwX,g-w,o= "$install_dir"/seafile_image/opt/seafile
 
@@ -67,6 +69,7 @@ set_permission() {
     test -e "$install_dir"/seahub-data && setfacl -m user:www-data:rX "$data_dir"
     test -e "$install_dir"/seahub-data && setfacl -R -m user:www-data:rX "$data_dir"/seahub-data
 
+    chmod u=rwx,g=rx,o= "$data_dir"
     find "$data_dir" \(   \! -perm -o= \
                      -o \! -user "$app" \
                      -o \! -group "$app" \) \
@@ -76,14 +79,11 @@ set_permission() {
 
 clean_url_in_db_config() {
     sql_request='DELETE FROM `constance_config` WHERE `constance_key`= "SERVICE_URL"'
-    ynh_mysql_execute_as_root --sql="$sql_request" --database=seahubdb
+    ynh_mysql_db_shell <<< "$sql_request" --database=seahubdb
     sql_request='DELETE FROM `constance_config` WHERE `constance_key`= "FILE_SERVER_ROOT"'
-    ynh_mysql_execute_as_root --sql="$sql_request" --database=seahubdb
+    ynh_mysql_db_shell <<< "$sql_request" --database=seahubdb
 }
 
 ensure_vars_set() {
-    if [ -z "${jwt_private_key_notification_server:-}" ]; then
-        jwt_private_key_notification_server=$(ynh_string_random -l 32)
-        ynh_app_setting_set --app="$app" --key=jwt_private_key_notification_server --value="$jwt_private_key_notification_server"
-    fi
+    ynh_app_setting_set_default --key=jwt_private_key_notification_server --value=$(ynh_string_random -l 32)
 }
diff --git a/scripts/backup b/scripts/backup
index c5d9791..c3a91c8 100644
--- a/scripts/backup
+++ b/scripts/backup
@@ -15,7 +15,7 @@ seafile_version=$(ynh_app_upstream_version)
 seafile_code="$install_dir/seafile_image/opt/seafile/seafile-server-$seafile_version"
 
 if systemctl is-active seafile --quiet || systemctl is-active seahub --quiet; then
-    ynh_print_warn --message="It's hightly recommended to make your backup when the service is stopped. Please stop seafile service and seahub service with this command before to run the backup 'systemctl stop seafile.service seahub.service'"
+    ynh_print_warn "It's hightly recommended to make your backup when the service is stopped. Please stop seafile service and seahub service with this command before to run the backup 'systemctl stop seafile.service seahub.service'"
 fi
 
 #=================================================
@@ -23,24 +23,25 @@ fi
 #=================================================
 
 # # Backup app files
-ynh_print_info --message="Backing up code..."
-ynh_backup --src_path="$install_dir"
-ynh_print_info --message="Backing up user data..."
-ynh_backup --src_path="$data_dir" --dest_path="data" --is_big=1
-ynh_print_info --message="Backing up configuration..."
-ynh_backup --src_path="/etc/nginx/conf.d/$domain.d/${app}.conf"
-ynh_backup --src_path=/etc/systemd/system/seafile.service
-ynh_backup --src_path=/etc/systemd/system/seahub.service
-ynh_backup --src_path=/etc/fail2ban/jail.d/"$app".conf
-ynh_backup --src_path=/etc/fail2ban/filter.d/"$app".conf
+ynh_print_info "Backing up code..."
+ynh_backup "$install_dir"
+ynh_print_info "Backing up user data..."
+ynh_backup "$data_dir" --dest_path="data"
+
+ynh_print_info "Backing up configuration..."
+ynh_backup "/etc/nginx/conf.d/$domain.d/${app}.conf"
+ynh_backup /etc/systemd/system/seafile.service
+ynh_backup /etc/systemd/system/seahub.service
+ynh_backup /etc/fail2ban/jail.d/"$app".conf
+ynh_backup /etc/fail2ban/filter.d/"$app".conf
 
 # Backup logs
-ynh_backup --src_path="/var/log/$app"
+ynh_backup "/var/log/$app"
 
 # Backup mysql
-ynh_print_info --message="Backing up database"
-ynh_mysql_dump_db --database="$db_name" > "${YNH_CWD}"/seafiledb.dmp
-ynh_mysql_dump_db --database=ccnetdb > "${YNH_CWD}"/ccnetdb.dmp
-ynh_mysql_dump_db --database=seahubdb > "${YNH_CWD}"/seahubdb.dmp
+ynh_print_info "Backing up database"
+ynh_mysql_dump_db > "${YNH_CWD}"/seafiledb.dmp
+ynh_mysql_dump_db ccnetdb > "${YNH_CWD}"/ccnetdb.dmp
+ynh_mysql_dump_db seahubdb > "${YNH_CWD}"/seahubdb.dmp
 
-ynh_print_info --message="Backup script completed for $app. (YunoHost will then actually copy those files to the archive)."
+ynh_print_info "Backup script completed for $app. (YunoHost will then actually copy those files to the archive)."
diff --git a/scripts/change_url b/scripts/change_url
index cdbb140..58f847c 100644
--- a/scripts/change_url
+++ b/scripts/change_url
@@ -14,35 +14,33 @@ source /usr/share/yunohost/helpers
 seafile_version="$(ynh_app_upstream_version)"
 seafile_code="$install_dir/seafile_image/opt/seafile/seafile-server-$seafile_version"
 
-#=================================================
-# STANDARD MODIFICATIONS
 #=================================================
 
-ynh_script_progression --message="Updating NGINX web server configuration..." --weight=1
-ynh_change_url_nginx_config
+ynh_script_progression "Updating NGINX web server configuration..."
+ynh_config_change_url_nginx
 
 #=================================================
 # SPECIFIC MODIFICATIONS
 #=================================================
 
-ynh_script_progression --message="Stoping services..."
+ynh_script_progression "Stoping services..."
 
 # Stop service before any change
-ynh_systemd_action --service_name=seafile --action=stop
-ynh_systemd_action --service_name=seahub --action=stop
+ynh_systemctl --service=seafile --action=stop
+ynh_systemctl --service=seahub --action=stop
 sleep 2
 pkill -f seafile-controller || true
 pkill -f seaf-server || true
 pkill -f ccnet-server || true
 pkill -f seahub || true
 
-ynh_script_progression --message="Updating seafile configuration..."
+ynh_script_progression "Updating seafile configuration..."
 
 # Update Seafile Config
-ynh_add_config --jinja --template=seahub_settings.py --destination="$install_dir"/conf/seahub_settings.py
-ynh_add_config --template=ccnet.conf --destination="$install_dir"/conf/ccnet.conf
-ynh_add_config --template=gunicorn.conf.py --destination="$install_dir"/conf/gunicorn.conf.py
-ynh_add_config --template=seafdav.conf --destination="$install_dir"/conf/seafdav.conf
+ynh_config_add --jinja --template=seahub_settings.py --destination="$install_dir"/conf/seahub_settings.py
+ynh_config_add --template=ccnet.conf --destination="$install_dir"/conf/ccnet.conf
+ynh_config_add --template=gunicorn.conf.py --destination="$install_dir"/conf/gunicorn.conf.py
+ynh_config_add --template=seafdav.conf --destination="$install_dir"/conf/seafdav.conf
 
 # Update permissions
 ynh_permission_url --permission=file_server --url="$domain"/seafhttp
@@ -55,9 +53,10 @@ clean_url_in_db_config
 sleep 2
 
 # Reload services
-ynh_script_progression --message="Starting services..."
-ynh_systemd_action --service_name=seafile -l "spawned seaf-server, pid " -p /var/log/seafile/controller.log
-ynh_systemd_action --service_name=seahub -l "Started Seafile hub." -p "systemd"
+ynh_script_progression "Starting services..."
+ynh_systemctl --service=seafile --wait_until="spawned seaf-server, pid " --log_path=/var/log/seafile/controller.log
+sleep 2
+ynh_systemctl --service=seahub --wait_until="Started Seafile hub." --log_path="systemd"
 sleep 2
 
-ynh_script_progression --message="Change of URL completed for $app" --time=--last
+ynh_script_progression "Change of URL completed for $app" --time=
diff --git a/scripts/install b/scripts/install
index b883257..329ad01 100644
--- a/scripts/install
+++ b/scripts/install
@@ -17,11 +17,9 @@ seafile_code="$install_dir/seafile_image/opt/seafile/seafile-server-$seafile_ver
 
 ensure_vars_set
 
-#=================================================
-# STANDARD MODIFICATIONS
 #=================================================
 
-ynh_script_progression --message="Creating base directory..."
+ynh_script_progression "Creating base directory..."
 
 if [ -n "$(ls -A "$data_dir")" ]; then
     old_data_dir_path="${data_dir}_$(date '+%Y%m%d.%H%M%S')"
@@ -35,25 +33,25 @@ mkdir -p "$data_dir"/{seafile-data,seahub-data}
 mkdir -p "$install_dir"/{conf,ccnet}
 
 # Download new version from sources
-ynh_script_progression --message="Installing sources files..." --weight=7
+ynh_script_progression "Installing sources files..."
 install_source
 
 # init databases
-ynh_script_progression --message="Configuring MySQL database..."
+ynh_script_progression "Configuring MySQL database..."
 db_user=seafile
-ynh_''mysql_setup_db --db_user="$db_user" --db_name=ccnetdb --db_pwd="$db_pwd"
-ynh_''mysql_setup_db --db_user="$db_user" --db_name=seahubdb --db_pwd="$db_pwd"
+ynh_''mysql_create_db ccnetdb "$db_user" "$db_pwd"
+ynh_''mysql_create_db seahubdb "$db_user" "$db_pwd"
 
-ynh_script_progression --message="Configuring application..." --weight=3
+ynh_script_progression "Configuring application..."
 
 # Run install script
 set_permission
-ynh_replace_special_string --match_string='seafile_config.seafile_dir = seafile_config.validate_seafile_dir(seafile_dir)' \
-                           --replace_string='seafile_config.seafile_dir = seafile_dir' \
-                           --target_file="$seafile_code/setup-seafile-mysql.py"
-ynh_replace_special_string --match_string="Utils.error('Ccnet config dir \\\"%s\\\" already exists.' % ccnet_config.ccnet_dir)" \
-                           --replace_string='patched = 1' \
-                           --target_file="$seafile_code/setup-seafile-mysql.py"
+ynh_replace_regex --match='seafile_config.seafile_dir = seafile_config.validate_seafile_dir(seafile_dir)' \
+                           --replace='seafile_config.seafile_dir = seafile_dir' \
+                           --file="$seafile_code/setup-seafile-mysql.py"
+ynh_replace_regex --match="Utils.error('Ccnet config dir \\\"%s\\\" already exists.' % ccnet_config.ccnet_dir)" \
+                           --replace='patched = 1' \
+                           --file="$seafile_code/setup-seafile-mysql.py"
 run_seafile_cmd bash "/opt/seafile/seafile-server-$seafile_version/setup-seafile-mysql.sh" auto \
     --server-name "$server_name" \
     --server-ip "$domain" \
@@ -69,79 +67,77 @@ run_seafile_cmd bash "/opt/seafile/seafile-server-$seafile_version/setup-seafile
 
 # Retrive values from auto generated config file
 seahub_secret_key=$(grep -P 'SECRET_KEY\s*=\s*".+"' "$install_dir"/conf/seahub_settings.py | cut -d'"' -f2)
-ynh_app_setting_set --app="$app" --key=seahub_secret_key --value="$seahub_secret_key"
+ynh_app_setting_set --key=seahub_secret_key --value="$seahub_secret_key"
 
 # Update seafile config files
-ynh_add_config --jinja --template=seahub_settings.py --destination="$install_dir"/conf/seahub_settings.py
-ynh_add_config --template=seafile.conf --destination="$install_dir"/conf/seafile.conf
-ynh_add_config --template=ccnet.conf --destination="$install_dir"/conf/ccnet.conf
-ynh_add_config --template=gunicorn.conf.py --destination="$install_dir"/conf/gunicorn.conf.py
-ynh_add_config --template=seafdav.conf --destination="$install_dir"/conf/seafdav.conf
-ynh_add_config --template=seafevents.conf --destination="$install_dir"/conf/seafevents.conf
+ynh_config_add --jinja --template=seahub_settings.py --destination="$install_dir"/conf/seahub_settings.py
+ynh_config_add --template=seafile.conf --destination="$install_dir"/conf/seafile.conf
+ynh_config_add --template=ccnet.conf --destination="$install_dir"/conf/ccnet.conf
+ynh_config_add --template=gunicorn.conf.py --destination="$install_dir"/conf/gunicorn.conf.py
+ynh_config_add --template=seafdav.conf --destination="$install_dir"/conf/seafdav.conf
+ynh_config_add --template=seafevents.conf --destination="$install_dir"/conf/seafevents.conf
 
 # Configure admin info
 # It will be used the first start
 admin_email=$(ynh_user_get_info --username="$admin" --key='mail')
-cp ../conf/create_admin.json $install_dir/conf/admin.txt
-ynh_replace_string         --match_string=__ADMIN__ --replace_string="$admin_email" --target_file=$install_dir/conf/admin.txt
-ynh_replace_special_string --match_string=__PASSWORD__ --replace_string="$admin_password" --target_file=$install_dir/conf/admin.txt
+cp ../conf/create_admin.json "$install_dir"/conf/admin.txt
+ynh_replace         --match=__ADMIN__ --replace="$admin_email" --file="$install_dir"/conf/admin.txt
+ynh_replace_regex --match=__PASSWORD__ --replace="$admin_password" --file="$install_dir"/conf/admin.txt
 
 # Use symlink to store data
 if [ -e "$install_dir"/seafile-data ]; then
     mv -t "$data_dir"/seafile-data "$install_dir"/seafile-data/*
-    ynh_secure_remove --file="$install_dir"/seafile-data
+    ynh_safe_rm "$install_dir"/seafile-data
 fi
 if [ -e "$install_dir"/seahub-data ]; then
     mv -t "$data_dir"/seahub-data "$install_dir"/seahub-data/*
-    ynh_secure_remove --file="$install_dir"/seahub-data
+    ynh_safe_rm "$install_dir"/seahub-data
 fi
 if [ -e "$install_dir"/logs ]; then
     mv -t /var/log/"$app" "$install_dir"/logs/*
-    ynh_secure_remove --file="$install_dir"/logs
+    ynh_safe_rm "$install_dir"/logs
 fi
 ln -s "$data_dir"/seafile-data "$install_dir"/seafile-data
 ln -s "$data_dir"/seahub-data "$install_dir"/seahub-data
 ln -s /var/log/"$app" "$install_dir"/logs
 
 # Fix local warning
-ynh_replace_string --match_string=en_US.UTF-8 --replace_string="${LANG:-'en_US.UTF-8'}" --target_file="$seafile_code/seahub.sh"
+ynh_replace --match=en_US.UTF-8 --replace="${LANG:-'en_US.UTF-8'}" --file="$seafile_code/seahub.sh"
 
 # Add Seafile Server to startup
-ynh_script_progression --message="Configuring a systemd service..."
-ynh_add_systemd_config --service=seafile --template=seafile.service
-ynh_add_systemd_config --service=seahub --template=seahub.service
+ynh_script_progression "Configuring $app's systemd service..."
+ynh_config_add_systemd --service=seafile --template=seafile.service
+ynh_config_add_systemd --service=seahub --template=seahub.service
 
 # register yunohost service
 yunohost service add seafile --description 'Main service for seafile server.'
 yunohost service add seahub --description 'Seafile server web interface.'
 
 # Config nginx
-ynh_script_progression --message="Configuring nginx..."
-ynh_add_nginx_config
+ynh_script_progression "Configuring nginx..."
+ynh_config_add_nginx
 
 # Add logrotate
-ynh_script_progression --message="Configuring log rotation..."
-ynh_use_logrotate --logfile=/var/log/"$app"
+ynh_script_progression "Configuring log rotation..."
+ynh_config_add_logrotate /var/log/"$app"
 
 # Add fail2ban
-ynh_script_progression --message="Configuring fail2ban..."
-ynh_add_fail2ban_config --use_template
+ynh_script_progression "Configuring fail2ban..."
+ynh_config_add_fail2ban
 
-#=================================================
-# GENERIC FINALIZATION
 #=================================================
 
 # Set all permissions
-ynh_script_progression --message="Protecting directory..."
+ynh_script_progression "Protecting directory..."
 set_permission
 
 # Start service
 sleep 3
 
-ynh_script_progression --message="Starting seafile services..."
-ynh_systemd_action --service_name=seafile -l "spawned seaf-server, pid " -p /var/log/seafile/controller.log
+ynh_script_progression "Starting seafile services..."
+ynh_systemctl --service=seafile --wait_until="spawned seaf-server, pid " --log_path=/var/log/seafile/controller.log
 sleep 2
-ynh_systemd_action --service_name=seahub -l "Started Seafile hub." -p "systemd"
+ynh_systemctl --service=seahub --wait_until="Started Seafile hub." --log_path="systemd"
 sleep 2
 
-ynh_script_progression --message="Installation of $app completed" --last
+ynh_script_progression "Installation of $app completed"
diff --git a/scripts/remove b/scripts/remove
index dd8fbd5..6e25f86 100644
--- a/scripts/remove
+++ b/scripts/remove
@@ -18,11 +18,11 @@ seafile_code="$install_dir/seafile_image/opt/seafile/seafile-server-$seafile_ver
 # STANDARD REMOVE
 #=================================================
 
-ynh_script_progression --message="Stoping services..."
+ynh_script_progression "Stoping services..."
 
 # Stop all services
-ynh_systemd_action --service_name=seafile --action=stop
-ynh_systemd_action --service_name=seahub --action=stop
+ynh_systemctl --service=seafile --action=stop
+ynh_systemctl --service=seahub --action=stop
 
 # Force to kill all process in case of a process is not stoped cleanly
 pkill -f seafile-controller || true
@@ -30,35 +30,35 @@ pkill -f seaf-server || true
 pkill -f ccnet-server || true
 pkill -f seahub || true
 
-ynh_script_progression --message="Removing code..."
-ynh_secure_remove --file=/var/www/"$app"
-ynh_secure_remove --file=/opt/yunohost/"$app"
+ynh_script_progression "Removing code..."
+ynh_safe_rm /var/www/"$app"
+ynh_safe_rm /opt/yunohost/"$app"
 
 # Remove databases
-ynh_script_progression --message="Removing databases..."
-db_helper=ynh_"mysql"_remove_db
-$db_helper --db_name ccnetdb --db_user seafile
-$db_helper --db_name seahubdb --db_user seafile
+ynh_script_progression "Removing databases..."
+ynh_''mysql_drop_db ccnetdb
+ynh_''mysql_drop_db seahubdb
 
 # Remove systemd service
-ynh_script_progression --message="Removing systemd units..."
-ynh_remove_systemd_config --service=seafile
-ynh_remove_systemd_config --service=seahub
+ynh_script_progression "Removing systemd units..."
+ynh_config_remove_systemd seafile
+ynh_config_remove_systemd seahub
 
 # Remove nginx config
-ynh_script_progression --message="Removing nginx configuration..."
-ynh_remove_nginx_config
+ynh_script_progression "Removing nginx configuration..."
+ynh_config_remove_nginx
 
 # Remove logrotate
-ynh_remove_logrotate
+ynh_config_remove_logrotate
 
 # Remove the dedicated fail2ban config
-ynh_script_progression --message="Removing fail2ban configuration..."
-ynh_remove_fail2ban_config
+ynh_script_progression "Removing fail2ban configuration..."
+ynh_config_remove_fail2ban
 
-ynh_script_progression --message="Removing seafile service..."
+ynh_script_progression "Removing seafile service..."
 yunohost service remove seafile
 yunohost service remove seahub
 
-ynh_script_progression --message="Removal of $app completed" --last
+ynh_script_progression "Removal of $app completed"
+
 sleep 1
diff --git a/scripts/restore b/scripts/restore
index 95587b1..6a780ea 100644
--- a/scripts/restore
+++ b/scripts/restore
@@ -14,64 +14,61 @@ source /usr/share/yunohost/helpers
 seafile_version="$(ynh_app_upstream_version)"
 seafile_code="$install_dir/seafile_image/opt/seafile/seafile-server-$seafile_version"
 
-ynh_script_progression --message="Loading settings..."
+ynh_script_progression "Loading settings..."
 
 #=================================================
 # STANDARD RESTORATION STEPS
 #=================================================
 
 # Restore all config and data
-ynh_script_progression --message="Restoring files..." --weight=10
-ynh_restore
-
+ynh_script_progression "Restoring files..."
+ynh_restore_everything
 # Restore mysql dump
-ynh_script_progression --message="Restoring database..." --weight=3
-db_helper=ynh_"mysql"_setup_db
-$db_helper --db_user "$db_user" --db_name ccnetdb --db_pwd "$db_pwd"
-$db_helper --db_user "$db_user" --db_name seahubdb --db_pwd "$db_pwd"
+ynh_script_progression "Restoring database..."
+ynh_''mysql_create_db ccnetdb "$db_user" "$db_pwd"
+ynh_''mysql_create_db seahubdb "$db_user" "$db_pwd"
 su -c "mysql -u ${app} -p$db_pwd $db_name < ${YNH_CWD}/seafiledb.dmp"
 su -c "mysql -u ${app} -p$db_pwd ccnetdb < ${YNH_CWD}/ccnetdb.dmp"
 su -c "mysql -u ${app} -p$db_pwd seahubdb < ${YNH_CWD}/seahubdb.dmp"
 
-#=================================================
-# GENERIC FINALIZATION
 #=================================================
 
 # Add logrotate
-ynh_script_progression --message="Configuring log rotation..."
+ynh_script_progression "Configuring log rotation..."
 mkdir -p /var/log/"$app"
-ynh_use_logrotate --logfile="$install_dir"/logs
+ynh_config_add_logrotate "$install_dir"/logs
 
 # Set all permissions
-ynh_script_progression --message="Protecting directory..."
+ynh_script_progression "Protecting directory..."
 set_permission
 
 # Enable service and start seafile
-ynh_script_progression --message="Reconfiguring application..."
+ynh_script_progression "Reconfiguring application..."
 systemctl daemon-reload
 systemctl enable seafile --quiet
 systemctl enable seahub --quiet
 
 # Add Seafile to YunoHost's monitored services
-ynh_script_progression --message="Register seafile service..."
+ynh_script_progression "Register seafile service..."
 yunohost service add seafile --description 'Main service for seafile server.'
 yunohost service add seahub --description 'Seafile server web interface.'
 
-ynh_script_progression --message="Reloading services..."
+ynh_script_progression "Reloading services..."
 
 # Reload nginx
 systemctl reload nginx.service
 
 # Reload fail2ban
-ynh_systemd_action --service_name=fail2ban --action=reload
+ynh_systemctl --service=fail2ban --action=reload
 
 # Avoid the current effect
 sleep 5
 
 # Restart service
-ynh_script_progression --message="Starting seafile services..." --weight=3
-ynh_systemd_action --service_name=seafile -l "spawned seaf-server, pid " -p /var/log/seafile/controller.log
-ynh_systemd_action --service_name=seahub -l "Started Seafile hub." -p "systemd"
+ynh_script_progression "Starting seafile services..."
+ynh_systemctl --service=seafile --wait_until="spawned seaf-server, pid " --log_path=/var/log/seafile/controller.log
+sleep 2
+ynh_systemctl --service=seahub --wait_until="Started Seafile hub." --log_path="systemd"
 sleep 2
 
-ynh_script_progression --message="Restoration completed for $app" --last
+ynh_script_progression "Restoration completed for $app"
diff --git a/scripts/upgrade b/scripts/upgrade
index 4b037bd..55e6ef8 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -23,10 +23,10 @@ if [ "$YNH_APP_CURRENT_VERSION" == '-' ] || ynh_compare_current_package_version
     ynh_die "Upgrade from this version not supported"
 fi
 
-ynh_script_progression --message="Stoping services..."
+ynh_script_progression "Stoping services..."
 
-ynh_systemd_action --service_name=seafile --action=stop
-ynh_systemd_action --service_name=seahub --action=stop
+ynh_systemctl --service=seafile --action=stop
+ynh_systemctl --service=seahub --action=stop
 sleep 5
 pkill -f seafile-controller || true
 pkill -f seaf-server || true
@@ -42,15 +42,12 @@ if mysqlshow | grep -q seafiledb; then
         $mysqlconn -e "RENAME TABLE seafiledb.$name to $db_name.$name";
     done;
     $mysqlconn -e "DROP DATABASE seafiledb"
-    ynh_replace_string --match_string='db_name = seafiledb' --replace_string='db_name = seafile' --target_file="$install_dir"/conf/seafile.conf
+    ynh_replace --match='db_name = seafiledb' --replace='db_name = seafile' --file="$install_dir"/conf/seafile.conf
     sed -i "s|password\s*=\s*.*^|password = $db_pwd|g" "$install_dir"/conf/seafile.conf
 fi
 
 # Set missing settings
-if [ -z "${seahub_secret_key:-}" ]; then
-    seahub_secret_key="$(grep -P 'SECRET_KEY\s*=\s*".+"' "$install_dir"/conf/seahub_settings.py | cut -d'"' -f2)"
-    ynh_app_setting_set --app="$app" --key=seahub_secret_key --value="$seahub_secret_key"
-fi
+ynh_app_setting_set_default --key=seahub_secret_key --value="$(grep -P 'SECRET_KEY\s*=\s*".+"' "$install_dir"/conf/seahub_settings.py | cut -d'"' -f2)"
 
 #
 # Update data dir if needed
@@ -97,15 +94,15 @@ if [ ! -L "$install_dir"/logs ]; then
     ln -s /var/log/"${app}" "$install_dir"/logs
 fi
 
-ynh_script_progression --message="Upgrading source files..." --weight=6
+ynh_script_progression "Upgrading source files..."
 
 # Download new version from sources
-ynh_script_progression --message="Installing sources files..." --weight=7
+ynh_script_progression "Installing sources files..."
 if [ "$YNH_APP_UPGRADE_TYPE" == UPGRADE_APP ]; then
     install_source
 fi
 
-ynh_script_progression --message="Configuring application..."
+ynh_script_progression "Configuring application..."
 
 # permission to execute update script and expect helper
 set_permission
@@ -128,7 +125,7 @@ case "$installed_version" in
     run_seafile_cmd "/opt/seafile/seafile-server-$seafile_version/seahub.sh" python-env python3 "/opt/seafile/seafile-server-$seafile_version/seahub/manage.py" migrate_file_comment
 
     # Update seafile by script
-    ynh_replace_string --match_string='read dummy' --replace_string='# patched' --target_file="$seafile_code/upgrade/upgrade_7.0_7.1.sh"
+    ynh_replace --match='read dummy' --replace='# patched' --file="$seafile_code/upgrade/upgrade_7.0_7.1.sh"
     run_seafile_cmd "/opt/seafile/seafile-server-$seafile_version/upgrade/upgrade_7.0_7.1.sh"
 
     # Fix seafile data link. Look like that the upgrade script of seafile don't always work correctly
@@ -139,90 +136,87 @@ case "$installed_version" in
     ln -s "$data_dir" "$install_dir"/seafile-data
 ;&
 "7.1."* )
-    ynh_replace_string --match_string='read dummy' --replace_string='# patched' --target_file="$seafile_code/upgrade/upgrade_8.0_9.0.sh"
+    ynh_replace --match='read dummy' --replace='# patched' --file="$seafile_code/upgrade/upgrade_8.0_9.0.sh"
     run_seafile_cmd "/opt/seafile/seafile-server-$seafile_version/upgrade/upgrade_8.0_9.0.sh"
 ;&
 "8.0."* )
-    ynh_replace_string --match_string='read dummy' --replace_string='# patched' --target_file="$seafile_code/upgrade/upgrade_7.1_8.0.sh"
+    ynh_replace --match='read dummy' --replace='# patched' --file="$seafile_code/upgrade/upgrade_7.1_8.0.sh"
     run_seafile_cmd "/opt/seafile/seafile-server-$seafile_version/upgrade/upgrade_7.1_8.0.sh"
 ;&
 "9."* )
-    ynh_replace_string --match_string='read dummy' --replace_string='# patched' --target_file="$seafile_code/upgrade/upgrade_8.0_9.0.sh"
+    ynh_replace --match='read dummy' --replace='# patched' --file="$seafile_code/upgrade/upgrade_8.0_9.0.sh"
     run_seafile_cmd "/opt/seafile/seafile-server-$seafile_version/upgrade/upgrade_8.0_9.0.sh"
 ;&
 "10."* )
-    ynh_replace_string --match_string='read dummy' --replace_string='# patched' --target_file="$seafile_code/upgrade/upgrade_9.0_10.0.sh"
+    ynh_replace --match='read dummy' --replace='# patched' --file="$seafile_code/upgrade/upgrade_9.0_10.0.sh"
     run_seafile_cmd "/opt/seafile/seafile-server-$seafile_version/upgrade/upgrade_9.0_10.0.sh"
     run_seafile_cmd "/opt/seafile/seafile-server-$seafile_version/seahub.sh" python-env python3 "/opt/seafile/seafile-server-$seafile_version/migrate_ldapusers.py"
 ;&
 esac
 
-ynh_replace_string --match_string='read dummy' --replace_string='# patched' --target_file="$seafile_code/upgrade/minor-upgrade.sh"
+ynh_replace --match='read dummy' --replace='# patched' --file="$seafile_code/upgrade/minor-upgrade.sh"
 run_seafile_cmd "/opt/seafile/seafile-server-$seafile_version/upgrade/minor-upgrade.sh"
 
 # Clean url in config in DB
 clean_url_in_db_config
 
 # Update seafile config files
-ynh_add_config --jinja --template=seahub_settings.py --destination="$install_dir"/conf/seahub_settings.py
-ynh_add_config --template=seafile.conf --destination="$install_dir"/conf/seafile.conf
-ynh_add_config --template=ccnet.conf --destination="$install_dir"/conf/ccnet.conf
-ynh_add_config --template=gunicorn.conf.py --destination="$install_dir"/conf/gunicorn.conf.py
-ynh_add_config --template=seafdav.conf --destination="$install_dir"/conf/seafdav.conf
-ynh_add_config --template=seafevents.conf --destination="$install_dir"/conf/seafevents.conf
+ynh_config_add --jinja --template=seahub_settings.py --destination="$install_dir"/conf/seahub_settings.py
+ynh_config_add --template=seafile.conf --destination="$install_dir"/conf/seafile.conf
+ynh_config_add --template=ccnet.conf --destination="$install_dir"/conf/ccnet.conf
+ynh_config_add --template=gunicorn.conf.py --destination="$install_dir"/conf/gunicorn.conf.py
+ynh_config_add --template=seafdav.conf --destination="$install_dir"/conf/seafdav.conf
+ynh_config_add --template=seafevents.conf --destination="$install_dir"/conf/seafevents.conf
 
 # Fix local warning
-ynh_replace_string --match_string=en_US.UTF-8 --replace_string="${LANG:-'en_US.UTF-8'}" --target_file="$seafile_code/seahub.sh"
+ynh_replace --match=en_US.UTF-8 --replace="${LANG:-'en_US.UTF-8'}" --file="$seafile_code/seahub.sh"
 
-#=================================================
-# STANDARD UPGRADE STEPS
 #=================================================
 
 # Config nginx
-ynh_add_nginx_config 'seahub_port fileserver_port webdav_port'
+ynh_config_add_nginx 'seahub_port fileserver_port webdav_port'
 
 # Add Seafile Server to startup
-ynh_script_progression --message="Updating systemd units..."
-ynh_add_systemd_config --service=seafile --template=seafile.service
-ynh_add_systemd_config --service=seahub --template=seahub.service
+ynh_script_progression "Updating systemd units..."
+ynh_config_add_systemd --service=seafile --template=seafile.service
+ynh_config_add_systemd --service=seahub --template=seahub.service
 
-#=================================================
-# GENERIC FINALIZATION
 #=================================================
 
 # Set all permissions
-ynh_script_progression --message="Protecting directory..."
+ynh_script_progression "Protecting directory..."
 set_permission
 
 # Add logrotate
-ynh_script_progression --message="Configuring log rotation..."
-ynh_use_logrotate --logfile=/var/log/"$app" --nonappend
+ynh_script_progression "Configuring log rotation..."
+ynh_config_add_logrotate /var/log/"$app"
 
 # Add fail2ban
-ynh_script_progression --message="Configuring fail2ban..." --weight=10
-ynh_add_fail2ban_config --use_template
+ynh_script_progression "Configuring fail2ban..."
+ynh_config_add_fail2ban
 
 # register yunohost service
-ynh_script_progression --message="Register seafile service..."
+ynh_script_progression "Register seafile service..."
 yunohost service add seafile --description 'Main service for seafile server.'
 yunohost service add seahub --description 'Seafile server web interface.'
 
 # delete seafile cache
 
 # restart seafile server
-ynh_script_progression --message="Starting seafile services..." --weight=3
+ynh_script_progression "Starting seafile services..."
 sleep 5
-ynh_systemd_action --service_name=memcached.service -p "systemd"
-ynh_systemd_action --service_name=seafile -l "spawned seaf-server, pid " -p /var/log/seafile/controller.log
-ynh_systemd_action --service_name=seahub -l "Started Seafile hub." -p "systemd"
+ynh_systemctl --service=memcached.service -p "systemd"
+ynh_systemctl --service=seafile --wait_until="spawned seaf-server, pid " --log_path=/var/log/seafile/controller.log
+sleep 2
+ynh_systemctl --service=seahub --wait_until="Started Seafile hub." --log_path="systemd"
 sleep 2
 
 # remove old version files
-ynh_script_progression --message="Cleaning system and updating settings..."
+ynh_script_progression "Cleaning system and updating settings..."
 for f in "$install_dir"/seafile-server-*;do
     if [[ ! "$f" =~ ${seafile_version//./\\.}|latest ]]; then
-        ynh_secure_remove --file="$f"
+        ynh_safe_rm "$f"
     fi
 done
 
-ynh_script_progression --message="Upgrade of $app completed" --last
+ynh_script_progression "Upgrade of $app completed"
diff --git a/scripts/ynh_setup_source b/scripts/ynh_setup_source
index 70a58f0..b845c5f 100644
--- a/scripts/ynh_setup_source
+++ b/scripts/ynh_setup_source
@@ -1,80 +1,62 @@
-# Download, check integrity, uncompress and patch the source from app.src
+# Download, check integrity, uncompress and patch upstream sources
 #
-# Requires YunoHost version 2.6.4 or higher.
+# NOTE this is a full copy of upstream ynh_setup_source but with some specific patch releated to seafile docker archive
 ynh_setup_source_custom() {
-    # Declare an array to define the options of this helper.
-    local legacy_args=dsk
-    local -A args_array=([d]=dest_dir= [s]=source_id= [k]=keep= [r]=full_replace=)
+    # ============ Argument parsing =============
+    local -A args_array=([d]=dest_dir= [s]=source_id= [k]=keep= [r]=full_replace)
     local dest_dir
     local source_id
     local keep
     local full_replace
-    # Manage arguments with getopts
     ynh_handle_getopts_args "$@"
     keep="${keep:-}"
     full_replace="${full_replace:-0}"
+    source_id="${source_id:-main}"
+    # ===========================================
 
-    if test -e $YNH_APP_BASEDIR/manifest.toml && cat $YNH_APP_BASEDIR/manifest.toml | toml_to_json | jq -e '.resources.sources' >/dev/null
+    local sources_json=$(ynh_read_manifest "resources.sources[\"$source_id\"]")
+    if jq -re ".url" <<< "$sources_json"
     then
-        source_id="${source_id:-main}"
-        local sources_json=$(cat $YNH_APP_BASEDIR/manifest.toml | toml_to_json | jq ".resources.sources[\"$source_id\"]")
-        if jq -re ".url" <<< "$sources_json"
-        then
-            local arch_prefix=""
-        else
-            local arch_prefix=".$YNH_ARCH"
-        fi
-
-        local src_url="$(jq -r "$arch_prefix.url" <<< "$sources_json" | sed 's/^null$//')"
-        local src_sum="$(jq -r "$arch_prefix.sha256" <<< "$sources_json" | sed 's/^null$//')"
-        local src_sumprg="sha256sum"
-        local src_format="$(jq -r ".format" <<< "$sources_json" | sed 's/^null$//')"
-        local src_in_subdir="$(jq -r ".in_subdir" <<< "$sources_json" | sed 's/^null$//')"
-        local src_extract="$(jq -r ".extract" <<< "$sources_json" | sed 's/^null$//')"
-        local src_platform="$(jq -r ".platform" <<< "$sources_json" | sed 's/^null$//')"
-        local src_rename="$(jq -r ".rename" <<< "$sources_json" | sed 's/^null$//')"
-
-        [[ -n "$src_url" ]] || ynh_die "No URL defined for source $source_id$arch_prefix ?"
-        [[ -n "$src_sum" ]] || ynh_die "No sha256 sum defined for source $source_id$arch_prefix ?"
-
-        if [[ -z "$src_format" ]]
-        then
-            if [[ "$src_url" =~ ^.*\.zip$ ]] || [[ "$src_url" =~ ^.*/zipball/.*$ ]]
-            then
-                src_format="zip"
-            elif [[ "$src_url" =~ ^.*\.tar\.gz$ ]] || [[ "$src_url" =~ ^.*\.tgz$ ]] || [[ "$src_url" =~ ^.*/tar\.gz/.*$ ]] || [[ "$src_url" =~ ^.*/tarball/.*$ ]]
-            then
-                src_format="tar.gz"
-            elif [[ "$src_url" =~ ^.*\.tar\.xz$ ]]
-            then
-                src_format="tar.xz"
-            elif [[ "$src_url" =~ ^.*\.tar\.bz2$ ]]
-            then
-                src_format="tar.bz2"
-            elif [[ -z "$src_extract" ]]
-            then
-                src_extract="false"
-            fi
-        fi
+        local arch_prefix=""
     else
-        source_id="${source_id:-app}"
-        local src_file_path="$YNH_APP_BASEDIR/conf/${source_id}.src"
-
-        # Load value from configuration file (see above for a small doc about this file
-        # format)
-        local src_url=$(grep 'SOURCE_URL=' "$src_file_path" | cut --delimiter='=' --fields=2-)
-        local src_sum=$(grep 'SOURCE_SUM=' "$src_file_path" | cut --delimiter='=' --fields=2-)
-        local src_sumprg=$(grep 'SOURCE_SUM_PRG=' "$src_file_path" | cut --delimiter='=' --fields=2-)
-        local src_format=$(grep 'SOURCE_FORMAT=' "$src_file_path" | cut --delimiter='=' --fields=2-)
-        local src_in_subdir=$(grep 'SOURCE_IN_SUBDIR=' "$src_file_path" | cut --delimiter='=' --fields=2-)
-        local src_rename=$(grep 'SOURCE_FILENAME=' "$src_file_path" | cut --delimiter='=' --fields=2-)
-        local src_extract=$(grep 'SOURCE_EXTRACT=' "$src_file_path" | cut --delimiter='=' --fields=2-)
-        local src_platform=$(grep 'SOURCE_PLATFORM=' "$src_file_path" | cut --delimiter='=' --fields=2-)
+        local arch_prefix=".$YNH_ARCH"
     fi
 
-    # Default value
-    src_sumprg=${src_sumprg:-sha256sum}
+    local src_url="$(jq -r "$arch_prefix.url" <<< "$sources_json" | sed 's/^null$//')"
+    local src_sum="$(jq -r "$arch_prefix.sha256" <<< "$sources_json" | sed 's/^null$//')"
+    local src_format="$(jq -r ".format" <<< "$sources_json" | sed 's/^null$//')"
+    local src_in_subdir="$(jq -r ".in_subdir" <<< "$sources_json" | sed 's/^null$//')"
     src_in_subdir=${src_in_subdir:-true}
+    local src_extract="$(jq -r ".extract" <<< "$sources_json" | sed 's/^null$//')"
+    local src_platform="$(jq -r ".platform" <<< "$sources_json" | sed 's/^null$//')"
+    local src_rename="$(jq -r ".rename" <<< "$sources_json" | sed 's/^null$//')"
+
+    [[ -n "$src_url" ]] || ynh_die "No URL defined for source $source_id$arch_prefix ?"
+    [[ -n "$src_sum" ]] || ynh_die "No sha256 sum defined for source $source_id$arch_prefix ?"
+
+    if [[ -z "$src_format" ]]
+    then
+        if [[ "$src_url" =~ ^.*\.zip$ ]] || [[ "$src_url" =~ ^.*/zipball/.*$ ]]
+        then
+            src_format="zip"
+        elif [[ "$src_url" =~ ^.*\.tar\.gz$ ]] || [[ "$src_url" =~ ^.*\.tgz$ ]] || [[ "$src_url" =~ ^.*/tar\.gz/.*$ ]] || [[ "$src_url" =~ ^.*/tarball/.*$ ]]
+        then
+            src_format="tar.gz"
+        elif [[ "$src_url" =~ ^.*\.tar\.xz$ ]]
+        then
+            src_format="tar.xz"
+        elif [[ "$src_url" =~ ^.*\.tar\.bz2$ ]]
+        then
+            src_format="tar.bz2"
+        elif [[ "$src_url" =~ ^.*\.tar$ ]]
+        then
+            src_format="tar"
+        elif [[ -z "$src_extract" ]]
+        then
+            src_extract="false"
+        fi
+    fi
+
     src_format=${src_format:-tar.gz}
     src_format=$(echo "$src_format" | tr '[:upper:]' '[:lower:]')
     src_extract=${src_extract:-true}
@@ -84,10 +66,6 @@ ynh_setup_source_custom() {
         ynh_die "For source $source_id, expected either 'true' or 'false' for the extract parameter"
     fi
 
-
-    # (Unused?) mecanism where one can have the file in a special local cache to not have to download it...
-    local local_src="/opt/yunohost-apps-src/${YNH_APP_ID}/${source_id}"
-
     # Gotta use this trick with 'dirname' because source_id may contain slashes x_x
     mkdir -p $(dirname /var/cache/yunohost/download/${YNH_APP_ID}/${source_id})
     src_filename="/var/cache/yunohost/download/${YNH_APP_ID}/${source_id}"
@@ -100,14 +78,10 @@ ynh_setup_source_custom() {
         fi
         # END APP CUSTOMIZATION
     else
-        if test -e "$local_src"; then
-            cp $local_src $src_filename
-        fi
-
         [ -n "$src_url" ] || ynh_die "Couldn't parse SOURCE_URL from $src_file_path ?"
 
         # If the file was prefetched but somehow doesn't match the sum, rm and redownload it
-        if [ -e "$src_filename" ] && ! echo "${src_sum} ${src_filename}" | ${src_sumprg} --check --status
+        if [ -e "$src_filename" ] && ! echo "${src_sum} ${src_filename}" | sha256sum --check --status
         then
             rm -f "$src_filename"
         fi
@@ -121,16 +95,16 @@ ynh_setup_source_custom() {
             local out
             # Timeout option is here to enforce the timeout on dns query and tcp connect (c.f. man wget)
             out=$(wget --tries 3 --no-dns-cache --timeout 900 --no-verbose --output-document=$src_filename $src_url 2>&1) \
-                || ynh_die --message="$out"
+                || ynh_die "$out"
         fi
 
         # Check the control sum
-        if ! echo "${src_sum} ${src_filename}" | ${src_sumprg} --check --status
+        if ! echo "${src_sum} ${src_filename}" | sha256sum --check --status
         then
-            local actual_sum="$(${src_sumprg} ${src_filename} | cut --delimiter=' ' --fields=1)"
+            local actual_sum="$(sha256sum ${src_filename} | cut --delimiter=' ' --fields=1)"
             local actual_size="$(du -hs ${src_filename} | cut --fields=1)"
             rm -f ${src_filename}
-            ynh_die --message="Corrupt source for ${src_url}: Expected sha256sum to be ${src_sum} but got ${actual_sum} (size: ${actual_size})."
+            ynh_die "Corrupt source for ${src_url}: Expected sha256sum to be ${src_sum} but got ${actual_sum} (size: ${actual_size})."
         fi
     fi
 
@@ -150,19 +124,12 @@ ynh_setup_source_custom() {
     fi
 
     if [ "$full_replace" -eq 1 ]; then
-        ynh_secure_remove --file="$dest_dir"
+        ynh_safe_rm "$dest_dir"
     fi
 
     # Extract source into the app dir
     mkdir --parents "$dest_dir"
 
-    if [ -n "${install_dir:-}" ] && [ "$dest_dir" == "$install_dir" ]; then
-        _ynh_apply_default_permissions $dest_dir
-    fi
-    if [ -n "${final_path:-}" ] && [ "$dest_dir" == "$final_path" ]; then
-        _ynh_apply_default_permissions $dest_dir
-    fi
-
     if [[ "$src_extract" == "false" ]]; then
         if [[ -z "$src_rename" ]]
         then
@@ -179,11 +146,11 @@ ynh_setup_source_custom() {
             local tmp_dir=$(mktemp --directory)
             unzip -quo $src_filename -d "$tmp_dir"
             cp --archive $tmp_dir/*/. "$dest_dir"
-            ynh_secure_remove --file="$tmp_dir"
+            ynh_safe_rm "$tmp_dir"
         else
             unzip -quo $src_filename -d "$dest_dir"
         fi
-        ynh_secure_remove --file="$src_filename"
+        ynh_safe_rm "$src_filename"
     else
         local strip=""
         if [ "$src_in_subdir" != "false" ]; then
@@ -194,30 +161,29 @@ ynh_setup_source_custom() {
             fi
             strip="--strip-components $sub_dirs"
         fi
-        if [[ "$src_format" =~ ^tar.gz|tar.bz2|tar.xz$ ]]; then
+        if [[ "$src_format" =~ ^tar.gz|tar.bz2|tar.xz|tar$ ]]; then
             tar --extract --file=$src_filename --directory="$dest_dir" $strip
         else
-            ynh_die --message="Archive format unrecognized."
+            ynh_die "Archive format unrecognized."
         fi
-        ynh_secure_remove --file="$src_filename"
+        ynh_safe_rm "$src_filename"
     fi
 
     # Apply patches
-    if [ -d "$YNH_APP_BASEDIR/sources/patches/" ]; then
-        local patches_folder=$(realpath $YNH_APP_BASEDIR/sources/patches/)
-        if (($(find $patches_folder -type f -name "${source_id}-*.patch" 2>/dev/null | wc --lines) > "0")); then
-            pushd "$dest_dir"
-            for p in $patches_folder/${source_id}-*.patch; do
-                echo $p
-                patch --strip=1 <$p || ynh_print_warn --message="Packagers /!\\ patch $p failed to apply"
-            done
-            popd
-        fi
-    fi
-
-    # Add supplementary files
-    if test -e "$YNH_APP_BASEDIR/sources/extra_files/${source_id}"; then
-        cp --archive $YNH_APP_BASEDIR/sources/extra_files/$source_id/. "$dest_dir"
+    if [ -d "$YNH_APP_BASEDIR/patches/" ]; then
+        local patches_folder=$(realpath "$YNH_APP_BASEDIR/patches/$source_id")
+        pushd "$dest_dir"
+        for patchfile in "$patches_folder/"*.patch; do
+            echo "Applying $patchfile"
+            if ! patch --strip=1 < "$patchfile"; then
+                if ynh_in_ci_tests; then
+                    ynh_die "Patch $patchfile failed to apply!"
+                else
+                    ynh_print_warn "Warn your packagers /!\\ Patch $patchfile failed to apply"
+                fi
+            fi
+        done
+        popd
     fi
 
     # Keep files to be backup/restored at the end of the helper
@@ -239,4 +205,8 @@ ynh_setup_source_custom() {
         done
     fi
     rm -rf /var/cache/yunohost/files_to_keep_during_setup_source/
+
+    if [ -n "${install_dir:-}" ] && [ "$dest_dir" == "$install_dir" ]; then
+        _ynh_apply_default_permissions $dest_dir
+    fi
 }
diff --git a/tests.toml b/tests.toml
index 88b42ba..fe49775 100644
--- a/tests.toml
+++ b/tests.toml
@@ -24,3 +24,4 @@ test_format = 1.0
     test_upgrade_from.8d41482.name = "Version 7.1 (Old_version_for_CI_4 branch)"
     test_upgrade_from.c11c24b.name = "Version 8.x (Old_version_for_CI_5 branch)"
     test_upgrade_from.7a4d00a.name = "Version 9.x"
+    test_upgrade_from.5a4717a.name = "Before helper 2.1"