diff --git a/data/helpers.d/setting b/data/helpers.d/setting
index b8c57e158..af358d274 100644
--- a/data/helpers.d/setting
+++ b/data/helpers.d/setting
@@ -16,7 +16,11 @@ ynh_app_setting_get() {
     # Manage arguments with getopts
     ynh_handle_getopts_args "$@"
 
-    ynh_app_setting "get" "$app" "$key"
+    if [[ $key =~ (unprotected|protected|skipped)_ ]]; then
+        yunohost app setting $app $key
+    else
+        ynh_app_setting "get" "$app" "$key"
+    fi
 }
 
 # Set an application setting
@@ -37,7 +41,11 @@ ynh_app_setting_set() {
     # Manage arguments with getopts
     ynh_handle_getopts_args "$@"
 
-    ynh_app_setting "set" "$app" "$key" "$value"
+    if [[ $key =~ (unprotected|protected|skipped)_ ]]; then
+        yunohost app setting $app $key -v $value
+    else
+        ynh_app_setting "set" "$app" "$key" "$value"
+    fi
 }
 
 # Delete an application setting
@@ -56,7 +64,11 @@ ynh_app_setting_delete() {
     # Manage arguments with getopts
     ynh_handle_getopts_args "$@"
 
-    ynh_app_setting "delete" "$app" "$key"
+    if [[ "$key" =~ (unprotected|skipped|protected)_ ]]; then
+        yunohost app setting $app $key -d
+    else
+        ynh_app_setting "delete" "$app" "$key"
+    fi
 }
 
 # Small "hard-coded" interface to avoid calling "yunohost app" directly each
@@ -66,11 +78,6 @@ ynh_app_setting_delete() {
 #
 ynh_app_setting()
 {
-    if [[ "$1" == "delete" ]] && [[ "$3" =~ ^(unprotected|skipped)_ ]] 
-    then
-        current_value=$(ynh_app_setting_get --app=$app --key=$3)
-    fi
-
     ACTION="$1" APP="$2" KEY="$3" VALUE="${4:-}" python2.7 - <<EOF
 import os, yaml, sys
 app, action = os.environ['APP'], os.environ['ACTION'].lower()
@@ -89,27 +96,12 @@ else:
     elif action == "set":
         if key in ['redirected_urls', 'redirected_regex']:
             value = yaml.load(value)
-        if any(key.startswith(word+"_") for word in ["unprotected", "protected", "skipped"]):
-            sys.stderr.write("/!\\ Packagers! This app is still using the skipped/protected/unprotected_uris/regex settings which are now obsolete and deprecated... Instead, you should use the new helpers 'ynh_permission_{create,urls,update,delete}' and the 'visitors' group to initialize the public/private access. Check out the documentation at the bottom of yunohost.org/groups_and_permissions to learn how to use the new permission mechanism.\n")
         settings[key] = value
     else:
         raise ValueError("action should either be get, set or delete")
     with open(setting_file, "w") as f:
         yaml.safe_dump(settings, f, default_flow_style=False)
 EOF
-
-    # Fucking legacy permission management.
-    # We need this because app temporarily set the app as unprotected to configure it with curl...
-    if [[ "$3" =~ ^(unprotected|skipped)_ ]]
-    then
-        if [[ "$1" == "set" ]] && [[ "${4:-}" == "/" ]]
-        then
-            ynh_permission_update --permission "main" --add "visitors"
-        elif [[ "$1" == "delete" ]] && [[ "${current_value:-}" == "/" ]] && [[ -n "$(ynh_app_setting_get --app=$2 --key='is_public' )" ]]
-        then
-            ynh_permission_update --permission "main" --remove "visitors"
-        fi
-    fi
 }
 
 # Check availability of a web path
@@ -305,7 +297,7 @@ ynh_permission_create() {
             protected=",protected=False"
         fi
     fi
-    
+
     yunohost tools shell -c "from yunohost.permission import permission_create; permission_create('$app.$permission' $url $additional_urls $auth_header $allowed $label $show_tile $protected , sync_perm=False)"
 }
 
diff --git a/locales/en.json b/locales/en.json
index 56aac443e..166fdcc2d 100644
--- a/locales/en.json
+++ b/locales/en.json
@@ -439,6 +439,7 @@
     "migration_0018_failed_to_migrate_iptables_rules": "Failed to migrate legacy iptables rules to nftables: {error}",
     "migration_0018_failed_to_reset_legacy_rules": "Failed to reset legacy iptables rules: {error}",
     "migration_0019_add_new_attributes_in_ldap": "Add new attributes for permissions in LDAP database",
+    "migration_0019_migrate_old_app_settings": "Migrate old apps settings 'skipped_uris', 'unprotected_uris', 'protected_uris' in permissions system.",
     "migration_0019_backup_before_migration": "Creating a backup of LDAP database and apps settings prior to the actual migration.",
     "migration_0019_can_not_backup_before_migration": "The backup of the system could not be completed before the migration failed. Error: {error:s}",
     "migration_0019_migration_failed_trying_to_rollback": "Could not migrate... trying to roll back the system.",
diff --git a/src/yunohost/app.py b/src/yunohost/app.py
index 79e9cfdf8..360f31abc 100644
--- a/src/yunohost/app.py
+++ b/src/yunohost/app.py
@@ -936,8 +936,6 @@ def app_install(operation_logger, app, label=None, args=None, no_remove_on_failu
         permission_url(app_instance_name + ".main", url='/', sync_perm=False)
     user_permission_update(app_instance_name + ".main", show_tile=True, sync_perm=False)
 
-    _migrate_legacy_permissions(app_instance_name)
-
     permission_sync_to_user()
 
     logger.success(m18n.n('installation_complete'))
@@ -990,34 +988,6 @@ def dump_app_log_extract_for_debugging(operation_logger):
         logger.info(line)
 
 
-def _migrate_legacy_permissions(app):
-
-    from yunohost.permission import user_permission_list, user_permission_update
-
-    # Check if app is apparently using the legacy permission management, defined by the presence of something like
-    # ynh_app_setting_set on unprotected_uris (or yunohost app setting)
-    install_script_path = os.path.join(APPS_SETTING_PATH, app, 'scripts/install')
-    install_script_content = open(install_script_path, "r").read()
-    if not re.search(r"(yunohost app setting|ynh_app_setting_set) .*(unprotected|skipped)_uris", install_script_content):
-        return
-
-    app_settings = _get_app_settings(app)
-    app_perm_currently_allowed = user_permission_list()["permissions"][app + ".main"]["allowed"]
-
-    settings_say_it_should_be_public = (app_settings.get("unprotected_uris", None) == "/"
-                                        or app_settings.get("skipped_uris", None) == "/")
-
-    # If the current permission says app is protected, but there are legacy rules saying it should be public...
-    if app_perm_currently_allowed == ["all_users"] and settings_say_it_should_be_public:
-        # Make it public
-        user_permission_update(app + ".main", add="visitors", sync_perm=False)
-
-    # If the current permission says app is public, but there are no setting saying it should be public...
-    if app_perm_currently_allowed == ["visitors"] and not settings_say_it_should_be_public:
-        # Make is private
-        user_permission_update(app + ".main", remove="visitors", sync_perm=False)
-
-
 @is_unit_operation()
 def app_remove(operation_logger, app):
     """
@@ -1224,31 +1194,109 @@ def app_setting(app, key, value=None, delete=False):
     """
     app_settings = _get_app_settings(app) or {}
 
-    if value is None and not delete:
-        try:
-            return app_settings[key]
-        except Exception as e:
-            logger.debug("cannot get app setting '%s' for '%s' (%s)", key, app, e)
-            return None
+    #
+    # Legacy permission setting management
+    # (unprotected, protected, skipped_uri/regex)
+    #
 
+    is_legacy_permission_setting = any(key.startswith(word+"_") for word in ["unprotected", "protected", "skipped"])
+
+    if is_legacy_permission_setting:
+
+        logger.warning("/!\\ Packagers! This app is still using the skipped/protected/unprotected_uris/regex settings which are now obsolete and deprecated... Instead, you should use the new helpers 'ynh_permission_{create,urls,update,delete}' and the 'visitors' group to initialize the public/private access. Check out the documentation at the bottom of yunohost.org/groups_and_permissions to learn how to use the new permission mechanism.")
+        from permission import user_permission_list, user_permission_update, permission_create, permission_delete, permission_url
+        permissions = user_permission_list(full=True, full_path=False)['permissions']
+        permission_name = "%s.legacy_%s_uris" % (app, key.split('_')[0])
+        permission = permissions.get(permission_name)
+
+        # GET
+        if value is None and not delete:
+            # FIXME FIXME FIXME : what about the main url ...?
+            return ','.join(permission['additional_urls']) if permission else None
+
+        # DELETE
+        if delete:
+            if key in app_settings:
+
+                # If 'is_public' setting still exists, we interpret this as
+                # coming from a legacy app (because new apps should manage the
+                # is_public state themselves anymore...)
+                #
+                # In that case, we interpret the request for "deleting
+                # unprotected/skipped" setting as willing to make the app
+                # private
+                if 'is_public' in app_settings and 'visitors' in permissions[app + ".main"]['allowed']:
+                    if key.startswith('unprotected_') or key.startswith('skipped_'):
+                        user_permission_update(app + ".main", remove="visitors")
+                else:
+                    if permission:
+                        permission_delete(permission_name)
+
+        # SET
+        else:
+            urls = value
+            # If the request is about the root of the app (/), ( = the vast majority of cases)
+            # we interpret this as a change for the main permission
+            # (i.e. allowing/disallowing visitors)
+            if urls == '/':
+                if key.startswith("unprotected_") or key.startswith("skipped_"):
+                    permission_url(app + ".main", url='/', sync_perm=False)
+                    user_permission_update(app + ".main", add="visitors")
+                else:
+                    user_permission_update(app + ".main", remove="visitors")
+            else:
+                # Add re: in case of regex, as we distingish regex by this since the new permission system
+                if key.endswith('_regex'):
+                    urls = 're:' + urls
+
+                if permission:
+                    # In case of new regex, save the urls, to add a new time in the additional_urls
+                    # In case of new urls, we do the same thing but inversed
+                    if key.endswith('_regex'):
+                        # List of urls to save
+                        current_urls_or_regex = [url for url in permission['additional_urls'] if not url.startswith('re:')]
+                    else:
+                        # List of regex to save
+                        current_urls_or_regex = [url for url in permission['additional_urls'] if url.startswith('re:')]
+
+                    new_urls = urls.split(',') + current_urls_or_regex
+                    # We need to clear urls because in the old setting the new setting override the old one and dont just add some urls
+                    permission_url(permission_name, clear_urls=True, sync_perm=False)
+                    permission_url(permission_name, add_url=new_urls)
+                else:
+                    from utils.legacy import legacy_permission_label
+                    # Let's create a "special" permission for the legacy settings
+                    permission_create(permission=permission_name,
+                                      # FIXME find a way to limit to only the user allowed to the main permission
+                                      allowed=['all_users'] if key.startswith('protected_') else ['all_users', 'visitors'],
+                                      url=None,
+                                      additional_urls=urls.split(','),
+                                      auth_header=not key.startswith('skipped_'),
+                                      label=legacy_permission_label(app, key.split('_')[0]),
+                                      show_tile=False,
+                                      protected=True)
+
+
+    #
+    # Regular setting management
+    #
+
+    # GET
+    if value is None and not delete:
+        return app_settings.get(key, None)
+
+    # DELETE
     if delete:
         if key in app_settings:
             del app_settings[key]
+
+    # SET
     else:
-        # FIXME: Allow multiple values for some keys?
         if key in ['redirected_urls', 'redirected_regex']:
             value = yaml.load(value)
-        if any(key.startswith(word+"_") for word in ["unprotected", "protected", "skipped"]):
-            logger.warning("/!\\ Packagers! This app is still using the skipped/protected/unprotected_uris/regex settings which are now obsolete and deprecated... Instead, you should use the new helpers 'ynh_permission_{create,urls,update,delete}' and the 'visitors' group to initialize the public/private access. Check out the documentation at the bottom of yunohost.org/groups_and_permissions to learn how to use the new permission mechanism.")
-
         app_settings[key] = value
-    _set_app_settings(app, app_settings)
 
-    # Fucking legacy permission management.
-    # We need this because app temporarily set the app as unprotected to configure it with curl...
-    if key.startswith("unprotected_") or key.startswith("skipped_") and value == "/":
-        from permission import user_permission_update
-        user_permission_update(app + ".main", add="visitors")
+    _set_app_settings(app, app_settings)
 
 
 def app_register_url(app, domain, path):
@@ -1314,104 +1362,10 @@ def app_ssowatconf():
     redirected_regex = {main_domain + '/yunohost[\/]?$': 'https://' + main_domain + '/yunohost/sso/'}
     redirected_urls = {}
 
-    def _get_setting(settings, name):
-        s = settings.get(name, None)
-        return s.split(',') if s else []
-
     for app in _installed_apps():
 
         app_settings = read_yaml(APPS_SETTING_PATH + app + '/settings.yml')
 
-        ## BEGIN Legacy part ##
-
-        if 'domain' not in app_settings:
-            continue
-        if 'path' not in app_settings:
-            continue
-
-        # This 'no_sso' settings sound redundant to not having $path defined ....
-        # At least from what I can see, all apps using it don't have a path defined ...
-        if 'no_sso' in app_settings:
-            continue
-
-        domain = app_settings['domain']
-        path = app_settings['path'].rstrip('/')
-
-        def _sanitized_absolute_url(perm_url):
-            # Nominal case : url is relative to the app's path
-            if perm_url.startswith("/"):
-                perm_domain = domain
-                perm_path = path + perm_url.rstrip("/")
-            # Otherwise, the urls starts with a domain name, like domain.tld/foo/bar
-            # We want perm_domain = domain.tld and perm_path = "/foo/bar"
-            else:
-                perm_domain, perm_path = perm_url.split("/", 1)
-                perm_path = "/" + perm_path.rstrip("/")
-
-            return perm_domain + perm_path
-
-        # Skipped
-        skipped_urls = [_sanitized_absolute_url(uri) for uri in _get_setting(app_settings, 'skipped_uris')]
-        skipped_urls += ['re:' + regex for regex in _get_setting(app_settings, 'skipped_regex')]
-
-        # Legacy permission system using (un)protected_uris and _regex managed in app settings...
-        unprotected_urls = [_sanitized_absolute_url(uri) for uri in _get_setting(app_settings, 'unprotected_uris')]
-        protected_urls = [_sanitized_absolute_url(uri) for uri in _get_setting(app_settings, 'protected_uris')]
-        unprotected_urls += ['re:' + regex for regex in _get_setting(app_settings, 'unprotected_regex')]
-        protected_urls += ['re:' + regex for regex in _get_setting(app_settings, 'protected_regex')]
-
-        if skipped_urls == [] and unprotected_urls == [] and protected_urls == []:
-            continue
-
-        # Manage compatibility with old protected, unprotected, skipped urls !!
-        this_app_perms = {name: info for name, info in all_permissions.items() if name.startswith(app + ".")}
-        for perm_name, perm_info in this_app_perms.items():
-
-            # Ignore permissions for which there's no url defined
-            if not perm_info["url"]:
-                continue
-
-            url = _sanitized_absolute_url(perm_info["url"])
-            perm_info["url"] = url
-            if "visitors" in perm_info["allowed"]:
-                # Legacy stuff : we remove now protected-urls that might have been declared as unprotected earlier...
-                protected_urls = [u for u in protected_urls if u != url]
-            else:
-                # Legacy stuff : we remove now unprotected-urls / skipped-urls that might have been declared as protected earlier...
-                unprotected_urls = [u for u in unprotected_urls if u != url]
-                skipped_urls = [u for u in skipped_urls if u != url]
-
-        # Create special permission for legacy apps
-        if skipped_urls != []:
-            permissions[app + ".legacy_skipped_urls"] = {
-                "users": [],
-                "label": "Legacy permission - skipped_urls for app :" + app,
-                "show_tile": False,
-                "auth_header": False,
-                "public": True,
-                "uris": skipped_urls
-            }
-        if unprotected_urls != []:
-            permissions[app + ".legacy_unprotected_urls"] =  {
-                "users": all_permissions[app + '.main']['corresponding_users'],
-                "label": "Legacy permission - unprotected_urls for app :" + app,
-                "show_tile": False,
-                "auth_header": True,
-                "public": True,
-                "uris": unprotected_urls
-            }
-        if protected_urls != []:
-            permissions[app + ".legacy_protected_urls"] = {
-                "users": all_permissions[app + '.main']['corresponding_users'],
-                "label": "Legacy permission - protected_urls for app :" + app,
-                "show_tile": False,
-                "auth_header": True,
-                "public": False,
-                "uris": protected_urls
-            }
-
-        ## END Legacy part ##
-
         # Redirected
         redirected_urls.update(app_settings.get('redirected_urls', {}))
         redirected_regex.update(app_settings.get('redirected_regex', {}))
diff --git a/src/yunohost/backup.py b/src/yunohost/backup.py
index d81dbc9eb..336f68af4 100644
--- a/src/yunohost/backup.py
+++ b/src/yunohost/backup.py
@@ -1257,6 +1257,7 @@ class RestoreManager():
                              name should be already install)
         """
         from yunohost.user import user_group_list
+        from yunohost.app import app_setting
         from yunohost.permission import permission_create, permission_delete, user_permission_list, permission_sync_to_user
 
         def copytree(src, dst, symlinks=False, ignore=None):
@@ -1353,6 +1354,14 @@ class RestoreManager():
                 from yunohost.utils.legacy import SetupGroupPermissions
                 SetupGroupPermissions.migrate_app_permission(app=app_instance_name)
 
+            # Migrate old settings
+            if app_setting(app_instance_name, 'skipped_uris') is not None or \
+               app_setting(app_instance_name, 'unprotected_uris') is not None or \
+               app_setting(app_instance_name, 'protected_uris') is not None:
+                from yunohost.tools import _get_migration_by_name
+                extends_permissions_features_1 = _get_migration_by_name("extends_permissions_features_1")
+                extends_permissions_features_1.migrate_skipped_unprotected_protected_uris(app=app_instance_name)
+
             # Prepare env. var. to pass to script
             env_dict = self._get_env_var(app_instance_name)
 
diff --git a/src/yunohost/data_migrations/0019_extends_permissions_features_1.py b/src/yunohost/data_migrations/0019_extends_permissions_features_1.py
index d45209207..53a3854c7 100644
--- a/src/yunohost/data_migrations/0019_extends_permissions_features_1.py
+++ b/src/yunohost/data_migrations/0019_extends_permissions_features_1.py
@@ -76,6 +76,51 @@ class MyMigration(Migration):
                     })
 
 
+    def migrate_skipped_unprotected_protected_uris(self, app=None):
+        from utils.legacy import legacy_permission_label
+        logger.info(m18n.n("migration_0019_migrate_old_app_settings"))
+        apps = _installed_apps()
+
+        if app:
+            if app not in apps:
+                logger.error("Can't migrate permission for app %s because it ain't installed..." % app)
+                apps = []
+            else:
+                apps = [app]
+
+        def _get_setting(app, name):
+            s = app_setting(app, name)
+            return s.split(',') if s else []
+
+        for app in apps:
+            skipped_urls = [_sanitized_absolute_url(uri) for uri in _get_setting(app, 'skipped_uris') if uri != '/']
+            skipped_urls += ['re:' + regex for regex in _get_setting(app, 'skipped_regex')]
+            unprotected_urls = [_sanitized_absolute_url(uri) for uri in _get_setting(app, 'unprotected_uris') if uri != '/']
+            unprotected_urls += ['re:' + regex for regex in _get_setting(app, 'unprotected_regex')]
+            protected_urls = [_sanitized_absolute_url(uri) for uri in _get_setting(app, 'protected_uris') if uri != '/']
+            protected_urls += ['re:' + regex for regex in _get_setting(app, 'protected_regex')]
+
+            if skipped_urls != []:
+                permission_create(app+".legacy_skipped_uris", additional_urls=skipped_urls,
+                                  auth_header=False, label=legacy_permission_label(app, "skipped"),
+                                  show_tile=False, allowed='visitors', protected=True, sync_perm=False)
+            if unprotected_urls != []:
+                permission_create(app+".legacy_unprotected_uris", additional_urls=unprotected_urls,
+                                  auth_header=True, label=legacy_permission_label(app, "unprotected"),
+                                  show_tile=False, allowed='visitors', protected=True, sync_perm=False)
+            if protected_urls != []:
+                permission_create(app+".legacy_protected_uris", additional_urls=protected_urls,
+                                  auth_header=True, label=legacy_permission_label(app, "protected"),
+                                  show_tile=False, allowed=permission_list()['permissions']['allowed'],
+                                  protected=True, sync_perm=False)
+
+            app_setting(app, 'skipped_uris', delete=True)
+            app_setting(app, 'unprotected_uris', delete=True)
+            app_setting(app, 'protected_uris', delete=True)
+
+        permission_sync_to_user()
+
+
     def run(self):
 
         # FIXME : what do we really want to do here ...
@@ -100,7 +145,8 @@ class MyMigration(Migration):
             # Update LDAP database
             self.add_new_ldap_attributes()
 
-            app_ssowatconf()
+            # Migrate old settings
+            self.migrate_skipped_unprotected_protected_uris()
 
         except Exception as e:
             logger.warn(m18n.n("migration_0019_migration_failed_trying_to_rollback"))
diff --git a/src/yunohost/utils/legacy.py b/src/yunohost/utils/legacy.py
index e7f584d6a..1045bf9f2 100644
--- a/src/yunohost/utils/legacy.py
+++ b/src/yunohost/utils/legacy.py
@@ -112,3 +112,35 @@ class SetupGroupPermissions():
                 user_permission_update(app + ".main", add="visitors", sync_perm=False)
 
         permission_sync_to_user()
+
+LEGACY_PERMISSION_LABEL = {
+        ("nextcloud": "skipped"): "api ",            # .well-known
+        ("libreto": "skipped"): "pad access",        # /[^/]+
+        ("leed": "skipped"): "api",                  # /action.php, for cron task ...
+        ("mailman": "protected"): "admin",           # /admin
+        ("prettynoemiecms": "protected"): "admin",   # /admin
+        ("etherpad_mypads": "skipped"): "admin",     # /admin
+        ("baikal": "protected"): "admin",            # /admin/
+        ("couchpotato": "unprotected"): "api",       # /api
+        ("freshrss": "skipped"): "api",              # /api/,
+        ("portainer": "skipped"): "api",             # /api/webhooks/
+        ("jeedom": "unprotected"): "api",            # /core/api/jeeApi.php
+        ("bozon": "protected"): "user interface",    # /index.php
+        ("limesurvey": "protected"): "admin ",       # /index.php?r=admin,/index.php?r=plugins,/scripts
+        ("kanboard": "unprotected"): "api ",         # /jsonrpc.php
+        ("seafile": "unprotected"): "medias",        # /media
+        ("ttrss": "skipped"): "api",                 # /public.php,/api,/opml.php?op=publish
+        ("libreerp": "protected"): "admin ",         # /web/database/manager
+        ("z-push": "skipped"): "api ",               # $domain/[Aa]uto[Dd]iscover/.*
+        ("radicale": "skipped"): "?",                # $domain$path_url
+        ("jirafeau": "protected"): "user interface", # $domain$path_url/$","$domain$path_url/admin.php.*$
+        ("opensondage": "protected"): "admin",       # $domain$path_url/admin/
+        ("lstu": "protected"): "user interface",     # $domain$path_url/login$","$domain$path_url/logout$","$domain$path_url/api$","$domain$path_url/extensions$","$domain$path_url/stats$","$domain$path_url/d/.*$","$domain$path_url/a$","$domain$path_url/$
+        ("lutim": "protected"): "user interface",    # $domain$path_url/stats/?$","$domain$path_url/manifest.webapp/?$","$domain$path_url/?$","$domain$path_url/[d-m]/.*$
+        ("lufi": "protected"): "user interface",     # $domain$path_url/stats$","$domain$path_url/manifest.webapp$","$domain$path_url/$","$domain$path_url/d/.*$","$domain$path_url/m/.*$
+        ("gogs": "skipped"): "api ",                 # $excaped_domain$excaped_path/[%w-.]*/[%w-.]*/git%-receive%-pack,$excaped_domain$excaped_path/[%w-.]*/[%w-.]*/git%-upload%-pack,$excaped_domain$excaped_path/[%w-.]*/[%w-.]*/info/refs
+
+ }
+
+def legacy_permission_label(app, permission_type):
+    return LEGACY_PERMISSION_LABEL.get((app, permission_type), "Legacy %s urls" % permission_type)