Annnnd I forgot to add the migration

src/yunohost/data_migrations/0012_futureproof_appslist_system.py

@@ -0,0 +1,46 @@
+
+import os
+import shutil
+
+from moulinette.utils.log import getActionLogger
+from moulinette.utils.filesystem import read_json
+
+from yunohost.tools import Migration
+from yunohost.app import (_initialize_appslists_system,
+                          _update_appslist,
+                          APPSLISTS_CACHE,
+                          APPSLISTS_CONF)
+
+logger = getActionLogger('yunohost.migration')
+
+LEGACY_APPSLISTS_CONF = '/etc/yunohost/appslists.json'
+LEGACY_APPSLISTS_CONF_BACKUP = LEGACY_APPSLISTS_CONF + ".old"
+
+
+class MyMigration(Migration):
+
+    "Migrate to the new future-proof appslist system"
+
+    def migrate(self):
+
+        if not os.path.exists(LEGACY_APPSLISTS_CONF):
+            logger.info("No need to do anything")
+
+        # Destroy old lecacy cache
+        if os.path.exists(APPSLISTS_CACHE):
+            shutil.rmtree(APPSLISTS_CACHE)
+
+        # Backup the legacy file
+        try:
+            legacy_list = read_json(LEGACY_APPSLISTS_CONF)
+            # If there's only one list, we assume it's just the old official list
+            # Otherwise, warn the (power-?)users that they should migrate their old list manually
+            if len(legacy_list) > 1:
+                logger.warning("It looks like you had additional appslist in the configuration file %s! YunoHost now uses %s instead, but it won't migrate your custom appslist. You should do this manually. The old file has been backuped in %s." % (LEGACY_APPSLISTS_CONF, APPSLISTS_CONF, LEGACY_APPSLISTS_CONF_BACKUP))
+        except Exception as e:
+            logger.warning("Unable to parse the legacy conf %s (error : %s) ... migrating anyway" % (LEGACY_APPSLISTS_CONF, str(e)))
+
+        os.rename(LEGACY_APPSLISTS_CONF, LEGACY_APPSLISTS_CONF_BACKUP)
+
+        _initialize_appslists_system()
+        _update_appslist()