fix: add missing deleted_at columns to all plugin tables, fix system-settings response schema, fix transaction rollback in permissions

app/plugins/builtins/mcp_client/migrations/0001_initial.sql

@@ -8,6 +8,7 @@ CREATE TABLE IF NOT EXISTS mcp_server_configs (
     description TEXT,
     last_connected_at TIMESTAMPTZ,
     created_by UUID,
+    deleted_at TIMESTAMPTZ,
     created_at TIMESTAMPTZ DEFAULT NOW(),
     updated_at TIMESTAMPTZ DEFAULT NOW()
 );