fix: run additional passes before setting the parent of the system

Author: AayushSabharwal

src/systems/systems.jl

@@ -46,12 +46,12 @@ function structural_simplify(
             not yet supported.
         """)
     end
+    for pass in additional_passes
+        newsys = pass(newsys)
+    end
     if newsys isa ODESystem || has_parent(newsys)
         @set! newsys.parent = complete(sys; split, flatten = false)
     end
-    for pass in additional_passes 
-        newsys = pass(newsys)
-    end
     newsys = complete(newsys; split)
     if has_defaults(newsys) && (defs = get_defaults(newsys)) !== nothing
         ks = collect(keys(defs))  # take copy to avoid mutating defs while iterating.