Here's an idea... How about if we throw away the xml files (treexml.xml and menustyle.xml) then the extension would recreate them based on the code in our menu.php and menu.css
This would solve the problems currently found when having to rewrite the the files ourselves or when other updates are required to our files. In the current case if you have extensive changes to your css or menu file Menu Writer overwrites and destroys your changes. Or you have to spend loads of time playing with the extensions interface to recreate what you can do manually in little time.
If possible this would be a great addition to the extension and solve many problems for those of us who like an extension to speed site deployment but still have to make manual changes either due to the extension no updating properly or because we already have our list of links available.