Those "boxes" folders were for adding menu items. That approach is now obsolete. Those folders are ignored - intentionally.
But converting addons for v1.5 compatibility requires two primary things:
a) rebuilding the menu options by inserting the required page associations into the database.
b) rewriting all forms to use the POST method instead of GET whenever those forms trigger UPDATE statements of any sort into the database. GET parameters should only be used for things like filters, and even then they need to be sanitized. In fact, the other part of form rewriting is that ALL inputs need to be sanitized before use.
If you don't do those things then your admin won't show the menu options, and even if they did they might be non-functional because if the forms aren't rewritten and sanitized then all updates will just redirect you to the admin home screen instead of doing the action required/expected.
There are other forum threads discussing the "how to" of these things.
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