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I upgraded my kickstart 2 RC1 store to 2.5 today, aside from a few issues with a view that I was told by the upgrade to disable, it went great. However the cool collection term to menu mapping feature is now broken.
I noticed when I edited a product and saved it, it started adding terms to the menu even if they were already there. So now I have a really huge menu messing up the site with many duplicates in it.
I tried disabling and uninstalling Commerce Kickstart Taxonomy which cleaned out the menu but as I edit or add products its still adding redundant entries into the menu.
For now I dont have any other choice but to disable sync on taxonomy menu and manually edit the menu. this seems to stop the redundand copies until this gets fixed.