I was using 7.x-3.1 beta 3 then I updated to 7.x-3.x and then my menu stopped being overriden.

My function is subtheme_menu_tree__primary, it was working good before the update.

I also noticed that there are 2 bootstrap_menu_tree__primary, one inside templates/menu and another inside theme/menu.

It seems that the one inside theme/menu is the one being used, I've tried to put my subtheme file inside those directories (recreated in my subtheme) but they don't seem to work.

Any idea?

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Jorgee created an issue. See original summary.

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My file is named menu-tree.func.php and is located in subtheme/templates directory.

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I just noticed that also menu-link.func.php is not working.
Maybe all *.func.php?

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Status: Active » Closed (cannot reproduce)

Sorry, I badly updated copying over the new download without deleting the entire directory.