Enlightenment 17, adding apps to the menu

I just installed Enlightenment 17 and the only way I know to add items to the menu is with the configuration tool but it doesn't show all the apps on my sytstem only some of them.
Also, the docs say to put themes in ~/.e/e/themes but that's a hidden folder. The configuration tool doesn't show the hidden folders so how do you add themes? Is there a way to manually edit the config?
 
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