The whole point of creating a custom theme is to get a website to look the way you want it to. So, it's important for the output that modules generate to be themeable.

I will give a simple example of modifying the markup that is used to display some links. The Flag module provides a mechanism to do things such as "liking" a post or reporting a post as spam. A post may have a link for each flag that is associated with it.

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