WordPress filters offer a great way to control many aspects of the way the WordPress engine processes or publishes information, without hacking any of the core code.
In recent projects I've found filters to be the easiest way to manage many of the functionality requests the client has made. Some examples of the are: RSS formatting, custom Avatars, auto rendering images/links in comments, controlling the Category used in permalinks, reformatting legacy data in posts, and even tweaking the behaviour of Admin pages.
All these changes can add up to quite a chunk of code and functions.php was getting quite large and difficult to maintain with all the other general functions in there. I decided to move all the filter functions and add_filter statements into a separate file called functions_filters.php and include it from functions.php. This made it much easier to add/maintain filters and localised the changes to that dedicated file.
It's an incredibly simple idea, but I highly recommend taking this approach if you are implementing filters to any degree.
If you've not used filters but want to learn more, you can find a good introduction here: http://codex.wordpress.org/Plugin_API/Filter_Reference
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