To ensure Robot Ninja continues to function correctly when the W3 Total Cache plugin is enabled you simply need to ensure that you have no other plugins enabled (or custom code) that removes the API link tag WordPress adds to each sites HTML by default. 

W3 Total Cache removes the WordPress API link header in cached responses so it is important we have access to the WordPress API link tag in order to be able to perform API Discovery

An example of a plugin that allows site managers to remove the API link tag is WP Disable.

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