I'm trying to integrate W3 Total Cache into our Workflow.
We have a base repository that our sites are forked from. I have installed W3TC into that base repository. On deploy, I add symlinks to the wp-content/*.php files. As far as I can tell it's not a problem having these there all the time, even if they're not currently used, but I still see a warning in the admin saying they should be deleted.
I also see warnings due to the wp-content folder being writable. It is mode 0775, but it is not writable as the owner is user:user.
I think everything is set up correctly now, but it would be nice to suppress these errors.