Am I correct in assuming W3 Total Cache (W3TC) will affect only the WordPress driven content (pages/posts/CCT) of a site?
Especially if WP is installed in the root level of a site, but there is a combination of js/jquery used within the content of a wordpress Page, AND various non-wordpress js/php files used in other directories in the site root, all used as part of one overall website?
Is it possible that W3TC (or any wp caching plugin for that matter) can have effects on site pages/files outside the wordpress install? I realize that's a loaded question, especially with W3TC as its got a huge amount of potential settings. We had it set up very basic and conservative, no Minify, really only using Page caching using Disk Enhanced on a shared server, no CDN or anything like that.
Does W3TC affect htaccess file(s) in such a way that non-wp files could not load correctly or seem to revert to older versions? I admit to being fuzzy on what exactly caching plugins are all doing behind the scenes (I get the idea of what caching is, but the how/what/why of htaccess comes into play?)
This topic stems from a real world situation where other programming was affected and we're trying to narrow down the cause (specifically, if W3TC could have had a role).
Would greatly appreciate some enlightenment here. Thanks!