Update 4th Feb: the HTML minify bug was fixed in W3TC v. 0.9.7.2, released a couple of days ago.
Update 19th Feb: I’m still seeing issues caused by W3TC, seems like not all is fixed fully yet.
Quick heads-up for users that have both W3 Total Cache and Autoptimize installed; the latest W3TC update (version 0.9.7.1) introduces a nasty bug in the HTML minifier which also impacts Autoptimize as that uses the same minifier class (Minify_HTML, part of Mr. Clay’s Minify). When W3TC is running the Minify_HTML class is loaded by and from W3TC, meaning AO’s autoload does not have to load the Minify_HTML from AO proper (which does not have that problem).
So since Autoptimize 2.0.0 got released half a year ago, minified files are not re-minified any more, which can yield important performance-gains. Or that, at least, is the goal. But as checking if a file is minified is non-trivial, AO reverts to a simpler check; does the filename indicate the file is minified. So for example whatever-min.js and thisone_too.min.css would be considered minified and will simply be aggregated, whereas not_minified.js would get minified. Mr Clay’s Minify (which is used by WP Minify, BWP Minify and W3 Total Cache and of which the core minification components are in Autoptimize as well) applies the same logic.
But apparently plugins often lie about their JS and CSS, with some files claiming to be minified which clearly are not and with some files (even WordPress core files) being minified but not having the min-suffix in the name. It’s obvious that lying like that is kind of stupid: saying your files is minified when in fact it is not, offers you no advantages. Not confirming your file is minified in the name when it is, saves you 4 characters in the filename, but I suspect you were just being lazy, sloppy or tired, no?
So, ladies and gentlemen, can we agree on the following:
Ideally you ship your plugin/ theme with minified JS & CSS.
If your files are minified, you confirm that in the filename by adding the “.min”-suffix and minification plugins will skip them.
If your files are not minified, you don’t include the “.min”-suffix in the filename, allowing for those minification plugins tot minify them.