Appledoc not only includes the HTML files that where generated from the markdown files, but also seems to copy the original template files to the html folder. These files are unnecessary.
At present I specify --keep-intermediate-files to keep the html output so that I can publish that on a webserver. That might be what's causing this. If this is the case, is there a method to get the HTML output that does not include intermediate files?
I get the content out of the docset itself, if you do a Show Package Contents and then get look in Contents/Resources/Documents - the Documents folder itself will hold all the HTML you're interested in. I extract this via a script to create the HTML