They are part of the quest folder download detailed on step 5 a). Looking at the repository online, these folders exist.
To do it manually without using Subversion to get the latest version, you can download quests_2015-02-13-07-59.tar.gz from
https://drive.google.com/folderview?...p=sharing#list and use something like 7-zip to unzip then untar it. This will give you a folder called "quests", which definitely does have the lua_modules and plugins folders in it.