I am reading on the article how to generate an Apple-like HTML documentation at here. My questions are what the command lines are used for. How can we combine command lines and appledoc xcode project to generate a HTML.
I haven't used 'appledoc', but from a quick look at the page you linked it appears that it's an open-source command-line utility. So the first step will be to compile the 'appledoc' program itself, and then stick it in a directory that's in your path, such as /usr/local/bin or ~/bin/.
The next step is to try to use it to generate some documentation (assuming that you've already created the markdown files that it consumes). Open a terminal window, navigate to the directory where your files are, and then use the command given at the top of the page that you linked:
appledoc --project-name appledoc --project-company "Gentle Bytes" --company-id com.gentlebytes --output ~/help .
If you want to use 'appledoc' to regenerate your documentation every time you build some project, you can add a "Run Script" build phase to an existing target in your project, or create a new target just for documentation that has nothing but a "Run Script" build phase. Either way, the script in that phase should be shell script containing a command similar to the one above (though you'll probably want to specify the source directory explicitly rather than just using the 'current' directory, i.e. .).