I'm similarly confused by this issue. If somebody can help me understand what's going on, I'll put my understanding into a documentation patch.

I have created this minimal example to demonstrate what I don't understand: I've created a directory structure within /tmp like this:

issue22021
└── root
    └── structure
        ├── content
        │   └── please_add.txt
        └── do_not_add.txt


Now I'd like to create a zip archive that contains the directories "structure" and "content", and the file "please_add.txt", but not the file "do_not_add.txt". My understanding of the documentation was that I'd have to do this:

>>> shutil.make_archive(base_name='/tmp/issue22021archive', format='zip', root_dir='/tmp/issue22021/root', base_dir='/tmp/issue22021/root/structure/content')

But on my system, the created file (/tmp/issue22021archive.zip) looks like this according to unzip -l:

Archive:  issue22021archive.zip
  Length      Date    Time    Name
---------  ---------- -----   ----
        0  2018-05-30 00:26   tmp/issue22021/root/structure/content/
        0  2018-05-30 00:26   tmp/issue22021/root/structure/content/please_add.txt
---------                     -------
        0                     2 files

This is consistent with my experience that created archives will always contain directories from / on, which is unexpected to me.

It appears this happens whenever base_dir and root_dir is set, but to my understanding the documentation does not warn against this.

I've confirmed this behaviour with Python 3.6.5 and Python 3.5.3, but I suspect that doesn't really matter, as it seems to be a documentation issue.