The `site` module documentation says that in .pth files, "Blank lines and lines beginning with # are skipped.". However, the implementation does not actually skip blank lines. It then joins the empty string to the site-packages directory, resulting in the site-packages directory being added to sys.path a second time.

Example:

$ python -c 'import sys; print(sys.path)'
['', '/home/smith/.virtualenvs/foo/lib/python36.zip', '/home/smith/.virtualenvs/foo/lib/python3.6', '/home/smith/.virtualenvs/foo/lib/python3.6/lib-dynload', '/usr/lib/python3.6', '/home/smith/.virtualenvs/foo/lib/python3.6/site-packages']
$ echo > /home/smith/.virtualenvs/foo/lib/python3.6/site-packages/test.pth
$ python -c 'import sys; print(sys.path)'
['', '/home/smith/.virtualenvs/foo/lib/python36.zip', '/home/smith/.virtualenvs/foo/lib/python3.6', '/home/smith/.virtualenvs/foo/lib/python3.6/lib-dynload', '/usr/lib/python3.6', '/home/smith/.virtualenvs/foo/lib/python3.6/site-packages', '/home/smith/.virtualenvs/foo/lib/python3.6/site-packages']

A patch fixing this is attached to issue 29326, but was ignored when that issue turned out to be caused by something else.