pip uninstall does not remove symlinks created by flit install --symlink

[sbidoul]

Environment

• pip version: 19.2
• Python version: 3
• OS: linux

Description

pip uninstall does not remove symlinks created in a virtualenv by flit install --symlink,
because it thinks they are outside the virtualenv prefix.

Expected behavior

Such symlinks should be removed by pip uninstall

How to Reproduce

$ python3 -m venv venv
$ source venv/bin/activate
$ pip install -U pip
$ git clone https://github.com/pypa/pep517.git  # example flit project
$ cd pep517
$ pip install flit
$ flit install --symlink
$ pip uninstall pep517
Uninstalling pep517-0.6.0:
  Would remove:
    /home/my/.virtualenvs/tempenv-2d6243995df5/lib/python3.7/site-packages/pep517-0.6.0.dist-info/*
  Would not remove (outside of prefix):
    /home/my/.virtualenvs/tempenv-2d6243995df5/lib/python3.7/site-packages/pep517
Proceed (y/n)? 

Analysis

I could find work on this issue before in #2552 by @takluyver and #3154 by @qwcode. I did not find what commit caused the problem to surface again.

[chrahunt]

Do you know if there are any versions in which this does work? I tried the versions containing those fixes but did not have any that would remove the file (of 6.0.0, 6.1.0, 7.0.0, 8.0.0, 9.0.0, 10.0.0, 18.1).

[sbidoul]

After posting this, I confirmed #3154 does not work for the use case above.

A fix seems straightforward on the current code base (diff). But it reveals another issue: when uninstalling such symlinks, pip ends up modifying the permissions on the target directory to 0200...