"bundle clean" removes git dependencies with RubyGems 3+ when path involves symlink

[GUI]

The bundle clean command removes gems that are still being used if all 3 of these criteria are true:

1. RubyGems 3.0+ is being used.
2. The bundler installation path contains a symlink anywhere in the path (it could be the final directory, or any intermediate).
3. A git dependency is present in your Gemfile.

If all 3 of these situations apply, then bundle clean will always remove the git dependencies present in your Gemfile, despite the fact that those gems are still in use. This occurs in both Bundler 2 and Bundler 1.7.

I'm wondering if this is related to these symlink changes in RubyGems 3.0: rubygems/rubygems#2352 However, since this issue is specific to git dependencies supported by Bundler, that's why I'm filing the ticket here, but let me know if I should file this on RubyGems instead.

Here's a demonstration of the issue (with Bundler 2.0.2, but the same behavior is seen with Bundler 1.17.3 as long as RubyGems 3+ is used):

# Create a Gemfile with a git dependency.
mkdir test-bundler
cd test-bundler
printf 'source "https://rubygems.org"\ngem "rack", :git => "https://github.com/rack/rack.git"' > Gemfile

# Create a symlink
mkdir real-path
ln -s real-path symlink-path

# Ruby, RubyGems, and Bundler versions
ruby --version
# ruby 2.6.3p62 (2019-04-16 revision 67580) [x86_64-darwin16]
gem update --system 3.0.4
gem install bundler --version 2.0.2
gem --version
# 3.0.4
bundle --version
# Bundler version 2.0.2

# Install to symlink
bundle install --path=./symlink-path

# Run "bundle clean", which removes the git dependency.
bundle clean --verbose
# Running `bundle clean --verbose` with bundler 2.0.2
# Found no changes, using resolution from the lockfile
# Removing rack (70c838f7204f)

bundle exec ruby -e 'puts "Hello, world."'
# https://github.com/rack/rack.git (at master@70c838f) is not yet checked out. Run `bundle install` first.

Note that this issue does not occur if you're not using a symlink in RubyGems 3+:

gem --version
# 3.0.3
bundle --version
# Bundler version 2.0.2

bundle install --path=./real-path

bundle clean --verbose
# Running `bundle clean --verbose` with bundler 2.0.2
# Found no changes, using resolution from the lockfile

bundle exec ruby -e 'puts "Hello, world."'
# Hello, world.

It also does not occur if you are using a symlink, but are using RubyGems 2:

gem update --system 2.7.10

gem --version
# 2.7.10
bundle --version
# Bundler version 2.0.2

bundle install --path=./symlink-path

bundle clean --verbose
# Running `bundle clean --verbose` with bundler 2.0.2
# Found no changes, using resolution from the lockfile

bundle exec ruby -e 'puts "Hello, world."'
# Hello, world.

[deivid-rodriguez]

Thanks for the super clean repro. This should be fixed by #7211.