Merge #7211

7211: Use real paths for `bundle clean` r=colby-swandale a=deivid-rodriguez

Fixes #7208.

### What was the end-user problem that led to this PR?

The problem was that since rubygems 3.0, `bundle clean` incorrectly cleans git gems when they are installed to a symlinked location, but still being used.

### What was your diagnosis of the problem?

My diagnosis was that since rubygems/rubygems#2352, `Gem.dir` returns an array of realpaths, not symlinked ones. However, we don't do the same resolution on the `bundler` side, so in this situation git gems are not correctly skipped from the cleanup.

### What is your fix for the problem, implemented in this PR?

My fix is to resolve the array of paths `bundle clean` uses to do its thing into an array of real paths, just like rubygems does now.

### Why did you choose this fix out of the possible options?

I chose this fix because it fixes the problem.


Co-authored-by: David Rodríguez <deivid.rodriguez@riseup.net>

lib/bundler/definition.rb

@@ -317,7 +317,7 @@ def has_local_dependencies?
     end
 
     def spec_git_paths
-      sources.git_sources.map {|s| s.path.to_s }
+      sources.git_sources.map {|s| File.realpath(s.path) }
     end
 
     def groups

spec/commands/clean_spec.rb

@@ -183,6 +183,32 @@ def should_not_have_gems(*gems)
     expect(vendored_gems("bin/rackup")).to exist
   end
 
+  it "keeps used git gems even if installed to a symlinked location" do
+    build_git "foo", :path => lib_path("foo")
+    git_path = lib_path("foo")
+    revision = revision_for(git_path)
+
+    gemfile <<-G
+      source "file://#{gem_repo1}"
+
+      gem "rack", "1.0.0"
+      git "#{git_path}", :ref => "#{revision}" do
+        gem "foo"
+      end
+    G
+
+    FileUtils.mkdir_p(bundled_app("real-path"))
+    FileUtils.ln_sf(bundled_app("real-path"), bundled_app("symlink-path"))
+
+    bundle "install", forgotten_command_line_options(:path => bundled_app("symlink-path"))
+
+    bundle :clean
+
+    expect(out).not_to include("Removing foo (#{revision[0..11]})")
+
+    expect(bundled_app("symlink-path/#{Bundler.ruby_scope}/bundler/gems/foo-#{revision[0..11]}")).to exist
+  end
+
   it "removes old git gems" do
     build_git "foo-bar", :path => lib_path("foo-bar")
     revision = revision_for(lib_path("foo-bar"))