bundle clean native extensions for gems with a git source

[dylanahsmith]

The bug fix for #5596 didn't clean extensions for gems with a git source, which ironically was my original use case for opening that issue

Note that my actual use case was that I want to uninstall a gem installed through bundler from a git source, where gem uninstall can't be used.

The remaining issue can be reproduced as follows.

Create this Gemfile

gem 'cityhash', git: 'https://github.com/nashby/cityhash.git', ref: 'v0.9.0'

then install and uninstall the gem using bundler

$ bundle install --path .bundle
...
Using bundler 1.17.3
Using cityhash 0.9.0 from https://github.com/nashby/cityhash.git (at v0.9.0@f2a15ac)
...
$ find .bundle -name '*.bundle'
.bundle
.bundle/ruby/2.5.0/bundler/gems/cityhash-f2a15ac7cc71/ext/cityhash/cityhash.bundle
.bundle/ruby/2.5.0/bundler/gems/cityhash-f2a15ac7cc71/lib/cityhash/cityhash.bundle
.bundle/ruby/2.5.0/bundler/gems/extensions/x86_64-darwin-18/2.5.0-static/cityhash-f2a15ac7cc71/cityhash/cityhash.bundle
$ touch empty_gemfile
$ BUNDLE_GEMFILE=empty_gemfile bundle clean --force
Resolving dependencies...
Removing cityhash (f2a15ac7cc71)
$ find .bundle -type f
.bundle/config
.bundle/ruby/2.5.0/bundler/gems/extensions/x86_64-darwin-18/2.5.0-static/cityhash-f2a15ac7cc71/gem_make.out
.bundle/ruby/2.5.0/bundler/gems/extensions/x86_64-darwin-18/2.5.0-static/cityhash-f2a15ac7cc71/gem.build_complete
.bundle/ruby/2.5.0/bundler/gems/extensions/x86_64-darwin-18/2.5.0-static/cityhash-f2a15ac7cc71/cityhash/cityhash.bundle

so the extension wasn't completely cleaned. The presence of the gem.build_complete will prevent the extension from being rebuilt.

I was also able to reproduce this issue on master.

[dylanahsmith]

I think the fix for this is

diff --git a/lib/bundler/runtime.rb b/lib/bundler/runtime.rb
index 762e7b3ec..83945868f 100644
--- a/lib/bundler/runtime.rb
+++ b/lib/bundler/runtime.rb
@@ -163,7 +163,7 @@ module Bundler
       gem_dirs             = Dir["#{Gem.dir}/gems/*"]
       gem_files            = Dir["#{Gem.dir}/cache/*.gem"]
       gemspec_files        = Dir["#{Gem.dir}/specifications/*.gemspec"]
-      extension_dirs       = Dir["#{Gem.dir}/extensions/*/*/*"]
+      extension_dirs       = Dir["#{Gem.dir}/extensions/*/*/*"] + Dir["#{Gem.dir}/bundler/gems/extensions/*/*/*"]
       spec_gem_paths       = []
       # need to keep git sources around
       spec_git_paths       = @definition.spec_git_paths