Platform-specific gem ignored and Gemfile.lock unexpectedly changed by bundle install after upgrading to Ruby 3.3.0

Describe the problem as clearly as you can

When upgrading from Ruby 3.2.3 to 3.3.0, a bundle install on platform x86_64-linux seems to ignore the platform-specific versions, installs the gem with native extensions, and modifies the Gemfile.lock as follows:

--- Gemfile.lock-3.2.3	2024-03-05 17:16:44
+++ Gemfile.lock	2024-03-05 17:18:53
@@ -4,3 +4,3 @@
-    sqlite3 (1.6.7-arm64-darwin)
-    sqlite3 (1.6.7-x86_64-darwin)
-    sqlite3 (1.6.7-x86_64-linux)
+    mini_portile2 (2.8.5)
+    sqlite3 (1.6.7)
+      mini_portile2 (~> 2.8.0)

Did you try upgrading rubygems & bundler?

Yes, issue reproduced with 3.5.6/2.5.6

Post steps to reproduce the problem

With this setup script in setup_lockfile.sh on the host machine:

set -eux

gem update --system 3.5.6

bundle init
bundle lock --add-platform arm64-darwin
bundle lock --add-platform x86_64-darwin
bundle lock --remove-platform ruby

echo "gem 'sqlite3', '= 1.6.7'" >> Gemfile
bundle install

Run the script inside a Ruby 3.2.3 container:

docker run --rm --volume $(pwd):/repro --workdir /repro ruby:3.2.3-slim bash setup_lockfile.sh

Which will generate this Gemfile.lock:

GEM
  remote: https://rubygems.org/
  specs:
    sqlite3 (1.6.7-arm64-darwin)
    sqlite3 (1.6.7-x86_64-darwin)
    sqlite3 (1.6.7-x86_64-linux)

PLATFORMS
  arm64-darwin
  x86_64-darwin
  x86_64-linux

DEPENDENCIES
  sqlite3 (= 1.6.7)

BUNDLED WITH
   2.5.6

With this script in demonstrate_issue.sh on the host machine (in the same directory as the Gemfile{,.lock} as generated by the 3.2.3 container in the previous step):

set -eux

apt-get update
apt-get install -y build-essential pkg-config

gem update --system 3.5.6

bundle install

Run the script inside a Ruby 3.3.0 container:

docker run --rm --volume $(pwd):/repro --workdir /repro ruby:3.3.0-slim bash demonstrate_issue.sh

...then (after a delay to install the extension) the following Gemfile.lock is generated:

GEM
  remote: https://rubygems.org/
  specs:
    mini_portile2 (2.8.5)
    sqlite3 (1.6.7)
      mini_portile2 (~> 2.8.0)

PLATFORMS
  arm64-darwin
  x86_64-darwin
  x86_64-linux

DEPENDENCIES
  sqlite3 (= 1.6.7)

BUNDLED WITH
   2.5.6

Which command did you run?

bundle install after upgrading Ruby to 3.3.0.

What were you expecting to happen?

That sqlite3 (1.6.7-x86_64-linux) would be installed (thus not requiring build-essential and pkg-config) and the Gemfile.lock to not be modified.

What actually happened?

The platform-specific gem in the lockfile was ignored (with no output to say why) and the lockfile was modified to remove the other platform-specific versions.

If not included with the output of your command, run bundle env and paste the output below

In the Ruby 3.2.3 container:

Bundler       2.5.6
  Platforms   ruby, x86_64-linux
Ruby          3.2.3p157 (2024-01-18 revision 52bb2ac0a6971d0391efa2275f7a66bff319087c) [x86_64-linux]
  Full Path   /usr/local/bin/ruby
  Config Dir  /usr/local/etc
RubyGems      3.5.6
  Gem Home    /usr/local/bundle
  Gem Path    /root/.local/share/gem/ruby/3.2.0:/usr/local/lib/ruby/gems/3.2.0:/usr/local/bundle
  User Home   /root
  User Path   /root/.local/share/gem/ruby/3.2.0
  Bin Dir     /usr/local/bundle/bin
Tools
  Git         not installed
  RVM         not installed
  rbenv       not installed
  chruby      not installed

In the Ruby 3.3.0 container:

Bundler       2.5.6
  Platforms   ruby, x86_64-linux
Ruby          3.3.0p0 (2023-12-25 revision 5124f9ac7513eb590c37717337c430cb93caa151) [x86_64-linux]
  Full Path   /usr/local/bin/ruby
  Config Dir  /usr/local/etc
RubyGems      3.5.6
  Gem Home    /usr/local/bundle
  Gem Path    /root/.local/share/gem/ruby/3.3.0:/usr/local/lib/ruby/gems/3.3.0:/usr/local/bundle
  User Home   /root
  User Path   /root/.local/share/gem/ruby/3.3.0
  Bin Dir     /usr/local/bundle/bin
Tools
  Git         not installed
  RVM         not installed
  rbenv       not installed
  chruby      not installed

Start with setup_lockfile.sh and demonstrate_issue.sh, then reproduce the difference by running them in the Ruby 3.2.3 and Ruby 3.3.0 containers. Compare the resulting Gemfile.lock files and Bundler output; done means bundle install selects sqlite3 (1.6.7-x86_64-linux) and leaves the lockfile unchanged.