Preserve native extensions during implicit clean

[sjh9714]

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

Fixes #9795.

When a native gem is already activated from the system gem path, an implicit
clean after bundle install can use that system installation's extension path
for the project-local stub. It then treats the still-required extension under
BUNDLE_PATH as stale and removes it silently.

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

Reload a stub's own gemspec when Gem::StubSpecification#to_spec returns an
activated specification from a different installation. This keeps the local
specification and extension paths together when implicit clean computes its
stale directories.

The regression test activates the system copy of a native gem, installs the
same version into BUNDLE_PATH, and changes an unrelated locked gem while
BUNDLE_CLEAN=true. It verifies that cleanup removes the obsolete gem but
preserves the required local native extension.

Make sure the following tasks are checked

• Describe the problem / feature
• Write tests for features and bug fixes
• Write code to solve the problem
• Make sure you follow the current code style and write meaningful commit messages without tags

Testing

• bin/rspec spec/commands/install_spec.rb:2065
• bin/rspec spec/bundler/stub_specification_spec.rb spec/commands/install_spec.rb
• bin/rake rubocop
• PATH="/tmp/oss-rspec-bin:$PATH" bin/rake spec:all (3 existing non-TTY color expectation failures; the same examples fail on the recorded upstream commit)

[hsbt]

👍