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Fix bundler env being copied to Ruby runner
Fix issues with the wrong bundle of gems being used as context for the runner. This failed to find the Ruby gem as it was using this project's test suite Gemfile instead. Wrap commands with `Bundler.with_unbundled_env` so it removes any Bundler context from the environment. It also clears some other env vars, so explicitly set them again in the base `run_env` method.
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