Fix conflicts with upstream Galaxy

Summary of Changes

Should fix stop jobs, uploading, and stdout. Remember to use stdout, you need to have the "live_tool_output_reporting" parameter set to true in your job_conf.xml under the job destination.

eg

<destination id="test_pulsar_http" runner="pulsar_http">
    <param id="url">http://localhost:8913/managers/http_local</param>
    <param id="default_file_action">remote_copy</param>
    <param id="live_tool_output_reporting">true</param>
</destination>

Checklist

• The MR has a clear and concise title
• Code is self-documented and follows style guidelines.
• Automated tests are written and pass successfully.
• Regression tests (e.g. manually triggered system tests, manual GUI/tool tests, ...) are performed to make sure the MR does not break anything (when applicable)
• Readme file is present and up-to-date.

Documentation Updates

Additional Notes