feat: add run_command tool to fix_pipeline flow

What does this merge request do and why?

Adds the run_command tool to the execution step in the fix_pipeline flow, to allow the agent to check if changes fix issues with unit tests, linting, etc.

Relates to #1588

How to set up and validate locally

1. Set up Duo Agent Platform
2. Set up the Flow Registry in your GDK
3. Run a Fix Pipeline Flow
4. Check your Flow Output in Automate > Agent sessions

Merge request checklist

• Tests added for new functionality. If not, please raise an issue to follow up.
• Documentation added/updated, if needed.
• If this change requires executor implementation: verified that issues/MRs exist for both Go executor and Node executor or confirmed that changes are backward-compatible and don't break existing executor functionality.