[docs] Update documentation for features from 2025-11-21

[github-actions]

Documentation Updates - 2025-11-21

This PR updates the documentation based on features merged in the last 24 hours.

Features Documented

• --progress flag for run command (from Add --progress flag to run command for agent CLI keepalive #4450) - Enables timer-based progress messages for long-running workflows
• Noop message parsing in logs and audit commands (from Add noop message parsing to logs and audit commands #4428) - Displays noop stats in overview table and JSON output
• close-discussion safe output type (from Add safe output type to close discussion with comment and resolution #4411) - Allows workflows to close discussions with comments and resolution reasons
• debug-agentic-workflow custom agent (from Add debug-agentic-workflow custom agent for workflow troubleshooting #4449) - Built-in custom agent for debugging workflows
• Audit command suggestion in run output (from Add audit command suggestion to run command output #4445) - Provides guidance to analyze runs after triggering

Changes Made

• docs/setup/cli.md:

  • Added --progress flag to run command documentation
  • Updated logs command to mention noop message column
  • Updated audit command to mention noop messages in output
  • Added note about audit command suggestion after running workflows

• docs/reference/safe-outputs.md:

  • Added close-discussion to safe output types table
  • Created new section documenting close-discussion safe output
  • Documented target resolution modes, filters, and resolution reasons

• docs/reference/custom-agents.md:

  • Added "Built-in Custom Agents" section
  • Documented debug-agentic-workflow custom agent

Merged PRs Referenced

• Add --progress flag to run command for agent CLI keepalive #4450 - Add --progress flag to run command for agent CLI keepalive
• Add debug-agentic-workflow custom agent for workflow troubleshooting #4449 - Add debug-agentic-workflow custom agent for workflow troubleshooting
• Add audit command suggestion to run command output #4445 - Add audit command suggestion to run command output
• Add noop message parsing to logs and audit commands #4428 - Add noop message parsing to logs and audit commands
• Add safe output type to close discussion with comment and resolution #4411 - Add safe output type to close discussion with comment and resolution

Documentation Guidelines

All changes follow the Diátaxis framework and documentation guidelines from .github/instructions/documentation.instructions.md:

• Neutral, technical tone
• Reference-style documentation for CLI and safe outputs
• Concise descriptions without marketing language
• Proper markdown formatting and code block syntax

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