Add GitHub Remote MCP toolsets preflight check with graceful degradation

[Copilot]

GitHub Remote MCP auth-test fails when toolsets aren't loaded in the runner environment, producing "tool not found" errors misclassified as authentication failures. No preflight verification exists before agent execution.

Changes

Preflight check script (check_github_remote_mcp_toolsets.sh)

• Sends MCP tools/list request to verify toolset availability
• Distinguishes auth failures (401/403) from missing toolsets (empty tools list)
• Exit codes: 0=available, 1=unavailable, 2=skip (local mode/not configured)
• Provides context-specific remediation steps

Gateway startup integration (start_mcp_gateway.sh)

• Invokes preflight check after connectivity validation
• Graceful degradation: logs warning on toolset unavailability, continues execution
• Delegates missing tool handling to agent via safe-outputs reporting

Test coverage (check_github_remote_mcp_toolsets_test.sh)

• Validates argument handling, config parsing, mode detection, URL filtering

Behavior

Toolsets unavailable:

ERROR: GitHub Remote MCP returned empty tools list

Root Cause:
  The GitHub MCP toolsets (repos, issues, discussions, etc.) are not available.
  This is not an authentication issue - the server is reachable but the
  tools themselves are not loaded.

Remediation:
  1. Verify GitHub Copilot MCP service status
  2. Check if the toolsets feature is enabled for your GitHub organization
  3. Consider using local mode (mode: local) as a fallback

Workflow continues, agent detects missing tools and creates safe-outputs discussion with diagnostic context.

Original prompt

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This section details on the original issue you should resolve

<issue_title>[deep-report] Harden GitHub Remote MCP auth-test by ensuring toolsets load or fallback to local mode</issue_title>
<issue_description>### Description
The GitHub Remote MCP auth-test continues to fail because GitHub MCP toolsets are not loaded in the runner (tools missing, not auth failures). Add a preflight check to verify tool availability, and implement a documented fallback (e.g., switch to local mode or emit an actionable error with remediation) when remote toolsets are unavailable.

Expected Impact

Reduces false-negative auth-test failures and improves signal on actual MCP availability issues.

Suggested Agent

workflow-analysis or mcp-analysis agent

Estimated Effort

Medium (1-4 hours)

Data Source

DeepReport Intelligence Briefing 2026-01-26; auth-test discussion §21356644658

AI generated by DeepReport - Intelligence Gathering Agent

Comments on the Issue (you are @copilot in this section)

• Fixes [deep-report] Harden GitHub Remote MCP auth-test by ensuring toolsets load or fallback to local mode #11895

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