[docs] Document GitHub App token minting for GitHub MCP server

[github-actions]

Documentation Updates - January 24, 2026

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

Features Documented

• GitHub App token minting for GitHub MCP server (from Add GitHub App token minting for GitHub MCP server #11660)
  • Added new "GitHub App Authentication" section in tools reference
  • Documents configuration with app-id and private-key
  • Explains benefits: short-lived tokens, automatic revocation, no PAT rotation
  • Includes setup instructions and shared workflow pattern
  • Documents token precedence and permission mapping

Changes Made

• Updated docs/src/content/docs/reference/tools.md
  • Added comprehensive GitHub App authentication section after "Modes and Restrictions"
  • Includes configuration examples, benefits, setup instructions
  • Documents shared workflow pattern for reusable app configuration
  • Cross-references to GitHub Tokens page for complete auth options

Merged PRs Referenced

• Add GitHub App token minting for GitHub MCP server #11660 - Add GitHub App token minting for GitHub MCP server (merged 2026-01-24T16:52:02Z)
  • Major feature: Enables GitHub App authentication for GitHub MCP server
  • Uses repository variables APP_ID and secret APP_PRIVATE_KEY
  • Automatic token minting at workflow start, invalidation at end
  • Permissions auto-mapped from job permissions field
  • Works with both local (Docker) and remote (hosted) modes

Other Notable PRs (Last 24 Hours)

Documentation-related PRs (already completed):

• Document label-only exception for slash_command triggers #11672 - Document label-only exception for slash_command triggers
• Add agentic upgrade tip to documentation #11643 - Add agentic upgrade tip to documentation
• Add missing dispatch-workflow to safe output documentation #11642 - Add missing dispatch-workflow to safe output documentation

Internal improvements (no user-facing doc updates needed):

• Add report formatting guidelines to daily-compiler-quality workflow #11678, Add markdown formatting guidelines to daily-firewall-report workflow #11663, Standardize CLI verbose/info messages to use console formatters #11662, Abstract manual ANSI escape sequences to console package #11661, Add markdown formatting guidelines to daily-cli-performance workflow #11658, Add markdown style guidelines to daily-news workflow #11657, Add markdown formatting guidelines to daily-file-diet workflow #11659 - Workflow formatting guidelines and console package refactoring
• Add error wrapping to compiler activation job builders #11670, [code-simplifier] Consolidate duplicate file deletion logic in deleteOldAgentFiles #11667 - Code quality improvements
• Add codemod to delete legacy agent files from .github/agents/ #11654 - Codemod for legacy agent files cleanup
• Remove workdir field from generated MCP server configuration #11640 - Remove workdir field from MCP config (internal)
• Migrate mcp_inspect_mcp.go to console package abstraction #11636, Replace manual prompt with console.ConfirmAction() in remove command #11637, Standardize error messages to use console formatting with stderr #11638, Add console error formatting to MCP CLI commands #11606 - Console formatting standardization
• Update MCP Gateway to v0.0.78 and fix test version references #11633 - MCP Gateway version update
• Fix markdown code region balancer for mismatched fence lengths #11631 - Markdown code region balancer fix
• Run discussion-task-miner every 4 hours instead of daily #11629 - Discussion task miner frequency change
• Add action pin updates to upgrade command after codemods #11626, Update action pins to latest releases (checkout v6.0.2, download-artifact v7.0.0) #11618 - Action pin updates
• Fix template injection validator false positives when env: follows run: #11586, Refactor CodingAgentEngine using Interface Segregation Principle #11607, Refactor ParseWorkflowFile: extract three helper functions to reduce complexity #11592, Refactor schedule_parser: split 1163-line file into focused modules #11588 - Code refactoring and complexity reduction
• [ca] Fix GitHub MCP allowed_tools rendering and numeric reaction parsing #11603, [docs] Consolidate developer specifications with tone improvements #11617 - Bug fixes and spec consolidation

Notes

The GitHub App token minting feature (#11660) was the only user-facing feature requiring documentation updates from the last 24 hours. All other PRs were either:

• Documentation updates themselves (already complete)
• Internal refactoring/improvements (not user-visible)
• Workflow/tooling changes (internal to the project)

The documentation follows GitHub Docs voice guidelines and includes:

• Clear explanations of benefits and use cases
• Step-by-step setup instructions
• Configuration examples with proper syntax
• Cross-references to related documentation
• Notes about token precedence and behavior

AI generated by Daily Documentation Updater