Add comprehensive settings and configuration documentation

[Copilot]

Created centralized configuration reference for environment variables, Claude Code settings, MCP servers, Gemini API, and notification hooks.

Changes

• New documentation: docs/settings-guide.md (765 lines)

  • Environment variable priority hierarchy across 6 configuration levels
  • Claude Code settings.json configuration options
  • MCP server setup (Context7, Human MCP, Chrome DevTools, Sequential Thinking)
  • Gemini API integration (AI Studio & Vertex AI)
  • Discord/Telegram notification hooks
  • Quick setup scripts and troubleshooting

• Cross-references added:

  • README core documentation and Gemini/MCP sections
  • System architecture document (Secret Management, MCP Integration)
  • CLAUDE.md documentation list

Example: Environment Priority

# Highest priority
export GEMINI_API_KEY='from-shell'

# Project root (recommended)
echo 'GEMINI_API_KEY=from-root' > .env

# Claude-level override
echo 'GEMINI_API_KEY=from-claude' > .claude/.env

# Hooks-level (lowest)
echo 'GEMINI_API_KEY=from-hooks' > .claude/hooks/.env

The guide consolidates configuration scattered across .env.example, setup docs, and hook-specific READMEs into a single, scannable reference.

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