docs: Update all documentation to reflect v5.4.0 skill-based search

Documentation Updates:
- README.md: Updated version badge, What's New, and search section
- docs/usage/search-tools.mdx: Rewrote for skill-based natural language approach
- docs/architecture/mcp-search.mdx → search-architecture.mdx: Complete rewrite
- docs/architecture/overview.mdx: Updated components and search pipeline
- docs/usage/getting-started.mdx: Added skill-based search section
- docs/configuration.mdx: Updated search configuration for v5.4.0
- docs/introduction.mdx: Updated key features
- docs/docs.json: Updated navigation to search-architecture

Key Changes:
- Emphasized ~2,250 token savings per session start
- Converted all examples to natural language queries
- Documented 10 HTTP API endpoints
- Explained progressive disclosure pattern
- Added migration notes (transparent, no user action required)
- Removed outdated MCP references

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

docs/introduction.mdx

@@ -23,7 +23,7 @@ Restart Claude Code. Context from previous sessions will automatically appear in
 ## Key Features
 
 - 🧠 **Persistent Memory** - Context survives across sessions
-- 🔍 **9 Search Tools** - Query your project history via MCP
+- 🔍 **Skill-Based Search** - Query your project history with natural language (~2,250 token savings)
 - 🌐 **Web Viewer UI** - Real-time memory stream visualization at http://localhost:37777
 - 🎨 **Theme Toggle** - Light, dark, and system preference themes
 - 🤖 **Automatic Operation** - No manual intervention required