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- Removed outdated MCP references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/docs.json

@@ -66,7 +66,7 @@
           "architecture/hooks",
           "architecture/worker-service",
           "architecture/database",
-          "architecture/mcp-search"
+          "architecture/search-architecture"
         ]
       }
     ]