docs: consolidate MCP/ subdirectory into MCPHostConfiguration.md

Implement DRY compliance by eliminating content duplication:

Content Migration:
- Advanced synchronization patterns from MCP/synchronization_commands.md
- Management operations from MCP/direct_management_commands.md
- Pattern-based filtering and multi-host batch operations
- Server removal workflows and safety features
- Host validation and error handling

Benefits:
- Single source of truth for all MCP host configuration information
- Eliminated 458 lines of duplicated content across 2 files
- Reduced maintenance overhead and user confusion
- Improved navigation with consolidated reference documentation

Follows DRY compliance analysis v2 recommendations for Option A:
Complete MCP/ subdirectory elimination with content preservation.

All unique content preserved with proper cross-references to CLIReference.md
for command syntax specifications.

Author: LittleCoinCoin