docs(mcp): add user guide for direct management commands

Create comprehensive user documentation for Phase 3e direct MCP
management commands covering:

- Server removal from specific hosts with multi-host support
- Complete host configuration removal functionality
- Safety features: backup creation, dry-run mode, confirmations
- Error handling and troubleshooting guidance
- Best practices and usage examples

Follows organization documentation standards with focused technical
clarity and practical examples for end users.

Author: LittleCoinCoin

docs/articles/users/MCP/direct_management_commands.md

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+# Direct MCP Management Commands
+
+This article covers the direct MCP management commands for removing servers and host configurations:
+
+- Server removal from specific hosts
+- Complete host configuration removal
+- Multi-host operations and batch processing
+- Dry-run functionality for safe testing
+
+## Overview
+
+The direct MCP management commands provide precise control over MCP server configurations across different hosts. These commands follow the object-action pattern for clarity and consistency.
+
+## Server Removal
+
+### Remove Server from Specific Hosts
+
+Remove an MCP server from one or more hosts while preserving other servers:
+
+```bash
+# Remove from single host
+hatch mcp remove server <server-name> --host <host-name>
+
+# Remove from multiple hosts
+hatch mcp remove server <server-name> --host <host1>,<host2>,<host3>
+
+# Remove from all configured hosts
+hatch mcp remove server <server-name> --host all
+```
+
+### Examples
+
+```bash
+# Remove 'filesystem-server' from Claude Desktop
+hatch mcp remove server filesystem-server --host claude-desktop
+
+# Remove 'database-server' from multiple hosts
+hatch mcp remove server database-server --host claude-desktop,cursor
+
+# Remove 'old-server' from all hosts
+hatch mcp remove server old-server --host all
+```
+
+### Options
+
+- `--host <hosts>`: Comma-separated list of host names or 'all'
+- `--no-backup`: Skip backup creation before removal
+- `--dry-run`: Preview changes without executing them
+- `--auto-approve`: Skip confirmation prompts
+
+## Host Configuration Removal
+
+### Remove Complete Host Configuration
+
+Remove all MCP servers and configuration for a specific host:
+
+```bash
+hatch mcp remove host <host-name>
+```
+
+This command removes the entire configuration file for the specified host, effectively removing all MCP servers configured for that host.
+
+### Examples
+
+```bash
+# Remove all MCP configuration for Claude Desktop
+hatch mcp remove host claude-desktop
+
+# Remove Cursor configuration with automatic approval
+hatch mcp remove host cursor --auto-approve
+```
+
+### Options
+
+- `--no-backup`: Skip backup creation before removal
+- `--dry-run`: Preview changes without executing them
+- `--auto-approve`: Skip confirmation prompts
+
+## Multi-Host Operations
+
+### Host Specification
+
+The `--host` parameter accepts several formats:
+
+- **Single host**: `claude-desktop`
+- **Multiple hosts**: `claude-desktop,cursor,vscode`
+- **All hosts**: `all` (targets all detected hosts)
+
+### Host Validation
+
+The system validates host names against available MCP host types:
+- `claude-desktop`
+- `cursor`
+- `vscode`
+- Additional hosts as configured
+
+Invalid host names will result in an error with available options listed.
+
+## Safety Features
+
+### Backup Creation
+
+By default, all removal operations create backups before making changes:
+
+```bash
+# Backup created automatically
+hatch mcp remove server test-server --host claude-desktop
+# Output: Backup created: ~/.hatch/mcp_backups/claude-desktop_20231201_143022.json
+```
+
+Skip backup creation with `--no-backup`:
+
+```bash
+hatch mcp remove server test-server --host claude-desktop --no-backup
+```
+
+### Dry-Run Mode
+
+Test commands safely with `--dry-run`:
+
+```bash
+# Preview server removal
+hatch mcp remove server test-server --host claude-desktop --dry-run
+# Output: [DRY RUN] Would remove MCP server 'test-server' from hosts: claude-desktop
+
+# Preview host removal
+hatch mcp remove host claude-desktop --dry-run
+# Output: [DRY RUN] Would remove entire host configuration for 'claude-desktop'
+```
+
+### Confirmation Prompts
+
+Interactive confirmation for destructive operations:
+
+```bash
+hatch mcp remove host claude-desktop
+# Output: This will remove ALL MCP servers from 'claude-desktop'. Continue? [y/N]
+```
+
+Skip prompts with `--auto-approve`:
+
+```bash
+hatch mcp remove host claude-desktop --auto-approve
+```
+
+## Error Handling
+
+### Server Not Found
+
+When attempting to remove a non-existent server:
+
+```bash
+hatch mcp remove server nonexistent-server --host claude-desktop
+# Output: [ERROR] Failed to remove 'nonexistent-server' from 'claude-desktop': Server not found
+```
+
+### Invalid Host
+
+When specifying an invalid host:
+
+```bash
+hatch mcp remove server test-server --host invalid-host
+# Output: Error: Invalid host 'invalid-host'. Available: claude-desktop, cursor, vscode
+```
+
+### Missing Configuration
+
+When no configuration exists for a host:
+
+```bash
+hatch mcp remove host unconfigured-host
+# Output: No configuration file to remove for 'unconfigured-host'
+```
+
+## Best Practices
+
+### Before Removal
+
+1. **List current configuration**: Use `hatch mcp list servers` to see what's configured
+2. **Test with dry-run**: Always test with `--dry-run` first
+3. **Verify host names**: Ensure correct host specification
+
+### During Removal
+
+1. **Use specific hosts**: Prefer explicit host names over 'all' for precision
+2. **Keep backups**: Only use `--no-backup` when certain
+3. **Batch operations**: Remove from multiple hosts in single command when appropriate
+
+### After Removal
+
+1. **Verify removal**: Check configuration with `hatch mcp list servers`
+2. **Test functionality**: Ensure remaining servers work correctly
+3. **Clean up backups**: Manage backup files as needed
+
+## Related Commands
+
+- [`hatch mcp list`](./listing_commands.md): View current MCP configurations
+- [`hatch mcp configure`](./configuration_commands.md): Add or modify MCP servers
+- [`hatch mcp backup`](./backup_commands.md): Manage configuration backups
+
+## Troubleshooting
+
+### Permission Issues
+
+Ensure proper file permissions for configuration directories and backup locations.
+
+### Configuration Corruption
+
+If configuration becomes corrupted, use backup restoration:
+
+```bash
+hatch mcp backup restore <backup-file> --host <host-name>
+```
+
+### Multiple Host Failures
+
+When removing from multiple hosts, check individual host status if some operations fail.