Remove deprecated config-test.json and enhance documentation for upstream server management, including dynamic configuration, import mechanisms, and real-time updates. Update README with detailed MCP tools usage and configuration persistence details.

Author: Dumbris

DESIGN.md

@@ -151,3 +151,76 @@ Returns `{total_tools, top:[{tool_name,count}]}`.
 * Hybrid BM25 + vector search.
 * Auto‑update channel.
 * GUI front‑end built with Wails.
+
+## Upstream Server Management
+
+### Dynamic Server Configuration
+
+The proxy supports dynamic management of upstream MCP servers through the `upstream_servers` MCP tool. This enables:
+
+- **Runtime Configuration**: Add, remove, and modify servers without restart
+- **Batch Operations**: Import multiple servers simultaneously
+- **Hot Reloading**: Immediate connection attempts and tool index updates
+- **Persistent Storage**: Configuration automatically saved to disk
+
+### Configuration Persistence
+
+#### Storage Architecture
+
+```
+~/.mcpproxy/
+├── mcp_config.json          # Main configuration file
+├── data.bolt                # BoltDB storage (tool stats, metadata)
+└── index.bleve/             # Search index directory
+```
+
+#### Configuration Flow
+
+1. **Runtime Changes**: MCP tool calls modify server configurations
+2. **Storage Update**: Changes written to BoltDB for immediate persistence
+3. **Config Sync**: Configuration file updated with current state
+4. **Connection Management**: Upstream manager connects/disconnects servers
+5. **Index Update**: Tool discovery runs to update search index
+
+### Server Types
+
+#### HTTP Servers
+- **Transport**: HTTP/HTTPS requests
+- **Authentication**: Headers-based (API keys, tokens)
+- **Configuration**: URL + optional headers
+- **Example**: REST-based MCP servers
+
+#### Stdio Servers  
+- **Transport**: Standard input/output communication
+- **Process Management**: Command execution with arguments
+- **Environment**: Custom environment variables
+- **Example**: Python/Node.js MCP server scripts
+
+### Import Mechanisms
+
+#### Cursor IDE Compatibility
+- **Format**: Direct import of Cursor `mcp.json` configuration
+- **Conversion**: Automatic mapping to internal server configuration
+- **Validation**: Type detection and parameter validation
+
+#### Batch Import
+- **Multiple Servers**: Array of server configurations
+- **Mixed Types**: HTTP and stdio servers in single operation
+- **Error Handling**: Individual server failures don't block others
+
+### Real-time Updates
+
+#### Connection Management
+- **Background Connections**: Non-blocking server connection attempts
+- **Retry Logic**: Exponential backoff for failed connections
+- **Status Tracking**: Real-time connection status updates
+
+#### Tool Discovery
+- **Automatic Indexing**: New servers trigger tool discovery
+- **Search Updates**: BM25 index updated with new tools
+- **Statistics**: Tool usage tracking across servers
+
+#### UI Integration
+- **Tray Updates**: System tray reflects server changes
+- **Status Broadcasting**: Real-time status updates to UI components
+- **Configuration Sync**: UI displays current server state

README.md

@@ -373,4 +373,201 @@ MIT License - see LICENSE file for details.
    - Verify network connectivity
    - Check firewall settings
 
-For more detailed troubleshooting, see [TRAY_ICON_GUIDE.md](TRAY_ICON_GUIDE.md). 
+For more detailed troubleshooting, see [TRAY_ICON_GUIDE.md](TRAY_ICON_GUIDE.md).
+
+## MCP Tools
+
+The Smart MCP Proxy provides several MCP tools for managing servers and discovering tools:
+
+### `upstream_servers` - Server Management
+
+Comprehensive tool for managing upstream MCP servers with support for multiple operations:
+
+#### Operations
+
+- **`list`** - List all configured upstream servers
+- **`add`** - Add a single upstream server
+- **`add_batch`** - Add multiple servers at once
+- **`remove`** - Remove an upstream server
+- **`update`** - Update an existing server
+- **`patch`** - Partially update server configuration
+- **`import_cursor`** - Import servers from Cursor IDE format
+
+#### Adding Single Server
+
+```json
+{
+  "operation": "add",
+  "name": "github-tools",
+  "url": "http://localhost:3001",
+  "headers": {
+    "Authorization": "Bearer your-token-here"
+  },
+  "enabled": true
+}
+```
+
+```json
+{
+  "operation": "add",
+  "name": "sqlite-tools",
+  "command": "uvx",
+  "args": ["mcp-server-sqlite", "--db-path", "/path/to/db.sqlite"],
+  "env": {
+    "MCP_SQLITE_PATH": "/path/to/db.sqlite"
+  },
+  "enabled": true
+}
+```
+
+#### Batch Adding Servers
+
+```json
+{
+  "operation": "add_batch",
+  "servers": [
+    {
+      "name": "github-tools",
+      "url": "http://localhost:3001",
+      "headers": {
+        "Authorization": "Bearer token123"
+      },
+      "enabled": true
+    },
+    {
+      "name": "sqlite-tools", 
+      "command": "uvx",
+      "args": ["mcp-server-sqlite", "--db-path", "/tmp/test.db"],
+      "env": {
+        "MCP_SQLITE_PATH": "/tmp/test.db"
+      },
+      "enabled": true
+    }
+  ]
+}
+```
+
+#### Import from Cursor IDE
+
+You can directly import your Cursor IDE MCP configuration:
+
+```json
+{
+  "operation": "import_cursor",
+  "cursor_config": {
+    "mcp-server-sqlite": {
+      "command": "uvx",
+      "args": ["mcp-server-sqlite", "--db-path", "/path/to/db.sqlite"],
+      "env": {
+        "MCP_SQLITE_PATH": "/path/to/db.sqlite"
+      }
+    },
+    "mcp-server-github": {
+      "url": "http://localhost:3000/mcp",
+      "headers": {
+        "Authorization": "Bearer github-token"
+      }
+    }
+  }
+}
+```
+
+#### Patch/Update Server
+
+```json
+{
+  "operation": "patch",
+  "name": "github-tools",
+  "enabled": false,
+  "headers": {
+    "Authorization": "Bearer new-token"
+  }
+}
+```
+
+### `retrieve_tools` - Tool Discovery
+
+Search for tools across all upstream servers:
+
+```json
+{
+  "query": "github repository",
+  "limit": 10
+}
+```
+
+### `call_tool` - Tool Execution
+
+Execute tools on upstream servers:
+
+```json
+{
+  "name": "github:create_repository",
+  "args": {
+    "name": "my-new-repo",
+    "private": false
+  }
+}
+```
+
+### `tools_stats` - Usage Statistics
+
+Get tool usage statistics:
+
+```json
+{
+  "top_n": 10
+}
+```
+
+## Configuration Persistence
+
+The proxy automatically saves configuration changes to `~/.mcpproxy/mcp_config.json`. This includes:
+
+- All upstream server configurations
+- Server states (enabled/disabled)
+- Connection parameters (URLs, commands, environment variables)
+- Authentication headers
+
+### Configuration File Location
+
+The configuration file location can be customized:
+
+```bash
+# Via environment variable
+export MCPPROXY_DATA_DIR=/custom/path
+./mcpproxy
+
+# Via command line flag
+./mcpproxy --data-dir /custom/path
+```
+
+### Hot Reloading
+
+The proxy automatically:
+- Saves configuration after any server changes
+- Attempts to connect to newly added servers
+- Updates the tool index when servers are modified
+- Reflects changes in the system tray (if enabled)
+
+## Basic Usage Scenarios
+
+### Scenario 1: Import from Cursor IDE
+
+1. Copy your Cursor IDE `mcp.json` configuration
+2. Use the `import_cursor` operation with the `upstream_servers` tool
+3. All servers will be automatically added and connected
+4. Configuration is persisted to `~/.mcpproxy/mcp_config.json`
+
+### Scenario 2: Add Individual Servers
+
+1. Use `upstream_servers` with `add` operation
+2. Specify either `url` (for HTTP) or `command`/`args` (for stdio)
+3. Include authentication headers if needed
+4. Server is immediately connected and tools indexed
+
+### Scenario 3: Batch Server Management
+
+1. Use `add_batch` operation with array of server configurations
+2. Mix HTTP and stdio servers in the same request
+3. All servers processed and connected simultaneously 

config-test.json

@@ -17,14 +17,58 @@ type Config struct {
 
 // ServerConfig represents upstream MCP server configuration
 type ServerConfig struct {
-	Name    string            `json:"name,omitempty" mapstructure:"name"`
-	URL     string            `json:"url,omitempty" mapstructure:"url"`
-	Type    string            `json:"type,omitempty" mapstructure:"type"` // http, stdio, auto
-	Command string            `json:"command,omitempty" mapstructure:"command"`
-	Args    []string          `json:"args,omitempty" mapstructure:"args"`
-	Env     map[string]string `json:"env,omitempty" mapstructure:"env"`
-	Enabled bool              `json:"enabled" mapstructure:"enabled"`
-	Created time.Time         `json:"created" mapstructure:"created"`
+	Name     string            `json:"name,omitempty" mapstructure:"name"`
+	URL      string            `json:"url,omitempty" mapstructure:"url"`
+	Protocol string            `json:"protocol,omitempty" mapstructure:"protocol"` // stdio, http, sse, streamable-http, auto
+	Command  string            `json:"command,omitempty" mapstructure:"command"`
+	Args     []string          `json:"args,omitempty" mapstructure:"args"`
+	Env      map[string]string `json:"env,omitempty" mapstructure:"env"`
+	Headers  map[string]string `json:"headers,omitempty" mapstructure:"headers"` // For HTTP servers
+	Enabled  bool              `json:"enabled" mapstructure:"enabled"`
+	Created  time.Time         `json:"created" mapstructure:"created"`
+	Updated  time.Time         `json:"updated,omitempty" mapstructure:"updated"`
+}
+
+// CursorMCPConfig represents the structure for Cursor IDE MCP configuration
+type CursorMCPConfig struct {
+	MCPServers map[string]CursorServerConfig `json:"mcpServers"`
+}
+
+// CursorServerConfig represents a single server configuration in Cursor format
+type CursorServerConfig struct {
+	Command string            `json:"command,omitempty"`
+	Args    []string          `json:"args,omitempty"`
+	Env     map[string]string `json:"env,omitempty"`
+	URL     string            `json:"url,omitempty"`
+	Headers map[string]string `json:"headers,omitempty"`
+}
+
+// ConvertFromCursorFormat converts Cursor IDE format to our internal format
+func ConvertFromCursorFormat(cursorConfig *CursorMCPConfig) []*ServerConfig {
+	var servers []*ServerConfig
+
+	for name, serverConfig := range cursorConfig.MCPServers {
+		server := &ServerConfig{
+			Name:    name,
+			Enabled: true,
+			Created: time.Now(),
+		}
+
+		if serverConfig.Command != "" {
+			server.Command = serverConfig.Command
+			server.Args = serverConfig.Args
+			server.Env = serverConfig.Env
+			server.Protocol = "stdio"
+		} else if serverConfig.URL != "" {
+			server.URL = serverConfig.URL
+			server.Headers = serverConfig.Headers
+			server.Protocol = "http"
+		}
+
+		servers = append(servers, server)
+	}
+
+	return servers
 }
 
 // ToolMetadata represents tool information stored in the index