fix: prevent MCP server restart when toggling tool permissions

- Added isProgrammaticUpdate flag to track when config changes are made programmatically
- Modified debounceConfigChange to skip file watcher triggers during programmatic updates
- Updated updateServerToolList to set the flag when writing config changes
- Updated updateServerConfig to handle minor updates (alwaysAllow, disabledTools, timeout) without triggering restarts
- Added small delay after programmatic writes to ensure file watchers process the flag

This prevents unnecessary server restarts when users toggle the 'Always allow' checkbox
for MCP tools, improving the user experience by maintaining active connections.

Fixes #8231

src/services/mcp/McpHub.ts

@@ -151,6 +151,7 @@ export class McpHub {
 	isConnecting: boolean = false
 	private refCount: number = 0 // Reference counter for active clients
 	private configChangeDebounceTimers: Map<string, NodeJS.Timeout> = new Map()
+	private isProgrammaticUpdate: boolean = false // Flag to track programmatic config updates
 
 	constructor(provider: ClineProvider) {
 		this.providerRef = new WeakRef(provider)
@@ -278,6 +279,11 @@ export class McpHub {
 	 * Debounced wrapper for handling config file changes
 	 */
 	private debounceConfigChange(filePath: string, source: "global" | "project"): void {
+		// Skip if this is a programmatic update
+		if (this.isProgrammaticUpdate) {
+			return
+		}
+
 		const key = `${source}-${filePath}`
 
 		// Clear existing timer if any
@@ -1463,7 +1469,28 @@ export class McpHub {
 			mcpServers: config.mcpServers,
 		}
 
-		await fs.writeFile(configPath, JSON.stringify(updatedConfig, null, 2))
+		// Check if this is a minor update that shouldn't trigger a restart
+		const isMinorUpdate = Object.keys(configUpdate).every(
+			(key) => key === "alwaysAllow" || key === "disabledTools" || key === "timeout",
+		)
+
+		if (isMinorUpdate) {
+			// Set flag to indicate programmatic update
+			this.isProgrammaticUpdate = true
+
+			try {
+				await fs.writeFile(configPath, JSON.stringify(updatedConfig, null, 2))
+
+				// Give file system watchers a moment to process
+				await new Promise((resolve) => setTimeout(resolve, 100))
+			} finally {
+				// Always reset the flag
+				this.isProgrammaticUpdate = false
+			}
+		} else {
+			// For major updates, allow normal file watcher behavior
+			await fs.writeFile(configPath, JSON.stringify(updatedConfig, null, 2))
+		}
 	}
 
 	public async updateServerTimeout(
@@ -1686,7 +1713,18 @@ export class McpHub {
 			targetList.splice(toolIndex, 1)
 		}
 
-		await fs.writeFile(normalizedPath, JSON.stringify(config, null, 2))
+		// Set flag to indicate programmatic update
+		this.isProgrammaticUpdate = true
+
+		try {
+			await fs.writeFile(normalizedPath, JSON.stringify(config, null, 2))
+
+			// Give file system watchers a moment to process
+			await new Promise((resolve) => setTimeout(resolve, 100))
+		} finally {
+			// Always reset the flag
+			this.isProgrammaticUpdate = false
+		}
 
 		if (connection) {
 			connection.server.tools = await this.fetchToolsList(serverName, source)