fix(core): resolve MCP process leaks, deadlocks, and config regressions Fix #23344

help.txt

@@ -0,0 +1,41 @@
+Usage: gemini [options] [command]
+
+Gemini CLI - Defaults to interactive mode. Use -p/--prompt for non-interactive (headless) mode.
+
+Commands:
+  gemini [query..]             Launch Gemini CLI  [default]
+  gemini mcp                   Manage MCP servers
+  gemini extensions <command>  Manage Gemini CLI extensions.  [aliases: extension]
+  gemini skills <command>      Manage agent skills.  [aliases: skill]
+  gemini hooks <command>       Manage Gemini CLI hooks.  [aliases: hook]
+
+Positionals:
+  query  Initial prompt. Runs in interactive mode by default; use -p/--prompt for non-interactive.
+
+Options:
+  -d, --debug                     Run in debug mode (open debug console with F12)  [boolean] [default: false]
+  -m, --model                     Model  [string]
+  -p, --prompt                    Run in non-interactive (headless) mode with the given prompt. Appended to input on stdin (if any).  [string]
+  -i, --prompt-interactive        Execute the provided prompt and continue in interactive mode  [string]
+  -w, --worktree                  Start Gemini in a new git worktree. If no name is provided, one is generated automatically.  [string]
+  -s, --sandbox                   Run in sandbox?  [boolean]
+  -y, --yolo                      Automatically accept all actions (aka YOLO mode, see https://www.youtube.com/watch?v=xvFZjo5PgG0 for more details)?  [boolean] [default: false]
+      --approval-mode             Set the approval mode: default (prompt for approval), auto_edit (auto-approve edit tools), yolo (auto-approve all tools), plan (read-only mode)  [string] [choices: "default", "auto_edit", "yolo", "plan"]
+      --policy                    Additional policy files or directories to load (comma-separated or multiple --policy)  [array]
+      --admin-policy              Additional admin policy files or directories to load (comma-separated or multiple --admin-policy)  [array]
+      --acp                       Starts the agent in ACP mode  [boolean]
+      --experimental-acp          Starts the agent in ACP mode (deprecated, use --acp instead)  [boolean]
+      --allowed-mcp-server-names  Allowed MCP server names  [array]
+      --allowed-tools             [DEPRECATED: Use Policy Engine instead See https://geminicli.com/docs/core/policy-engine] Tools that are allowed to run without confirmation  [array]
+  -e, --extensions                A list of extensions to use. If not provided, all extensions are used.  [array]
+  -l, --list-extensions           List all available extensions and exit.  [boolean]
+  -r, --resume                    Resume a previous session. Use "latest" for most recent or index number (e.g. --resume 5)  [string]
+      --list-sessions             List available sessions for the current project and exit.  [boolean]
+      --delete-session            Delete a session by index number (use --list-sessions to see available sessions).  [string]
+      --include-directories       Additional directories to include in the workspace (comma-separated or multiple --include-directories)  [array]
+      --screen-reader             Enable screen reader mode for accessibility.  [boolean]
+  -o, --output-format             The format of the CLI output.  [string] [choices: "text", "json", "stream-json"]
+      --raw-output                Disable sanitization of model output (e.g. allow ANSI escape sequences). WARNING: This can be a security risk if the model output is untrusted.  [boolean]
+      --accept-raw-output-risk    Suppress the security warning when using --raw-output.  [boolean]
+  -v, --version                   Show version number  [boolean]
+  -h, --help                      Show help  [boolean]

packages/core/src/config/config.ts

@@ -1568,6 +1568,10 @@ export class Config implements McpContext, AgentLoopContext {
     return this.promptId;
   }
 
+  getCustomExcludes(): string[] {
+    return this.fileFiltering.customIgnoreFilePaths;
+  }
+
   getWorktreeSettings(): WorktreeSettings | undefined {
     return this.worktreeSettings;
   }
@@ -2508,20 +2512,6 @@ export class Config implements McpContext, AgentLoopContext {
     };
   }
 
-  /**
-   * Gets custom file exclusion patterns from configuration.
-   * TODO: This is a placeholder implementation. In the future, this could
-   * read from settings files, CLI arguments, or environment variables.
-   */
-  getCustomExcludes(): string[] {
-    // Placeholder implementation - returns empty array for now
-    // Future implementation could read from:
-    // - User settings file
-    // - Project-specific configuration
-    // - Environment variables
-    // - CLI arguments
-    return [];
-  }
 
   getCheckpointingEnabled(): boolean {
     return this.checkpointing;

packages/core/src/telemetry/sdk.ts

@@ -355,14 +355,6 @@ export async function initializeTelemetry(
   // Note: We don't use process.on('exit') here because that callback is synchronous
   // and won't wait for the async shutdownTelemetry() to complete.
   // Instead, telemetry shutdown is handled in runExitCleanup() in cleanup.ts
-  process.on('SIGTERM', () => {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    shutdownTelemetry(config);
-  });
-  process.on('SIGINT', () => {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    shutdownTelemetry(config);
-  });
 }
 
 /**

packages/core/src/tools/mcp-client-manager.ts

@@ -626,8 +626,13 @@ export class McpClientManager {
    * This is the cleanup method to be called on application exit.
    */
   async stop(): Promise<void> {
+    const pidsToKill: number[] = [];
+
     const disconnectionPromises = Array.from(this.clients.entries()).map(
       async ([name, client]) => {
+        const pid = client.getPid();
+        if (pid) pidsToKill.push(pid);
+
         try {
           await client.disconnect();
         } catch (error) {
@@ -641,6 +646,20 @@ export class McpClientManager {
     );
 
     await Promise.all(disconnectionPromises);
+
+    // Hard kill any processes that are still running after graceful disconnect
+    for (const pid of pidsToKill) {
+      try {
+        // Check if process is still running
+        process.kill(pid, 0);
+        // If it didn't throw, it's still there. Force it.
+        debugLogger.log(`Hard killing lingering MCP process ${pid}`);
+        process.kill(pid, 'SIGKILL');
+      } catch {
+        // Process is already gone, which is good
+      }
+    }
+
     this.clients.clear();
   }
 

packages/core/src/tools/mcp-client.test.ts

@@ -2420,7 +2420,7 @@ describe('connectToMcpServer with OAuth', () => {
       },
     );
 
-    const client = await connectToMcpServer(
+    const { client } = await connectToMcpServer(
       '0.0.1',
       'test-server',
       { httpUrl: serverUrl, oauth: { enabled: true } },
@@ -2465,7 +2465,7 @@ describe('connectToMcpServer with OAuth', () => {
       },
     );
 
-    const client = await connectToMcpServer(
+    const { client } = await connectToMcpServer(
       '0.0.1',
       'test-server',
       { httpUrl: serverUrl, oauth: { enabled: true } },
@@ -2505,7 +2505,7 @@ describe('connectToMcpServer with OAuth', () => {
 
     vi.mocked(mockedClient.connect).mockResolvedValueOnce(undefined);
 
-    const client = await connectToMcpServer(
+    const { client } = await connectToMcpServer(
       '0.0.1',
       'test-server',
       { httpUrl: serverUrl, oauth: { enabled: true } },
@@ -2549,7 +2549,7 @@ describe('connectToMcpServer with OAuth', () => {
 
     vi.mocked(mockedClient.connect).mockResolvedValueOnce(undefined);
 
-    const client = await connectToMcpServer(
+    const { client } = await connectToMcpServer(
       '0.0.1',
       'test-server',
       { httpUrl: serverUrl, oauth: { enabled: true } },
@@ -2644,7 +2644,7 @@ describe('connectToMcpServer - HTTP→SSE fallback', () => {
       .mockRejectedValueOnce(new StreamableHTTPError(500, 'Server error'))
       .mockResolvedValueOnce(undefined);
 
-    const client = await connectToMcpServer(
+    const { client } = await connectToMcpServer(
       '0.0.1',
       'test-server',
       { url: 'http://test-server' },
@@ -2685,7 +2685,7 @@ describe('connectToMcpServer - HTTP→SSE fallback', () => {
       .mockRejectedValueOnce(new StreamableHTTPError(404, 'Not Found'))
       .mockResolvedValueOnce(undefined);
 
-    const client = await connectToMcpServer(
+    const { client } = await connectToMcpServer(
       '0.0.1',
       'test-server',
       { url: 'http://test-server' },
@@ -2770,7 +2770,7 @@ describe('connectToMcpServer - OAuth with transport fallback', () => {
       .mockRejectedValueOnce(new StreamableHTTPError(401, 'Unauthorized'))
       .mockResolvedValueOnce(undefined);
 
-    const client = await connectToMcpServer(
+    const { client } = await connectToMcpServer(
       '0.0.1',
       'test-server',
       { url: 'http://test-server', oauth: { enabled: true } },