fix: destroy descendant processes on StdioClientTransport.closeGracefully

When `closeGracefully()` is called, the previous implementation invoked
only `process.destroy()` on the root process. With wrapper commands such
as `npx` (POSIX) or `cmd.exe /c npx.cmd ...` (Windows), the wrapper has
already forked child processes (`node.exe`, the MCP server itself);
destroying only the wrapper leaves those descendants orphaned. On Windows
this prevents the JVM from shutting down cleanly.

Walk `ProcessHandle.descendants()` (JDK 9+, available since the repo's
Java 17 baseline) and destroy each descendant before destroying the root.
This avoids the OS-specific `taskkill /pid X /F /T` approach suggested on
the issue: same effect, one cross-platform code path, no shelling out.

The descendant snapshot is best-effort — processes forked concurrently
with the destroy call may be missed, but the wider tree generally dies
with its parent.

Fixes #496

Author: k-krawczyk

mcp-core/src/main/java/io/modelcontextprotocol/client/transport/StdioClientTransport.java

@@ -327,9 +327,11 @@ protected void handleOutbound(Function<Flux<JSONRPCMessage>, Flux<JSONRPCMessage
 	}
 
 	/**
-	 * Gracefully closes the transport by destroying the process and disposing of the
-	 * schedulers. This method sends a TERM signal to the process and waits for it to exit
-	 * before cleaning up resources.
+	 * Gracefully closes the transport by destroying the server process tree and disposing
+	 * of the schedulers. This method sends a TERM signal to every process in the tree
+	 * (descendants first, then the root) and waits for the root to exit before cleaning
+	 * up resources. Tree-aware termination prevents leaked child processes when a wrapper
+	 * command such as {@code npx} or {@code cmd.exe /c npx.cmd} is used.
 	 * @return A Mono that completes when the transport is closed
 	 */
 	@Override
@@ -346,9 +348,9 @@ public Mono<Void> closeGracefully() {
 			// Give a short time for any pending messages to be processed
 			return Mono.delay(Duration.ofMillis(100)).then();
 		})).then(Mono.defer(() -> {
-			logger.debug("Sending TERM to process");
+			logger.debug("Sending TERM to process tree");
 			if (this.process != null) {
-				this.process.destroy();
+				destroyProcessTree(this.process);
 				return Mono.fromFuture(process.onExit());
 			}
 			else {
@@ -387,4 +389,21 @@ public <T> T unmarshalFrom(Object data, TypeRef<T> typeRef) {
 		return this.jsonMapper.convertValue(data, typeRef);
 	}
 
+	/**
+	 * Destroys {@code process} together with any descendant processes spawned beneath it.
+	 * Wrapper invocations such as {@code cmd.exe /c npx.cmd ...} on Windows or
+	 * {@code npx} on POSIX systems spawn additional child processes; destroying only the
+	 * wrapper leaves those descendants orphaned and prevents graceful JVM shutdown.
+	 * <p>
+	 * The descendant snapshot from {@link ProcessHandle#descendants()} is best-effort:
+	 * processes that fork concurrently with this call may not be signalled. The wider
+	 * tree typically dies anyway once its parent is gone.
+	 * <p>
+	 * Visible for tests.
+	 */
+	static void destroyProcessTree(Process process) {
+		process.descendants().forEach(ProcessHandle::destroy);
+		process.destroy();
+	}
+
 }

mcp-core/src/test/java/io/modelcontextprotocol/client/transport/StdioClientTransportDestroyTreeTests.java

@@ -0,0 +1,74 @@
+/*
+ * Copyright 2026-2026 the original author or authors.
+ */
+package io.modelcontextprotocol.client.transport;
+
+import java.time.Duration;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.condition.DisabledOnOs;
+import org.junit.jupiter.api.condition.OS;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.assertThatCode;
+import static org.awaitility.Awaitility.await;
+
+/**
+ * Tests for {@link StdioClientTransport#destroyProcessTree(Process)}.
+ *
+ * <p>
+ * Regression coverage for the case where {@code closeGracefully()} previously left
+ * orphaned descendant processes (e.g. {@code node} spawned beneath {@code npx} on
+ * Windows). The tree-aware destroy must terminate the entire descendant chain, not just
+ * the root.
+ */
+class StdioClientTransportDestroyTreeTests {
+
+	@Test
+	@DisabledOnOs(OS.WINDOWS) // sh + & + wait is POSIX; CI is ubuntu-latest
+	void destroyProcessTreeTerminatesRootAndDescendants() throws Exception {
+		// `sh` forks two long-sleeping children. Killing only `sh` would leave both
+		// children alive — exactly the bug reported in #496 (but reproduced portably).
+		Process root = new ProcessBuilder("sh", "-c", "sleep 60 & sleep 60 & wait").start();
+
+		await().atMost(Duration.ofSeconds(3)).until(() -> root.descendants().count() >= 2);
+		List<ProcessHandle> descendants = root.descendants().collect(Collectors.toList());
+		assertThat(descendants).hasSizeGreaterThanOrEqualTo(2);
+
+		StdioClientTransport.destroyProcessTree(root);
+
+		await().atMost(Duration.ofSeconds(5)).untilAsserted(() -> {
+			assertThat(root.isAlive()).as("root sh process").isFalse();
+			for (ProcessHandle d : descendants) {
+				assertThat(d.isAlive()).as("descendant pid=%s", d.pid()).isFalse();
+			}
+		});
+	}
+
+	@Test
+	@DisabledOnOs(OS.WINDOWS)
+	void destroyProcessTreeTerminatesRootWithNoDescendants() throws Exception {
+		Process root = new ProcessBuilder("sleep", "60").start();
+
+		assertThat(root.isAlive()).isTrue();
+
+		StdioClientTransport.destroyProcessTree(root);
+
+		await().atMost(Duration.ofSeconds(5)).until(() -> !root.isAlive());
+	}
+
+	@Test
+	void destroyProcessTreeIsSafeOnAlreadyTerminatedProcess() throws Exception {
+		// Pick a command that exists on every supported OS and exits immediately.
+		String[] cmd = System.getProperty("os.name").toLowerCase().contains("win")
+				? new String[] { "cmd.exe", "/c", "exit", "0" } : new String[] { "sh", "-c", "exit 0" };
+		Process root = new ProcessBuilder(cmd).start();
+		root.waitFor();
+		assertThat(root.isAlive()).isFalse();
+
+		assertThatCode(() -> StdioClientTransport.destroyProcessTree(root)).doesNotThrowAnyException();
+	}
+
+}