fix: prevent stdio MCP server subprocess from dying after connect (#24035)

## Problem

MCP servers configured in `.mcp.json` with stdio transport are
discovered successfully (tools appear) but die immediately after
connection, making all tool calls fail.

## Root Cause

In `connectServer`, the subprocess is spawned with `connectCtx` — a
30-second timeout context whose `cancel()` is deferred:

```go
connectCtx, cancel := context.WithTimeout(ctx, connectTimeout)
defer cancel()
if err := c.Start(connectCtx); err != nil { ... }
```

The mcp-go stdio transport calls `exec.CommandContext(connectCtx, ...)`.
When `connectServer` returns, `cancel()` fires, and
`exec.CommandContext` sends SIGKILL to the subprocess. The process
immediately becomes a zombie.

Confirmed by checking `/proc/<pid>/status` after context cancellation:
```
State: Z (zombie)
```

## Fix

Pass the parent `ctx` (which is `a.gracefulCtx` — the agent's long-lived
context) to `c.Start()`. `connectCtx` continues to bound only the
`Initialize()` handshake. The subprocess is cleaned up when the Manager
is closed or the parent context is canceled.

## Regression Test

Added `TestConnectServer_StdioProcessSurvivesConnect` which:
- Spawns a real subprocess (re-execs the test binary as a fake MCP
server)
- Calls `connectServer` and lets it return (internal `connectCtx` gets
canceled)
- Verifies the subprocess is still alive by calling `ListTools`

The test **fails** on the old code with `transport error: context
deadline exceeded` and **passes** with the fix.

> Generated with [Coder Agents](https://coder.com/agents)

agent/x/agentmcp/manager.go

@@ -187,7 +187,11 @@ func (*Manager) connectServer(ctx context.Context, cfg ServerConfig) (*client.Cl
 	connectCtx, cancel := context.WithTimeout(ctx, connectTimeout)
 	defer cancel()
 
-	if err := c.Start(connectCtx); err != nil {
+	// Use the parent ctx (not connectCtx) so the subprocess outlives
+	// the connect/initialize handshake. connectCtx bounds only the
+	// Initialize call below. The subprocess is cleaned up when the
+	// Manager is closed or ctx is canceled.
+	if err := c.Start(ctx); err != nil {
 		_ = c.Close()
 		return nil, xerrors.Errorf("start %q: %w", cfg.Name, err)
 	}

agent/x/agentmcp/manager_internal_test.go

@@ -1,6 +1,11 @@
 package agentmcp
 
 import (
+	"bufio"
+	"context"
+	"encoding/json"
+	"fmt"
+	"os"
 	"testing"
 
 	"github.com/mark3labs/mcp-go/mcp"
@@ -8,6 +13,7 @@ import (
 	"github.com/stretchr/testify/require"
 
 	"github.com/coder/coder/v2/codersdk/workspacesdk"
+	"github.com/coder/coder/v2/testutil"
 )
 
 func TestSplitToolName(t *testing.T) {
@@ -193,3 +199,118 @@ func TestConvertResult(t *testing.T) {
 		})
 	}
 }
+
+// TestConnectServer_StdioProcessSurvivesConnect verifies that a stdio MCP
+// server subprocess remains alive after connectServer returns. This is a
+// regression test for a bug where the subprocess was tied to a short-lived
+// connectCtx and killed as soon as the context was canceled.
+func TestConnectServer_StdioProcessSurvivesConnect(t *testing.T) {
+	t.Parallel()
+
+	if os.Getenv("TEST_MCP_FAKE_SERVER") == "1" {
+		// Child process: act as a minimal MCP server over stdio.
+		runFakeMCPServer()
+		return
+	}
+
+	// Get the path to the test binary so we can re-exec ourselves
+	// as a fake MCP server subprocess.
+	testBin, err := os.Executable()
+	require.NoError(t, err)
+
+	cfg := ServerConfig{
+		Name:      "fake",
+		Transport: "stdio",
+		Command:   testBin,
+		Args:      []string{"-test.run=^TestConnectServer_StdioProcessSurvivesConnect$"},
+		Env:       map[string]string{"TEST_MCP_FAKE_SERVER": "1"},
+	}
+
+	ctx := testutil.Context(t, testutil.WaitLong)
+	m := &Manager{}
+	client, err := m.connectServer(ctx, cfg)
+	require.NoError(t, err, "connectServer should succeed")
+	t.Cleanup(func() { _ = client.Close() })
+
+	// At this point connectServer has returned and its internal
+	// connectCtx has been canceled. The subprocess must still be
+	// alive. Verify by listing tools (requires a live server).
+	listCtx, listCancel := context.WithTimeout(ctx, testutil.WaitShort)
+	defer listCancel()
+	result, err := client.ListTools(listCtx, mcp.ListToolsRequest{})
+	require.NoError(t, err, "ListTools should succeed — server must be alive after connect")
+	require.Len(t, result.Tools, 1)
+	assert.Equal(t, "echo", result.Tools[0].Name)
+}
+
+// runFakeMCPServer implements a minimal JSON-RPC / MCP server over
+// stdin/stdout, just enough for initialize + tools/list.
+func runFakeMCPServer() {
+	scanner := bufio.NewScanner(os.Stdin)
+	for scanner.Scan() {
+		line := scanner.Bytes()
+
+		var req struct {
+			JSONRPC string          `json:"jsonrpc"`
+			ID      json.RawMessage `json:"id"`
+			Method  string          `json:"method"`
+		}
+		if err := json.Unmarshal(line, &req); err != nil {
+			continue
+		}
+
+		var resp any
+		switch req.Method {
+		case "initialize":
+			resp = map[string]any{
+				"jsonrpc": "2.0",
+				"id":      req.ID,
+				"result": map[string]any{
+					"protocolVersion": "2025-03-26",
+					"capabilities": map[string]any{
+						"tools": map[string]any{},
+					},
+					"serverInfo": map[string]any{
+						"name":    "fake-server",
+						"version": "0.0.1",
+					},
+				},
+			}
+		case "notifications/initialized":
+			// No response needed for notifications.
+			continue
+		case "tools/list":
+			resp = map[string]any{
+				"jsonrpc": "2.0",
+				"id":      req.ID,
+				"result": map[string]any{
+					"tools": []map[string]any{
+						{
+							"name":        "echo",
+							"description": "echoes input",
+							"inputSchema": map[string]any{
+								"type":       "object",
+								"properties": map[string]any{},
+							},
+						},
+					},
+				},
+			}
+		default:
+			resp = map[string]any{
+				"jsonrpc": "2.0",
+				"id":      req.ID,
+				"error": map[string]any{
+					"code":    -32601,
+					"message": "method not found",
+				},
+			}
+		}
+
+		out, err := json.Marshal(resp)
+		if err != nil {
+			continue
+		}
+		_, _ = fmt.Fprintf(os.Stdout, "%s\n", out)
+	}
+}