Fix shell process cleanup

.gitattributes

@@ -0,0 +1,28 @@
+# Auto detect text files and normalize to LF
+* text=auto eol=lf
+
+# Go source files
+*.go text eol=lf
+
+# Shell scripts
+*.sh text eol=lf
+
+# Windows specific files
+*.bat text eol=crlf
+*.cmd text eol=crlf
+*.ps1 text eol=crlf
+
+# Binary files
+*.exe binary
+*.dll binary
+*.so binary
+*.dylib binary
+*.png binary
+*.jpg binary
+*.jpeg binary
+*.gif binary
+*.ico binary
+*.pdf binary
+*.zip binary
+*.tar binary
+*.gz binary

go.mod

@@ -35,6 +35,7 @@ require (
 	go.opentelemetry.io/otel/sdk v1.38.0
 	go.opentelemetry.io/otel/trace v1.38.0
 	golang.org/x/oauth2 v0.32.0
+	golang.org/x/sys v0.37.0
 	golang.org/x/term v0.36.0
 	google.golang.org/genai v1.31.0
 	modernc.org/sqlite v1.39.1
@@ -116,7 +117,6 @@ require (
 	golang.org/x/exp v0.0.0-20250819193227-8b4c13bb791b // indirect
 	golang.org/x/net v0.46.0 // indirect
 	golang.org/x/sync v0.17.0 // indirect
-	golang.org/x/sys v0.37.0 // indirect
 	golang.org/x/text v0.30.0 // indirect
 	golang.org/x/time v0.14.0 // indirect
 	google.golang.org/genproto/googleapis/api v0.0.0-20250826171959-ef028d996bc1 // indirect

pkg/runtime/remote_runtime.go

@@ -65,13 +65,6 @@ func (r *RemoteRuntime) CurrentAgent() *agent.Agent {
 	return agent.New(r.currentAgent, fmt.Sprintf("Remote agent: %s", r.currentAgent))
 }
 
-// StopPendingProcesses stops all pending tool operations for the remote runtime
-func (r *RemoteRuntime) StopPendingProcesses(ctx context.Context) error {
-	// For remote runtime, stop the team's toolsets
-	// This will kill any spawned processes from shell tools
-	return r.team.StopToolSets(ctx)
-}
-
 // RunStream starts the agent's interaction loop and returns a channel of events
 func (r *RemoteRuntime) RunStream(ctx context.Context, sess *session.Session) <-chan Event {
 	slog.Debug("Starting remote runtime stream", "agent", r.currentAgent, "session_id", r.sessionID)

pkg/runtime/runtime.go

@@ -65,8 +65,6 @@ type ElicitationRequestHandler func(ctx context.Context, message string, schema
 type Runtime interface {
 	// CurrentAgent returns the currently active agent
 	CurrentAgent() *agent.Agent
-	// StopPendingProcesses stops all pending tool operations (e.g., running shell commands)
-	StopPendingProcesses(ctx context.Context) error
 	// RunStream starts the agent's interaction loop and returns a channel of events
 	RunStream(ctx context.Context, sess *session.Session) <-chan Event
 	// Run starts the agent's interaction loop and returns the final messages
@@ -180,10 +178,6 @@ func (r *runtime) CurrentAgent() *agent.Agent {
 	return current
 }
 
-func (r *runtime) StopPendingProcesses(ctx context.Context) error {
-	return r.team.StopToolSets(ctx)
-}
-
 // registerDefaultTools registers the default tool handlers
 func (r *runtime) registerDefaultTools() {
 	slog.Debug("Registering default tools")

pkg/server/server.go

@@ -126,8 +126,6 @@ func New(sessionStore session.Store, runConfig config.RuntimeConfig, teams map[s
 	group.POST("/sessions/:id/resume", s.resumeSession)
 	// Create a new session and run an agent loop
 	group.POST("/sessions", s.createSession)
-	// Stop a running session
-	group.POST("/sessions/:id/stop", s.stopSession)
 	// Delete a session
 	group.DELETE("/sessions/:id", s.deleteSession)
 
@@ -963,36 +961,6 @@ func (s *Server) resumeSession(c echo.Context) error {
 	return c.JSON(http.StatusOK, map[string]string{"message": "session resumed"})
 }
 
-func (s *Server) stopSession(c echo.Context) error {
-	sessionID := c.Param("id")
-
-	// Get the runtime for this session to access its team
-	rt, rtExists := s.runtimes[sessionID]
-
-	// Cancel the runtime context if it's still running
-	s.cancelsMu.Lock()
-	if cancel, exists := s.runtimeCancels[sessionID]; exists {
-		slog.Info("Stopping session execution", "session_id", sessionID)
-		cancel()
-		delete(s.runtimeCancels, sessionID)
-		s.cancelsMu.Unlock()
-
-		// Stop all pending tool operations (including killing shell-spawned processes)
-		if rtExists {
-			if err := rt.StopPendingProcesses(c.Request().Context()); err != nil {
-				slog.Error("Failed to stop pending tools for session", "session_id", sessionID, "error", err)
-				// Don't return error here, as we still want to report success for stopping the session
-			}
-		}
-
-		return c.JSON(http.StatusOK, map[string]string{"message": "session stopped successfully"})
-	}
-	s.cancelsMu.Unlock()
-
-	slog.Debug("No active runtime found for session", "session_id", sessionID)
-	return c.JSON(http.StatusNotFound, map[string]string{"error": "no active session found"})
-}
-
 func (s *Server) deleteSession(c echo.Context) error {
 	sessionID := c.Param("id")
 

pkg/tools/builtin/cmd_unix.go

@@ -7,12 +7,20 @@ import (
 	"syscall"
 )
 
+type processGroup struct {
+	// Unix doesn't need to store handles, process group is managed by kernel
+}
+
 func platformSpecificSysProcAttr() *syscall.SysProcAttr {
 	return &syscall.SysProcAttr{
 		Setpgid: true,
 	}
 }
 
-func kill(proc *os.Process) error {
+func createProcessGroup(proc *os.Process) (*processGroup, error) {
+	return &processGroup{}, nil
+}
+
+func kill(proc *os.Process, pg *processGroup) error {
 	return syscall.Kill(-proc.Pid, syscall.SIGTERM)
 }

pkg/tools/builtin/cmd_windows.go

@@ -3,12 +3,70 @@ package builtin
 import (
 	"os"
 	"syscall"
+	"unsafe"
+
+	"golang.org/x/sys/windows"
 )
 
+type processGroup struct {
+	jobHandle     windows.Handle
+	processHandle windows.Handle
+}
+
 func platformSpecificSysProcAttr() *syscall.SysProcAttr {
 	return nil
 }
 
-func kill(proc *os.Process) error {
+func createProcessGroup(proc *os.Process) (*processGroup, error) {
+	job, err := windows.CreateJobObject(nil, nil)
+	if err != nil {
+		return nil, err
+	}
+
+	info := windows.JOBOBJECT_EXTENDED_LIMIT_INFORMATION{
+		BasicLimitInformation: windows.JOBOBJECT_BASIC_LIMIT_INFORMATION{
+			LimitFlags: windows.JOB_OBJECT_LIMIT_KILL_ON_JOB_CLOSE,
+		},
+	}
+	if _, err := windows.SetInformationJobObject(
+		job,
+		windows.JobObjectExtendedLimitInformation,
+		uintptr(unsafe.Pointer(&info)),
+		uint32(unsafe.Sizeof(info))); err != nil {
+		_ = windows.CloseHandle(job)
+		return nil, err
+	}
+
+	handle, err := windows.OpenProcess(windows.PROCESS_SET_QUOTA|windows.PROCESS_TERMINATE, false, uint32(proc.Pid))
+	if err != nil {
+		_ = windows.CloseHandle(job)
+		return nil, err
+	}
+
+	if err := windows.AssignProcessToJobObject(job, handle); err != nil {
+		_ = windows.CloseHandle(handle)
+		_ = windows.CloseHandle(job)
+		return nil, err
+	}
+
+	return &processGroup{
+		jobHandle:     job,
+		processHandle: handle,
+	}, nil
+}
+
+func kill(proc *os.Process, pg *processGroup) error {
+	if pg != nil {
+		// Close handles to trigger JOB_OBJECT_LIMIT_KILL_ON_JOB_CLOSE
+		// which will terminate all processes in the job
+		if pg.processHandle != 0 {
+			_ = windows.CloseHandle(pg.processHandle)
+		}
+		if pg.jobHandle != 0 {
+			_ = windows.CloseHandle(pg.jobHandle)
+		}
+	}
+
+	// Also call Kill on the process as a fallback
 	return proc.Kill()
 }

pkg/tools/builtin/shell.go

@@ -8,7 +8,7 @@ import (
 	"os"
 	"os/exec"
 	"runtime"
-	"sync"
+	"strings"
 
 	"github.com/docker/cagent/pkg/tools"
 )
@@ -25,8 +25,6 @@ type shellHandler struct {
 	shell           string
 	shellArgsPrefix []string
 	env             []string
-	mu              sync.Mutex
-	processes       []*os.Process
 }
 
 type RunShellArgs struct {
@@ -40,74 +38,67 @@ func (h *shellHandler) RunShell(ctx context.Context, toolCall tools.ToolCall) (*
 		return nil, fmt.Errorf("invalid arguments: %w", err)
 	}
 
-	cmd := exec.CommandContext(ctx, h.shell, append(h.shellArgsPrefix, params.Cmd)...)
+	cmd := exec.Command(h.shell, append(h.shellArgsPrefix, params.Cmd)...)
 	cmd.Env = h.env
 	if params.Cwd != "" {
 		cmd.Dir = params.Cwd
 	} else {
-		// Use the current working directory; avoid PWD on Windows (may be MSYS-style like /c/...)
 		if wd, err := os.Getwd(); err == nil {
 			cmd.Dir = wd
 		}
 	}
 
-	// Set up process group for proper cleanup
-	// On Unix: create new process group so we can kill the entire tree
 	cmd.SysProcAttr = platformSpecificSysProcAttr()
 
-	// Note: On Windows, we would set CreationFlags, but that requires
-	// platform-specific code in a _windows.go file
-
-	// Capture output using buffers
-	var outBuf, errBuf bytes.Buffer
+	var outBuf bytes.Buffer
 	cmd.Stdout = &outBuf
-	cmd.Stderr = &errBuf
+	cmd.Stderr = &outBuf
 
-	// Start the command so we can track it
 	if err := cmd.Start(); err != nil {
 		return &tools.ToolCallResult{
 			Output: fmt.Sprintf("Error starting command: %s", err),
 		}, nil
 	}
 
-	// Track the process for cleanup
-	h.mu.Lock()
-	h.processes = append(h.processes, cmd.Process)
-	h.mu.Unlock()
-
-	// Remove from tracking once complete
-	defer func() {
-		h.mu.Lock()
-		for i, p := range h.processes {
-			if p != nil && p.Pid == cmd.Process.Pid {
-				h.processes = append(h.processes[:i], h.processes[i+1:]...)
-				break
-			}
-		}
-		h.mu.Unlock()
-	}()
-
-	// Wait for the command to complete and get the result
-	err := cmd.Wait()
-
-	// Combine stdout and stderr
-	output := outBuf.String() + errBuf.String()
-
+	pg, err := createProcessGroup(cmd.Process)
 	if err != nil {
 		return &tools.ToolCallResult{
-			Output: fmt.Sprintf("Error executing command: %s\nOutput: %s", err, output),
+			Output: fmt.Sprintf("Error creating process group: %s", err),
 		}, nil
 	}
 
-	if output == "" {
+	done := make(chan error, 1)
+	go func() {
+		done <- cmd.Wait()
+	}()
+
+	select {
+	case <-ctx.Done():
+		if cmd.Process != nil {
+			_ = kill(cmd.Process, pg)
+		}
 		return &tools.ToolCallResult{
-			Output: "<no output>",
+			Output: "Command cancelled",
 		}, nil
-	}
+	case err := <-done:
+		output := outBuf.String()
 
-	return &tools.ToolCallResult{
-		Output: output,
-	}, nil
+		if err != nil {
+			return &tools.ToolCallResult{
+				Output: fmt.Sprintf("Error executing command: %s\nOutput: %s", err, output),
+			}, nil
+		}
+
+		if strings.TrimSpace(output) == "" {
+			return &tools.ToolCallResult{
+				Output: "<no output>",
+			}, nil
+		}
+
+		return &tools.ToolCallResult{
+			Output: fmt.Sprintf("Output: %s", output),
+		}, nil
+	}
 }
 
 func NewShellTool(env []string) *ShellTool {
@@ -236,18 +227,5 @@ func (t *ShellTool) Start(context.Context) error {
 }
 
 func (t *ShellTool) Stop(context.Context) error {
-	t.handler.mu.Lock()
-	defer t.handler.mu.Unlock()
-
-	// Kill all tracked processes
-	for _, proc := range t.handler.processes {
-		if proc != nil {
-			_ = kill(proc)
-		}
-	}
-
-	// Clear the processes list
-	t.handler.processes = nil
-
 	return nil
 }