diff --git a/pkg/desktop/transport/transport_test.go b/pkg/desktop/transport/transport_test.go
index b7f06211fd..19514e30c3 100644
--- a/pkg/desktop/transport/transport_test.go
+++ b/pkg/desktop/transport/transport_test.go
@@ -243,7 +243,10 @@ func TestFallbackTransport_NonSocketErrorDoesNotDisableProxy(t *testing.T) {
 	req, err := http.NewRequestWithContext(t.Context(), http.MethodGet, "http://example.invalid/", http.NoBody)
 	require.NoError(t, err)
 
-	resp, err := ft.RoundTrip(req) //nolint:bodyclose // resp is nil on error, checked below
+	resp, err := ft.RoundTrip(req)
+	if resp != nil && resp.Body != nil {
+		resp.Body.Close()
+	}
 	require.Error(t, err)
 	require.Nil(t, resp)
 	assert.True(t, errors.Is(err, upstreamErr) || err.Error() == upstreamErr.Error())
diff --git a/pkg/selfupdate/exec_windows.go b/pkg/selfupdate/exec_windows.go
index 6517efcc91..2e33567594 100644
--- a/pkg/selfupdate/exec_windows.go
+++ b/pkg/selfupdate/exec_windows.go
@@ -3,6 +3,8 @@
 package selfupdate
 
 import (
+	"context"
+	"errors"
 	"fmt"
 	"os"
 	"os/exec"
@@ -27,9 +29,9 @@ func swapBinary(dst, src string) error {
 		if cpErr := atomicWriteFromFile(dst, src); cpErr != nil {
 			// Roll back so we never leave the install without a binary.
 			if rbErr := os.Rename(old, dst); rbErr != nil {
-				return fmt.Errorf("installing new binary: %w (copy fallback failed: %v; rollback also failed: %v)", err, cpErr, rbErr)
+				return fmt.Errorf("installing new binary: %w (copy fallback failed: %w; rollback also failed: %w)", err, cpErr, rbErr)
 			}
-			return fmt.Errorf("installing new binary: %w (copy fallback failed: %v)", err, cpErr)
+			return fmt.Errorf("installing new binary: %w (copy fallback failed: %w)", err, cpErr)
 		}
 		_ = os.Remove(src)
 	}
@@ -48,7 +50,7 @@ func reExecProcess(path string, args, env []string) error {
 		childArgs = args[1:]
 	}
 
-	cmd := exec.Command(path, childArgs...) //nolint:gosec // path is our own freshly installed binary
+	cmd := exec.CommandContext(context.Background(), path, childArgs...)
 	cmd.Env = env
 	cmd.Stdin = os.Stdin
 	cmd.Stdout = os.Stdout
@@ -69,9 +71,5 @@ func reExecProcess(path string, args, env []string) error {
 // asExitError is a tiny helper kept separate so exec_unix.go does not need to
 // import errors solely for this Windows branch.
 func asExitError(err error, target **exec.ExitError) bool {
-	if e, ok := err.(*exec.ExitError); ok { //nolint:errorlint // direct type assertion is intentional here
-		*target = e
-		return true
-	}
-	return false
+	return errors.As(err, target)
 }
diff --git a/pkg/tools/builtin/backgroundjobs/cmd_windows.go b/pkg/tools/builtin/backgroundjobs/cmd_windows.go
index d25a83ef15..2cbb43fa86 100644
--- a/pkg/tools/builtin/backgroundjobs/cmd_windows.go
+++ b/pkg/tools/builtin/backgroundjobs/cmd_windows.go
@@ -31,13 +31,13 @@ func createProcessGroup(proc *os.Process) (*processGroup, error) {
 	if _, err := windows.SetInformationJobObject(
 		job,
 		windows.JobObjectExtendedLimitInformation,
-		uintptr(unsafe.Pointer(&info)),
+		uintptr(unsafe.Pointer(&info)), //nolint:gosec // Windows API requires unsafe.Pointer
 		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))
+	handle, err := windows.OpenProcess(windows.PROCESS_SET_QUOTA|windows.PROCESS_TERMINATE, false, uint32(proc.Pid)) //nolint:gosec // proc.Pid fits in uint32 on Windows
 	if err != nil {
 		_ = windows.CloseHandle(job)
 		return nil, err
diff --git a/pkg/tools/builtin/rag/rag.go b/pkg/tools/builtin/rag/rag.go
index 8ca720492a..473067a389 100644
--- a/pkg/tools/builtin/rag/rag.go
+++ b/pkg/tools/builtin/rag/rag.go
@@ -49,6 +49,8 @@ type ToolSet struct {
 	manager       *rag.Manager
 	toolName      string
 	eventCallback EventCallback
+	cancelWatcher context.CancelFunc
+	watcherDone   chan struct{}
 }
 
 // Verify interface compliance.
@@ -84,9 +86,15 @@ func (t *ToolSet) Start(ctx context.Context) error {
 		return nil
 	}
 
+	// We create a child context so we can explicitly cancel the watcher and event goroutines
+	// when Stop() is called, preventing goroutine leaks if the parent context outlives this toolset.
+	watchCtx, cancel := context.WithCancel(ctx)
+	t.cancelWatcher = cancel
+	t.watcherDone = make(chan struct{})
+
 	// Forward RAG manager events if a callback is set.
 	if t.eventCallback != nil {
-		go t.forwardEvents(ctx)
+		go t.forwardEvents(watchCtx)
 	}
 
 	if err := t.manager.Initialize(ctx); err != nil {
@@ -94,8 +102,9 @@ func (t *ToolSet) Start(ctx context.Context) error {
 	}
 
 	go func() {
-		if err := t.manager.StartFileWatcher(ctx); err != nil {
-			slog.ErrorContext(ctx, "Failed to start RAG file watcher", "tool", t.toolName, "error", err)
+		defer close(t.watcherDone)
+		if err := t.manager.StartFileWatcher(watchCtx); err != nil && !errors.Is(err, context.Canceled) {
+			slog.ErrorContext(watchCtx, "Failed to start RAG file watcher", "tool", t.toolName, "error", err)
 		}
 	}()
 	return nil
@@ -106,6 +115,10 @@ func (t *ToolSet) Stop(_ context.Context) error {
 	if t.manager == nil {
 		return nil
 	}
+	if t.cancelWatcher != nil {
+		t.cancelWatcher()
+		<-t.watcherDone
+	}
 	return t.manager.Close()
 }
 
diff --git a/pkg/tools/builtin/shell/cmd_windows.go b/pkg/tools/builtin/shell/cmd_windows.go
index 05e11368ac..85d4145786 100644
--- a/pkg/tools/builtin/shell/cmd_windows.go
+++ b/pkg/tools/builtin/shell/cmd_windows.go
@@ -31,13 +31,13 @@ func createProcessGroup(proc *os.Process) (*processGroup, error) {
 	if _, err := windows.SetInformationJobObject(
 		job,
 		windows.JobObjectExtendedLimitInformation,
-		uintptr(unsafe.Pointer(&info)),
+		uintptr(unsafe.Pointer(&info)), //nolint:gosec // Windows API requires unsafe.Pointer
 		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))
+	handle, err := windows.OpenProcess(windows.PROCESS_SET_QUOTA|windows.PROCESS_TERMINATE, false, uint32(proc.Pid)) //nolint:gosec // proc.Pid fits in uint32 on Windows
 	if err != nil {
 		_ = windows.CloseHandle(job)
 		return nil, err
diff --git a/pkg/tools/builtin/shell/script_shell.go b/pkg/tools/builtin/shell/script_shell.go
index efb3176299..e363b892aa 100644
--- a/pkg/tools/builtin/shell/script_shell.go
+++ b/pkg/tools/builtin/shell/script_shell.go
@@ -248,7 +248,11 @@ func (t *ScriptToolSet) execute(ctx context.Context, rt tools.Runtime, toolConfi
 	// stay literal because env values may legitimately contain $ (issue
 	// #2615).
 	for _, key := range slices.Sorted(maps.Keys(toolConfig.Env)) {
-		envCopy = append(envCopy, key+"="+path.ExpandEnvRefs(toolConfig.Env[key]))
+		val := path.ExpandEnvRefs(toolConfig.Env[key])
+		if strings.ContainsRune(val, 0) {
+			return tools.ResultError(fmt.Sprintf("configured environment variable %q contains a NUL byte", key)), nil
+		}
+		envCopy = append(envCopy, key+"="+val)
 	}
 	for key, value := range params {
 		if value == nil {