diff --git a/README.md b/README.md
index c254a74..529cb54 100644
--- a/README.md
+++ b/README.md
@@ -115,7 +115,9 @@ Discovery is bounded and configurable:
 
 These settings are recorded in managed metadata, so `update` uses the same
 depth, command-count, and output policy. `--timeout` remains a global runtime
-override for all subprocess-based operations.
+override for all subprocess-based operations. While discovery is running in an
+interactive terminal, `generate` displays a spinner on stderr; redirected and
+piped output remains unchanged.
 
 It is deliberately conservative: only the three exact headings above and
 indented `name  description` rows are recognized as subcommands. In sections
@@ -124,11 +126,13 @@ the current command's direct children. Aliases,
 multi-word command columns, missing descriptions, unrecognized headings, and
 unusual layouts are omitted rather than guessed. Positionals are never assumed
 to be files, and descriptions are rendered inert — help text can't inject code
-into your shell. Reaching the depth limit leaves deeper commands listed but
-does not inspect their options; exceeding the command-count, output-size, or
-timeout limit fails generation without replacing the installed definition. If
-the tool has a working native command, `generate` refuses and points you at
-`install` unless you pass `--force`.
+into your shell. Advertised subcommands whose help command fails or has no
+recognizable structure remain listed but are not inspected. Reaching the depth
+limit similarly leaves deeper commands listed without inspecting their options;
+exceeding the command-count, output-size, or timeout limit fails generation
+without replacing the installed definition. If the tool has a working native
+command, `generate` refuses and points you at `install` unless you pass
+`--force`.
 
 ### Provenance
 
diff --git a/main.go b/main.go
index 380bb1c..92ae583 100644
--- a/main.go
+++ b/main.go
@@ -14,6 +14,7 @@ import (
 	"regexp"
 	"sort"
 	"strings"
+	"sync"
 	"time"
 
 	"github.com/spf13/cobra"
@@ -82,6 +83,60 @@ func paint(on bool, code, s string) string {
 	return "\x1b[" + code + "m" + s + "\x1b[0m"
 }
 
+type progressSpinner struct {
+	once    sync.Once
+	done    chan struct{}
+	stopped chan struct{}
+	w       io.Writer
+	enabled bool
+}
+
+func spinnerTTY(f *os.File) bool {
+	if os.Getenv("TERM") == "dumb" {
+		return false
+	}
+	st, err := f.Stat()
+	return err == nil && st.Mode()&os.ModeCharDevice != 0
+}
+
+func startSpinner(w io.Writer, label string, enabled bool) *progressSpinner {
+	s := &progressSpinner{w: w, enabled: enabled}
+	if !enabled {
+		return s
+	}
+	s.done = make(chan struct{})
+	s.stopped = make(chan struct{})
+	frames := []string{"⠋", "⠙", "⠹", "⠸", "⠼", "⠴", "⠦", "⠧", "⠇", "⠏"}
+	fmt.Fprintf(w, "\r%s %s", frames[0], label)
+	go func() {
+		defer close(s.stopped)
+		ticker := time.NewTicker(80 * time.Millisecond)
+		defer ticker.Stop()
+		i := 1
+		for {
+			select {
+			case <-ticker.C:
+				fmt.Fprintf(w, "\r%s %s", frames[i%len(frames)], label)
+				i++
+			case <-s.done:
+				return
+			}
+		}
+	}()
+	return s
+}
+
+func (s *progressSpinner) Stop() {
+	if !s.enabled {
+		return
+	}
+	s.once.Do(func() {
+		close(s.done)
+		<-s.stopped
+		fmt.Fprint(s.w, "\r\033[K")
+	})
+}
+
 // suggest appends copy-pasteable commands to a message, each bare on its own
 // indented line directly under it, so selecting a line yields a runnable
 // command with no quoting or prose to strip.
@@ -219,13 +274,17 @@ func captureLimit(path string, args []string, d time.Duration, limit int64) ([]b
 	c := exec.CommandContext(ctx, path, args...)
 	c.Stdin = nil
 	var out, er bytes.Buffer
-	c.Stdout = &limited{w: &out, n: limit}
-	c.Stderr = &limited{w: &er, n: limit}
+	budget := &outputBudget{n: limit}
+	c.Stdout = &limited{w: &out, budget: budget}
+	c.Stderr = &limited{w: &er, budget: budget}
 	e := c.Run()
 	if ctx.Err() != nil {
 		return nil, fmt.Errorf("command timed out")
 	}
 	if e != nil {
+		if strings.Contains(e.Error(), "output exceeds limit") {
+			return nil, errors.New("output exceeds limit")
+		}
 		// The tool's own stderr explains the failure better than an exit code;
 		// fall back to the exec error only when the command died silently.
 		if msg := stripErrorPrefix(er.String()); msg != "" {
@@ -250,16 +309,23 @@ func stripErrorPrefix(s string) string {
 }
 
 type limited struct {
-	w io.Writer
-	n int64
+	w      io.Writer
+	budget *outputBudget
+}
+
+type outputBudget struct {
+	mu sync.Mutex
+	n  int64
 }
 
 func (l *limited) Write(p []byte) (int, error) {
-	if int64(len(p)) > l.n {
+	l.budget.mu.Lock()
+	defer l.budget.mu.Unlock()
+	if int64(len(p)) > l.budget.n {
 		return 0, errors.New("output exceeds limit")
 	}
 	n, e := l.w.Write(p)
-	l.n -= int64(n)
+	l.budget.n -= int64(n)
 	return n, e
 }
 func validate(tool string, b []byte) error {
@@ -340,6 +406,9 @@ func (a *app) write(tool string, b []byte, m metadata) error {
 	if _, e = f.Write(body); e == nil {
 		e = f.Chmod(0644)
 	}
+	if e == nil {
+		e = f.Sync()
+	}
 	if e == nil {
 		e = f.Close()
 	} else {
@@ -348,6 +417,16 @@ func (a *app) write(tool string, b []byte, m metadata) error {
 	if e == nil {
 		e = os.Rename(n, p)
 	}
+	if e == nil {
+		if d, de := os.Open(a.dir); de != nil {
+			fmt.Fprintf(os.Stderr, "%s %s installed but completion directory was not synced: %v\n", paint(useColor.err, "1;33", "warning:"), tool, de)
+		} else {
+			if de = d.Sync(); de != nil {
+				fmt.Fprintf(os.Stderr, "%s %s installed but completion directory was not synced: %v\n", paint(useColor.err, "1;33", "warning:"), tool, de)
+			}
+			_ = d.Close()
+		}
+	}
 	if e == nil {
 		// The definition is installed at this point; a failed event write only
 		// costs the current shell's refresh, so warn instead of failing.
@@ -447,6 +526,7 @@ func (a *app) updateOne(tool string) error {
 func (a *app) update() *cobra.Command {
 	return &cobra.Command{Use: "update [TOOL]", Args: cobra.MaximumNArgs(1), RunE: func(c *cobra.Command, x []string) error {
 		tools := x
+		var fails []string
 		if len(tools) == 0 {
 			es, er := os.ReadDir(a.dir)
 			if er != nil && !os.IsNotExist(er) {
@@ -456,7 +536,7 @@ func (a *app) update() *cobra.Command {
 				if strings.HasPrefix(e.Name(), "_") && !e.IsDir() {
 					b, re := os.ReadFile(filepath.Join(a.dir, e.Name()))
 					if re != nil {
-						tools = append(tools, strings.TrimPrefix(e.Name(), "_"))
+						fails = append(fails, e.Name()+": "+re.Error())
 						continue
 					}
 					if _, er := decode(b); er == nil {
@@ -468,7 +548,6 @@ func (a *app) update() *cobra.Command {
 			}
 			sort.Strings(tools)
 		}
-		var fails []string
 		for _, t := range tools {
 			if e := a.updateOne(t); e != nil {
 				fails = append(fails, t+": "+e.Error())
@@ -598,6 +677,10 @@ func (a *app) generate() *cobra.Command {
 			if e := a.shadowGuard(x[0], "completionctl generate --force "+x[0]); e != nil {
 				return e
 			}
+		}
+		spinner := startSpinner(c.ErrOrStderr(), "Discovering "+x[0]+" commands…", c.ErrOrStderr() == os.Stderr && spinnerTTY(os.Stderr))
+		defer spinner.Stop()
+		if !force {
 			for _, ar := range nativeArgs {
 				if b, e := capture(exe, ar, a.timeout); e == nil && validate(x[0], b) == nil {
 					return errors.New(suggest(useColor.err,
@@ -615,6 +698,7 @@ func (a *app) generate() *cobra.Command {
 		if e != nil {
 			return e
 		}
+		spinner.Stop()
 		m := metadata{Version: 1, Tool: x[0], Source: "help", Executable: exe, Args: help, Parser: "command-tree-v1", MaxDepth: limits.MaxDepth, MaxCommands: limits.MaxCommands, MaxOutput: limits.MaxOutput}
 		if e = a.write(x[0], z, m); e != nil {
 			return e
@@ -707,11 +791,17 @@ func (a *app) discoverHelp(exe string, helpArgs []string, limits discoveryLimits
 		args := append(append([]string{}, path...), helpArgs...)
 		b, err := captureLimit(exe, args, a.timeout, remaining)
 		if err != nil {
+			if len(path) > 0 && !isDiscoveryLimitError(err) {
+				continue
+			}
 			return commandTree{}, fmt.Errorf("help for %s: %w", commandLabel(path), err)
 		}
 		remaining -= int64(len(b))
 		command, err := parseHelp(b)
 		if err != nil {
+			if len(path) > 0 {
+				continue
+			}
 			return commandTree{}, fmt.Errorf("help for %s: %w", commandLabel(path), err)
 		}
 		tree.Nodes = append(tree.Nodes, commandNode{Path: append([]string{}, path...), Command: command})
@@ -730,6 +820,11 @@ func (a *app) discoverHelp(exe string, helpArgs []string, limits discoveryLimits
 	return tree, nil
 }
 
+func isDiscoveryLimitError(err error) bool {
+	s := err.Error()
+	return strings.Contains(s, "timed out") || strings.Contains(s, "output exceeds limit")
+}
+
 func commandLabel(path []string) string {
 	if len(path) == 0 {
 		return "root command"
@@ -979,23 +1074,32 @@ func renderTree(tool string, tree commandTree) ([]byte, error) {
 	}
 	var b strings.Builder
 	fmt.Fprintf(&b, "#compdef %s\n# help-derived: recognized command sections and options only\n_completionctl_generated() {\n", tool)
-	b.WriteString("  local context state line _cc_key='' _cc_i=2\n  typeset -A opt_args\n")
-	// Consume only an exact, recognized command prefix. Once flags or unknown
-	// positionals begin, dispatch remains at the last confirmed node.
+	b.WriteString("  local context state line _cc_key='' _cc_i=2 _cc_start=2\n  typeset -A opt_args\n")
+	// Consume a recognized command path while allowing options before commands.
+	// Required option arguments are skipped so a value matching a command name
+	// cannot accidentally change completion context.
 	b.WriteString("  while (( _cc_i < CURRENT )); do\n    case \"$_cc_key|${words[_cc_i]}\" in\n")
 	for _, n := range tree.Nodes {
 		parent := strings.Join(n.Path, " ")
 		for _, sub := range n.Command.Subcommands {
 			child := strings.TrimSpace(parent + " " + sub.Name)
-			fmt.Fprintf(&b, "      %s) _cc_key=%s ;;\n", zshCaseWord(parent+"|"+sub.Name), zshWordUnsafe(child))
+			fmt.Fprintf(&b, "      %s) _cc_key=%s; _cc_start=$((_cc_i + 1)) ;;\n", zshCaseWord(parent+"|"+sub.Name), zshWordUnsafe(child))
+		}
+		for _, option := range n.Command.Options {
+			if option.Cardinality != valueRequired {
+				continue
+			}
+			for _, alias := range option.Aliases {
+				fmt.Fprintf(&b, "      %s) (( _cc_i++ )) ;;\n", zshCaseWord(parent+"|"+alias))
+			}
 		}
 	}
-	b.WriteString("      *) break ;;\n    esac\n    (( _cc_i++ ))\n  done\n  case \"$_cc_key\" in\n")
+	b.WriteString("      *'|-'*) ;;\n      *) break ;;\n    esac\n    (( _cc_i++ ))\n  done\n  case \"$_cc_key\" in\n")
 	for _, n := range tree.Nodes {
 		key := strings.Join(n.Path, " ")
 		fmt.Fprintf(&b, "    %s)\n", zshCaseWord(key))
 		if len(n.Path) > 0 {
-			fmt.Fprintf(&b, "      words=(\"$words[1]\" \"${words[%d,-1]}\")\n      (( CURRENT -= %d ))\n", len(n.Path)+2, len(n.Path))
+			b.WriteString("      words=(\"$words[1]\" \"${words[_cc_start,-1]}\")\n      (( CURRENT -= _cc_start - 2 ))\n")
 		}
 		specs := renderOptionSpecs(n.Command)
 		if len(n.Command.Subcommands) > 0 {
diff --git a/main_test.go b/main_test.go
index 4b3f6ff..334fc09 100644
--- a/main_test.go
+++ b/main_test.go
@@ -243,6 +243,40 @@ esac
 	}
 }
 
+func TestDiscoverHelpSkipsUnsupportedAdvertisedCommand(t *testing.T) {
+	bin := t.TempDir()
+	tool := filepath.Join(bin, "tool")
+	script := `#!/bin/sh
+case "$*" in
+  --help) printf '%s\n' 'Commands:' '  good  Works' '  plugin  External plugin' ;;
+  'good --help') printf '%s\n' 'Options:' '  --ok  works' ;;
+  'plugin --help') exit 2 ;;
+esac
+`
+	if err := os.WriteFile(tool, []byte(script), 0755); err != nil {
+		t.Fatal(err)
+	}
+	a := app{timeout: time.Second}
+	tree, err := a.discoverHelp(tool, []string{"--help"}, discoveryLimits{MaxDepth: 1, MaxCommands: 3, MaxOutput: 4096})
+	if err != nil {
+		t.Fatal(err)
+	}
+	if len(tree.Nodes) != 2 || strings.Join(tree.Nodes[1].Path, " ") != "good" {
+		t.Fatalf("tree=%#v", tree)
+	}
+}
+
+func TestCaptureLimitIsSharedAcrossOutputStreams(t *testing.T) {
+	tool := filepath.Join(t.TempDir(), "tool")
+	script := "#!/bin/sh\nprintf '%080d' 0\nprintf '%080d' 0 >&2\n"
+	if err := os.WriteFile(tool, []byte(script), 0755); err != nil {
+		t.Fatal(err)
+	}
+	if _, err := captureLimit(tool, nil, time.Second, 100); err == nil || !strings.Contains(err.Error(), "output exceeds limit") {
+		t.Fatalf("shared output limit error=%v", err)
+	}
+}
+
 func TestRenderTreeContainsContextSpecificOptions(t *testing.T) {
 	tree := commandTree{Nodes: []commandNode{
 		{Command: parsedCommand{Options: []parsedOption{{Aliases: []string{"--root"}, Description: "root"}}, Subcommands: []parsedSubcommand{{"run", "Run it"}}}},
@@ -263,6 +297,26 @@ func TestRenderTreeContainsContextSpecificOptions(t *testing.T) {
 	}
 }
 
+func TestRenderTreeAllowsOptionsBeforeSubcommands(t *testing.T) {
+	tree := commandTree{Nodes: []commandNode{
+		{Command: parsedCommand{
+			Options:     []parsedOption{{Aliases: []string{"--config"}, Cardinality: valueRequired}},
+			Subcommands: []parsedSubcommand{{"run", "Run it"}},
+		}},
+		{Path: []string{"run"}, Command: parsedCommand{Options: []parsedOption{{Aliases: []string{"--child"}}}}},
+	}}
+	b, err := renderTree("tool", tree)
+	if err != nil {
+		t.Fatal(err)
+	}
+	s := string(b)
+	// Keep the assertions tied to dispatch behavior rather than the complete
+	// generated function.
+	if !strings.Contains(s, "'|--config') (( _cc_i++ ))") || !strings.Contains(s, "*'|-'*) ;;") {
+		t.Fatal(s)
+	}
+}
+
 func TestRenderRequiredAndOptional(t *testing.T) {
 	c, _ := parseHelp([]byte("--required FILE  r\n--optional [DIR]  o"))
 	b, e := renderZsh("tool", c)
@@ -415,6 +469,23 @@ func TestPaintRespectsToggle(t *testing.T) {
 	}
 }
 
+func TestProgressSpinnerCanStopCleanly(t *testing.T) {
+	var out bytes.Buffer
+	spinner := startSpinner(&out, "Discovering tool commands…", true)
+	spinner.Stop()
+	spinner.Stop()
+	got := out.String()
+	if !strings.Contains(got, "Discovering tool commands…") || !strings.HasSuffix(got, "\r\033[K") {
+		t.Fatalf("spinner output=%q", got)
+	}
+
+	out.Reset()
+	startSpinner(&out, "hidden", false).Stop()
+	if out.Len() != 0 {
+		t.Fatalf("disabled spinner wrote %q", out.String())
+	}
+}
+
 func TestUpdateReimportsFromRecordedSource(t *testing.T) {
 	dir, src := t.TempDir(), t.TempDir()
 	t.Setenv(searchEnv, "")
diff --git a/tests/help-completion-live.zsh b/tests/help-completion-live.zsh
index 4bb0d0f..482c923 100644
--- a/tests/help-completion-live.zsh
+++ b/tests/help-completion-live.zsh
@@ -13,6 +13,7 @@ cat >"$tmp/bin/faketool" <<'EOF'
 case "$*" in
   --help)
     printf '  -o, --output <FILE>  Write output\n'
+	printf '  --verbose  Enable verbose output\n'
     printf '  --visibility <visibility>\n      Set thread visibility (private, unlisted, workspace, group)\n'
     printf '  --mode <fast|slow>  Select mode\n'
     printf 'Commands:\n  run  Run a job\n'
@@ -54,7 +55,8 @@ for want in -- --output --visibility --mode; do
 done
 
 # The dispatcher selects options from the confirmed nested command path.
-zpty -wn comp $'faketool run deep --\t'
+# Global flags before the command path must not pin dispatch at the root.
+zpty -wn comp $'faketool --verbose run deep --\t'
 zpty -wn comp $'\n'
 zpty -w comp "print 'LEAF''MARKER'"
 zpty -r comp nested "*LEAFMARKER*"