diff --git a/internal/cli/entry_test.go b/internal/cli/entry_test.go
index 7fd3605..b27ea7e 100644
--- a/internal/cli/entry_test.go
+++ b/internal/cli/entry_test.go
@@ -1347,20 +1347,22 @@ func TestGenerateDefaultOutput(t *testing.T) {
 func TestGenerateSeveralPathsDefaultOutput(t *testing.T) {
 	root := t.TempDir()
 	fs := afero.NewOsFs()
-	require.NoError(t, fs.MkdirAll(filepath.Join(root, "first"), 0o750))
-	require.NoError(t, fs.MkdirAll(filepath.Join(root, "second"), 0o750))
-	writeTestFile(t, fs, filepath.Join(root, "first", "one.txt"), "1")
-	writeTestFile(t, fs, filepath.Join(root, "second", "two.txt"), "2")
+	dirs := []string{"first", "second"}
+
+	for _, dir := range dirs {
+		require.NoError(t, fs.MkdirAll(filepath.Join(root, dir), 0o750))
+		writeTestFile(t, fs, filepath.Join(root, dir, dir+".txt"), dir)
+	}
 
 	t.Chdir(root)
 
-	opts := testOpts([]string{testApp, cmdGenerate, "-q", "first", "second"}, fs)
+	opts := testOpts(append([]string{testApp, cmdGenerate, "-q"}, dirs...), fs)
 	require.Equal(t, 0, runCLI(opts), "stderr: %s", testStderr(t, opts))
 
-	assert.ElementsMatch(t, []string{"one.txt", "two.txt"},
+	assert.ElementsMatch(t, []string{"first.txt", "second.txt"},
 		manifestPaths(t, fs, filepath.Join(root, defaultManifestName)))
 
-	for _, dir := range []string{"first", "second"} {
+	for _, dir := range dirs {
 		exists, err := afero.Exists(fs, filepath.Join(root, dir, defaultManifestName))
 		require.NoError(t, err)
 		assert.False(t, exists, "index.mf written in %s", dir)
diff --git a/internal/cli/gen.go b/internal/cli/gen.go
index 3c33e3a..4ea3e36 100644
--- a/internal/cli/gen.go
+++ b/internal/cli/gen.go
@@ -4,6 +4,7 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"io"
 	"os"
 	"os/signal"
 	"path/filepath"
@@ -235,6 +236,35 @@ func (mfa *CLIApp) runEnumeratePhase(cmd *cli.Command, s *mfer.Scanner) error {
 	return nil
 }
 
+// runScanPhase reads the enumerated files and writes the manifest to out,
+// with optional progress reporting.
+func (mfa *CLIApp) runScanPhase(
+	ctx context.Context, cmd *cli.Command, s *mfer.Scanner, out io.Writer,
+) error {
+	var (
+		scanProgress chan mfer.ScanStatus
+		scanWg       sync.WaitGroup
+	)
+
+	if cmd.Bool("progress") {
+		scanProgress = make(chan mfer.ScanStatus, 1)
+
+		scanWg.Add(1)
+
+		go reportScanProgress(scanProgress, &scanWg)
+	}
+
+	err := s.ToManifest(ctx, out, scanProgress)
+
+	scanWg.Wait()
+
+	if err != nil {
+		return fmt.Errorf("generate manifest: %w", err)
+	}
+
+	return nil
+}
+
 func (mfa *CLIApp) generateManifestOperation(
 	ctx context.Context, cmd *cli.Command,
 ) error {
@@ -253,8 +283,6 @@ func (mfa *CLIApp) generateManifestOperation(
 		return err
 	}
 
-	showProgress := cmd.Bool("progress")
-
 	// Check if output file exists
 	if exists, _ := afero.Exists(mfa.Fs, outputPath); exists && !cmd.Bool("force") {
 		return fmt.Errorf("output file %s %w", outputPath, errOutputExists)
@@ -286,25 +314,9 @@ func (mfa *CLIApp) generateManifestOperation(
 	}()
 
 	// Phase 2: Scan - read file contents and generate manifest
-	var (
-		scanProgress chan mfer.ScanStatus
-		scanWg       sync.WaitGroup
-	)
-
-	if showProgress {
-		scanProgress = make(chan mfer.ScanStatus, 1)
-
-		scanWg.Add(1)
-
-		go reportScanProgress(scanProgress, &scanWg)
-	}
-
-	err = s.ToManifest(ctx, outFile, scanProgress)
-
-	scanWg.Wait()
-
+	err = mfa.runScanPhase(ctx, cmd, s, outFile)
 	if err != nil {
-		return fmt.Errorf("generate manifest: %w", err)
+		return err
 	}
 
 	// Close file before rename to ensure all data is flushed