Fix --output-dir having no effect for single-skill runs

cmd/waza/cmd_run.go

@@ -182,6 +182,26 @@ func runCommandE(cmd *cobra.Command, args []string) error {
 
 	if len(specPaths) == 1 {
 		results, err := runCommandForSpec(cmd, specPaths[0])
+
+		// Only write outputs when the run produced meaningful results:
+		// either success (err == nil) or test failures (outcomes are still valid).
+		// For other errors (spec load/parse failures), skip writing and return early.
+		if err != nil {
+			if _, ok := errors.AsType[*TestFailureError](err); !ok {
+				return err
+			}
+		}
+
+		// Write structured directory output when --output-dir is specified
+		if outputDir != "" {
+			if wErr := writeOutputDir(outputDir, []skillRunResult{
+				{skillName: specPaths[0].skillName, outcomes: results},
+			}); wErr != nil {
+				return fmt.Errorf("failed to write output directory: %w", wErr)
+			}
+		}
+
+		// Auto-upload after all local writes succeed
 		autoUploadOutcomes(cmd, cfg, results)
 		return err
 	}

cmd/waza/cmd_run_test.go

@@ -1905,6 +1905,39 @@ func TestRunCommand_OutputDirMutualExclusion(t *testing.T) {
 	assert.Contains(t, err.Error(), "--output and --output-dir are mutually exclusive")
 }
 
+func TestRunCommand_OutputDirSingleSkill(t *testing.T) {
+	resetRunGlobals()
+	defer resetRunGlobals()
+
+	specPath := createTestSpec(t, "mock")
+	outDir := filepath.Join(t.TempDir(), "results")
+
+	cmd := newRunCommand()
+	cmd.SetArgs([]string{specPath, "--output-dir", outDir})
+
+	err := cmd.Execute()
+	require.NoError(t, err)
+
+	// Verify output directory was created with a result JSON file
+	entries, err := os.ReadDir(outDir)
+	require.NoError(t, err)
+	require.NotEmpty(t, entries, "expected output files in --output-dir")
+
+	// Find and validate the JSON result file
+	var found bool
+	for _, e := range entries {
+		if filepath.Ext(e.Name()) == ".json" {
+			data, err := os.ReadFile(filepath.Join(outDir, e.Name()))
+			require.NoError(t, err)
+			var outcome models.EvaluationOutcome
+			require.NoError(t, json.Unmarshal(data, &outcome))
+			assert.Equal(t, "test-eval", outcome.BenchName)
+			found = true
+		}
+	}
+	assert.True(t, found, "expected at least one .json result in output dir")
+}
+
 func TestWriteOutputDir_SingleSkill(t *testing.T) {
 	dir := t.TempDir()