diff --git a/internal/run/minimumViableSpec.go b/internal/run/minimumViableSpec.go
index dc8a77b5..7fa2a3c0 100644
--- a/internal/run/minimumViableSpec.go
+++ b/internal/run/minimumViableSpec.go
@@ -26,12 +26,19 @@ func (w *Workflow) retryWithMinimumViableSpec(ctx context.Context, parentStep *w
 	substep := parentStep.NewSubstep("Retrying with minimum viable document")
 	source := w.workflow.Sources[sourceID]
 
-	source.Transformations = append(source.Transformations, workflow.Transformation{
-		FilterOperations: &workflow.FilterOperationsOptions{
-			Operations: strings.Join(invalidOperations, ","),
-			Exclude:    pointer.ToBool(true),
-		},
-	})
+	if len(invalidOperations) > 0 {
+		source.Transformations = append(source.Transformations, workflow.Transformation{
+			FilterOperations: &workflow.FilterOperationsOptions{
+				Operations: strings.Join(invalidOperations, ","),
+				Exclude:    pointer.ToBool(true),
+			},
+		})
+	} else {
+		// Sometimes the document has invalid, unused sections
+		source.Transformations = append(source.Transformations, workflow.Transformation{
+			RemoveUnused: pointer.ToBool(true),
+		})
+	}
 	w.workflow.Sources[sourceID] = source
 
 	sourcePath, sourceRes, err := w.RunSource(ctx, substep, sourceID, targetID)
diff --git a/internal/run/transform.go b/internal/run/transform.go
index 534a7bb9..7fc842b7 100644
--- a/internal/run/transform.go
+++ b/internal/run/transform.go
@@ -47,20 +47,20 @@ func (t Transform) Do(ctx context.Context, inputPath string) (string, error) {
 		return "", err
 	}
 
-	var out bytes.Buffer
+	var out *bytes.Buffer
 	for _, transformation := range t.source.Transformations {
-		out = bytes.Buffer{}
+		out = &bytes.Buffer{}
 
 		if transformation.Cleanup != nil {
 			transformStep.NewSubstep("Cleaning up document")
 
-			if err := transform.CleanupFromReader(ctx, in, inputPath, &out, yamlOut); err != nil {
+			if err := transform.CleanupFromReader(ctx, in, inputPath, out, yamlOut); err != nil {
 				return "", err
 			}
 		} else if transformation.RemoveUnused != nil {
 			transformStep.NewSubstep("Removing unused nodes")
 
-			if err := transform.RemoveUnusedFromReader(ctx, in, inputPath, &out, yamlOut); err != nil {
+			if err := transform.RemoveUnusedFromReader(ctx, in, inputPath, out, yamlOut); err != nil {
 				return "", err
 			}
 		} else if transformation.FilterOperations != nil {
@@ -78,12 +78,12 @@ func (t Transform) Do(ctx context.Context, inputPath string) (string, error) {
 			}
 			transformStep.NewSubstep(fmt.Sprintf("Filtering %s %d operations", inOutString, len(operations)))
 
-			if err := transform.FilterOperationsFromReader(ctx, in, inputPath, operations, include, &out, yamlOut); err != nil {
+			if err := transform.FilterOperationsFromReader(ctx, in, inputPath, operations, include, out, yamlOut); err != nil {
 				return "", err
 			}
 		}
 
-		in = &out
+		in = bytes.NewReader(out.Bytes())
 	}
 
 	outFile, err := os.Create(outputPath)
@@ -91,7 +91,7 @@ func (t Transform) Do(ctx context.Context, inputPath string) (string, error) {
 	if err != nil {
 		return "", err
 	}
-	if _, err := io.Copy(outFile, &out); err != nil {
+	if _, err := io.Copy(outFile, out); err != nil {
 		return "", err
 	}
 
diff --git a/prompts/sources.go b/prompts/sources.go
index 46207357..1368e9ba 100644
--- a/prompts/sources.go
+++ b/prompts/sources.go
@@ -400,8 +400,6 @@ func PromptForNewSource(currentWorkflow *workflow.Workflow) (string, *workflow.S
 		return "", nil, err
 	}
 
-	println("FILE LOCATION: " + fileLocation)
-
 	document, err := formatDocument(fileLocation, authHeader, false)
 	if err != nil {
 		return "", nil, err