diff --git a/applier.go b/applier.go
index 27f93df..9e2897e 100644
--- a/applier.go
+++ b/applier.go
@@ -31,6 +31,8 @@ type Applier struct {
 	treeCache   map[string]*github.Tree
 	entries     map[string]*github.TreeEntry
 	uncommitted bool
+
+	applyOptions []gitdiff.ApplyOption
 }
 
 // NewApplier creates a new Applier for a repository. The Applier applies
@@ -45,6 +47,12 @@ func NewApplier(client *github.Client, repo Repository, c *github.Commit) *Appli
 	return a
 }
 
+// SetApplyOptions sets the options to use when calling [gitdiff.Apply]. Pass
+// an empty list to remove previously set options.
+func (a *Applier) SetApplyOptions(opts ...gitdiff.ApplyOption) {
+	a.applyOptions = opts
+}
+
 // Apply applies the changes in a file, adds the result to the list of pending
 // tree entries, and returns the entry. If the application succeeds, Apply
 // creates a blob in the repository with the modified content.
@@ -97,7 +105,7 @@ func (a *Applier) applyCreate(ctx context.Context, f *gitdiff.File) (*github.Tre
 		return nil, &Conflict{Type: ConflictNewFileExists, File: f.NewName}
 	}
 
-	c, err := base64Apply(nil, f.NewName, f)
+	c, err := base64Apply(nil, f.NewName, f, a.applyOptions...)
 	if err != nil {
 		return nil, err
 	}
@@ -130,7 +138,7 @@ func (a *Applier) applyDelete(ctx context.Context, f *gitdiff.File) (*github.Tre
 		return nil, fmt.Errorf("get blob content failed: %w", err)
 	}
 
-	if err := apply(io.Discard, bytes.NewReader(data), f.OldName, f); err != nil {
+	if err := apply(io.Discard, bytes.NewReader(data), f.OldName, f, a.applyOptions...); err != nil {
 		return nil, err
 	}
 
@@ -166,7 +174,7 @@ func (a *Applier) applyModify(ctx context.Context, f *gitdiff.File) (*github.Tre
 			return nil, fmt.Errorf("get blob content failed: %w", err)
 		}
 
-		c, err := base64Apply(data, f.OldName, f)
+		c, err := base64Apply(data, f.OldName, f, a.applyOptions...)
 		if err != nil {
 			return nil, err
 		}
@@ -346,11 +354,11 @@ func findTreeEntry(t *github.Tree, name, entryType string) (*github.TreeEntry, b
 
 // base64Apply applies the patch in f to data and returns the result as a
 // base64-encoded string.
-func base64Apply(data []byte, name string, f *gitdiff.File) (string, error) {
+func base64Apply(data []byte, name string, f *gitdiff.File, opts ...gitdiff.ApplyOption) (string, error) {
 	var b bytes.Buffer
 
 	enc := base64.NewEncoder(base64.StdEncoding, &b)
-	if err := apply(enc, bytes.NewReader(data), name, f); err != nil {
+	if err := apply(enc, bytes.NewReader(data), name, f, opts...); err != nil {
 		return "", err
 	}
 	if err := enc.Close(); err != nil {
@@ -361,8 +369,8 @@ func base64Apply(data []byte, name string, f *gitdiff.File) (string, error) {
 }
 
 // apply runs gitdiff.Apply, wrapping any conflicts in patch2pr's Conflict type.
-func apply(dst io.Writer, src io.ReaderAt, name string, f *gitdiff.File) error {
-	if err := gitdiff.Apply(dst, src, f); err != nil {
+func apply(dst io.Writer, src io.ReaderAt, name string, f *gitdiff.File, opts ...gitdiff.ApplyOption) error {
+	if err := gitdiff.Apply(dst, src, f, opts...); err != nil {
 		var applyErr *gitdiff.ApplyError
 		var conflict *gitdiff.Conflict
 		if errors.As(err, &applyErr) && errors.As(err, &conflict) {
diff --git a/go.mod b/go.mod
index db4c6d6..cc7499e 100644
--- a/go.mod
+++ b/go.mod
@@ -3,7 +3,7 @@ module github.com/bluekeyes/patch2pr
 go 1.25.0
 
 require (
-	github.com/bluekeyes/go-gitdiff v0.8.1
+	github.com/bluekeyes/go-gitdiff v0.9.0
 	github.com/google/go-github/v88 v88.0.0
 	github.com/shurcooL/githubv4 v0.0.0-20260209031235-2402fdf4a9ed
 )
diff --git a/go.sum b/go.sum
index 57fbc15..1c208cf 100644
--- a/go.sum
+++ b/go.sum
@@ -1,5 +1,5 @@
-github.com/bluekeyes/go-gitdiff v0.8.1 h1:lL1GofKMywO17c0lgQmJYcKek5+s8X6tXVNOLxy4smI=
-github.com/bluekeyes/go-gitdiff v0.8.1/go.mod h1:WWAk1Mc6EgWarCrPFO+xeYlujPu98VuLW3Tu+B/85AE=
+github.com/bluekeyes/go-gitdiff v0.9.0 h1:w+O6lkRBOqfGcwF0Lf6FFHQrhmxM0hCJW5+rbilGuSs=
+github.com/bluekeyes/go-gitdiff v0.9.0/go.mod h1:WWAk1Mc6EgWarCrPFO+xeYlujPu98VuLW3Tu+B/85AE=
 github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
 github.com/google/go-cmp v0.7.0 h1:wk8382ETsv4JYUZwIsn6YpYiWiBsYLSJiTsyBybVuN8=
 github.com/google/go-cmp v0.7.0/go.mod h1:pXiqmnSA92OHEEa9HXL2W4E7lf9JzCmGVUdgjX3N/iU=