Uploaded patches are empty

When I use the upload_patch command the file that is uploaded is empty. However, adding the same file manually in trac works.

Operating System:
Mac OS 10.11.16.

Copy of the file ( I had to change the extension from .diff to .txt to upload here )
39800.txt

git diff master --no-prefix output:

diff --git a/src/wp-includes/nav-menu-template.php b/src/wp-includes/nav-menu-template.php
index 737d6e6..ea7c22d 100644
--- a/src/wp-includes/nav-menu-template.php
+++ b/src/wp-includes/nav-menu-template.php
@@ -394,6 +394,18 @@ function _wp_menu_item_classes_by_context( &$menu_items ) {
                ) {
                        $classes[] = 'current-menu-item';
                        $menu_items[$key]->current = true;
+
+                       $_anc_id = (int) $menu_item->db_id;
+
+                       while(
+                               ( $_anc_id = get_post_meta( $_anc_id, '_menu_item_menu_item_parent', true ) ) &&
+                               ! in_array( $_anc_id, $active_ancestor_item_ids, true )
+                       ) {
+                               $active_ancestor_item_ids[] = $_anc_id;
+                       }
+
+                       $active_parent_item_ids[] = (int) $menu_item->menu_item_parent;
+
                // if the menu item corresponds to the currently-requested URL
                } elseif ( 'custom' == $menu_item->object && isset( $_SERVER['HTTP_HOST'] ) ) {
                        $_root_relative_current = untrailingslashit( $_SERVER['REQUEST_URI'] );
diff --git a/tests/phpunit/tests/post/nav-menu.php b/tests/phpunit/tests/post/nav-menu.php
index c6a028c..d0496a1 100644
--- a/tests/phpunit/tests/post/nav-menu.php
+++ b/tests/phpunit/tests/post/nav-menu.php
@@ -553,4 +553,63 @@ class Test_Nav_Menus extends WP_UnitTestCase {
                $this->assertNotInstanceOf( 'WP_Post', get_post( $nav_created_post_ids[0] ) );
                $this->assertNotInstanceOf( 'WP_Post', get_post( $nav_created_post_ids[1] ) );
        }
+
+
+       /**







diff --git src/wp-includes/nav-menu-template.php src/wp-includes/nav-menu-template.php
index 737d6e6..ea7c22d 100644
--- src/wp-includes/nav-menu-template.php
+++ src/wp-includes/nav-menu-template.php
@@ -394,6 +394,18 @@ function _wp_menu_item_classes_by_context( &$menu_items ) {
                ) {
                        $classes[] = 'current-menu-item';
                        $menu_items[$key]->current = true;
+
+                       $_anc_id = (int) $menu_item->db_id;
+
+                       while(
+                               ( $_anc_id = get_post_meta( $_anc_id, '_menu_item_menu_item_parent', true ) ) &&
+                               ! in_array( $_anc_id, $active_ancestor_item_ids, true )
+                       ) {
+                               $active_ancestor_item_ids[] = $_anc_id;
+                       }
+
+                       $active_parent_item_ids[] = (int) $menu_item->menu_item_parent;
+
                // if the menu item corresponds to the currently-requested URL
                } elseif ( 'custom' == $menu_item->object && isset( $_SERVER['HTTP_HOST'] ) ) {
                        $_root_relative_current = untrailingslashit( $_SERVER['REQUEST_URI'] );
                // if the menu item corresponds to the currently-requested URL
                } elseif ( 'custom' == $menu_item->object && isset( $_SERVER['HTTP_HOST'] ) ) {
                        $_root_relative_current = untrailingslashit( $_SERVER['REQUEST_URI'] );
diff --git tests/phpunit/tests/post/nav-menu.php tests/phpunit/tests/post/nav-menu.php
index c6a028c..d0496a1 100644
--- tests/phpunit/tests/post/nav-menu.php
+++ tests/phpunit/tests/post/nav-menu.php
@@ -553,4 +553,63 @@ class Test_Nav_Menus extends WP_UnitTestCase {
                $this->assertNotInstanceOf( 'WP_Post', get_post( $nav_created_post_ids[0] ) );
                $this->assertNotInstanceOf( 'WP_Post', get_post( $nav_created_post_ids[1] ) );
        }
+
+
+       /**
+        * @ticket 39800
+        */
+       function test_parent_ancestor_for_post_archive() {
+
+               register_post_type( 'books', array( 'label' => 'Books', 'public' => true, 'has_archive' => true ) );
+
+               $first_page_id  = self::factory()->post->create( array( 'post_type' => 'page', 'post_title' => 'Top Level Page') );
+               $second_page_id = self::factory()->post->create( array( 'post_type' => 'page', 'post_title' => 'Second Level Page') );
+
+
+               $first_menu_id = wp_update_nav_menu_item( $this->menu_id, 0, array(
+                       'menu-item-type'      => 'post_type',
+                       'menu-item-object'    => 'page',
+                       'menu-item-object-id' => $first_page_id,
+                       'menu-item-status'    => 'publish',
+               ));
+
+               $second_menu_id = wp_update_nav_menu_item( $this->menu_id, 0, array(
+                       'menu-item-type'      => 'post_type',
+                       'menu-item-object'    => 'page',
+                       'menu-item-object-id' => $second_page_id,
+                       'menu-item-status'    => 'publish',
+                       'menu-item-parent-id' => $first_menu_id
+               ));
+
+               wp_update_nav_menu_item( $this->menu_id, 0, array(
+                       'menu-item-type'      => 'post_type_archive',
+                       'menu-item-object'    => 'books',
+                       'menu-item-status'    => 'publish',
+                       'menu-item-parent-id' => $second_menu_id
+               ));
+
+               $this->go_to( get_post_type_archive_link( 'books') );
+
+               $menu_items = wp_get_nav_menu_items( $this->menu_id );
+               _wp_menu_item_classes_by_context( $menu_items );
+
+               $top_page_menu_item       = $menu_items[0];
+               $secondary_page_menu_item = $menu_items[1];
+               $post_archive_menu_item   = $menu_items[2];
+
+               $this->assertFalse( $top_page_menu_item->current_item_parent );
+               $this->assertTrue( $top_page_menu_item->current_item_ancestor );
+               $this->assertContains( 'current-menu-ancestor', $top_page_menu_item->classes );
+
+               $this->assertTrue( $secondary_page_menu_item->current_item_parent );
+               $this->assertTrue( $secondary_page_menu_item->current_item_ancestor  );
+               $this->assertContains( 'current-menu-parent', $secondary_page_menu_item->classes );
+               $this->assertContains( 'current-menu-ancestor', $secondary_page_menu_item->classes );
+
+               $this->assertFalse( $post_archive_menu_item->current_item_parent );
+               $this->assertFalse( $post_archive_menu_item->current_item_ancestor  );
+
+               $this->assertNotContains( 'current-menu-parent', $post_archive_menu_item->classes );
+               $this->assertNotContains( 'current-menu-ancestor', $post_archive_menu_item->classes );
+       }
 }
(END)

Start at the upload_patch command and reproduce the empty-upload behavior using the attached patch file, comparing it with a manual Trac upload. Trace how the command reads and submits the file; done means the uploaded patch retains the complete diff instead of being empty.