PHP `rename()` support for VirtualBox via a Must-Use plugin coupled with a "watcher" bash script.

php-rename-support-for-virtualbox.php

<?php

/**
 * Plugin Name: PHP <code>rename()</code> support for VirtualBox.
 * Description: Enables support for the PHP native rename() function.
 * Author:      WordPress Core Contributors
 * Author URI:  https://make.wordpress.org/core
 * License:     GPLv2 or later
 * Version:     1.0.0
 */

add_action(
	'pre_move_dir',
	function() {
		global $wp_filesystem;

		if ( ! $wp_filesystem ) {
			require_once ABSPATH . '/wp-admin/includes/file.php';
			WP_Filesystem();
		}

		$wp_filesystem->touch( trailingslashit( $wp_filesystem->wp_content_dir() ) . '.wpclearcache' );
	}
);

add_action(
	'post_move_dir',
	function() {
		global $wp_filesystem;

		# Wait 200ms to ensure that the `rename()` has completed.
		usleep( 200000 );

		if ( ! $wp_filesystem ) {
			require_once ABSPATH . '/wp-admin/includes/file.php';
			WP_Filesystem();
		}

		$wp_filesystem->delete( trailingslashit( $wp_filesystem->wp_content_dir() ) . '.wpclearcache' );
	}
);

wpclearcache.sh

#!/usr/bin/sh

# Name:        PHP rename() support for VirtualBox.
# Description: Enables support for the PHP native rename() function.
# Author:      WordPress Core Contributors
# Author URI:  https://make.wordpress.org/core
# License:     GPLv2 or later
# Version:     1.0.0
# 
# Usage:
#  1. Set WP_CONTENT_DIR to the path for the wp-content directory,
#     without a trailing slash.
# 
#  2. Ensure the script can be executed by using the following command:
#     chmod +x wpclearcache.sh
#
#  3. This script should be run continuously.
#     It is advised to use the following command:
#     ./wpclearcache.sh &

WP_CONTENT_DIR=.

while :
do
  if [ -f "$WP_CONTENT_DIR/.wpclearcache" ]; then
    # Free reclaimable slab objects (includes dentries and inodes).
    sudo sh -c 'echo 2 > /proc/sys/vm/drop_caches'
  fi

  # Wait 200ms.
  sleep 0.2s
done