Devkit - Alternative delete_plugins() - This allows additional protected plugins using a filter

admin__wp-reset.php

public function delete_plugins() {
    require_once ABSPATH . 'wp-admin/includes/plugin.php';
    require_once ABSPATH . 'wp-admin/includes/file.php';

    // Plugin basenames you NEVER want to delete
    $protected = array(
        DPDEV_BASE, // devkit itself
    );

    // Let other code add more protected plugins
    $protected = apply_filters('devkit_deleteplugin_exceptions', $protected);

    // 1) Deactivate active plugins except protected ones
    $active_plugins = get_option('active_plugins', array());

    // Remove all protected plugins from deactivation list
    $active_plugins = array_values(array_diff($active_plugins, $protected));

    if (!empty($active_plugins)) {
        deactivate_plugins($active_plugins, true);
    }

    // 2) Get all plugins, remove protected ones, delete the rest
    $plugins = get_plugins();

    foreach ($protected as $p) {
        unset($plugins[$p]);
    }

    if (!empty($plugins)) {
        delete_plugins(array_keys($plugins));
    }
}

example_filter.php

add_filter('devkit_deleteplugin_exceptions', function($protected) {
    $protected[] = 'ninja-updater/ninja-updater.php';
    return $protected;
});