A WordPress plugin that would allow you to update a plugin folder without producing a alert box for the user

remove_plugin.php

<?php

/**
 * olt_rename_plugin function.
 * removed the 
 * @access public
 * @param mixed $old_plugin. (default: null)
 * @param mixed $new_plugin. (default: null)
 * @param bool $add_to_network. (default: false)
 * @return void
 */

function olt_rename_plugin( $old_plugin = null, $new_plugin = null, $sitewide = false ) {
    
    $current = get_option( 'active_plugins' );
    
    $network_active_plugins = (array) get_site_option( 'active_sitewide_plugins', array() );
    
    
    $network_plugins = is_multisite() ? wp_get_active_network_plugins() : false;
    
    $old_plugin = plugin_basename( trim( $old_plugin ) );
    $new_plugin = plugin_basename( trim( $new_plugin ) );
    $update_current = false;
    $update_network_current = false;
    $old_plugin_gone = false;
    
   
    // don't remove the plugin if the file exists
    if( !file_exists( WP_PLUGIN_DIR . '/' . $old_plugin  ) ):
  	// remove the old plugin
		if( !empty( $old_plugin ) && in_array( $old_plugin, $current ) && !$sitewide):
			$current_count = 0; 
			
			foreach($current as $current_plugin):
			
				if( $current_plugin == $old_plugin )
					$remove_count = $current_count;	
				
				$current_count++;
				
			endforeach;
			
			if( isset($remove_count) ):
				unset($current[$remove_count]);
				unset($current[$remove_count]);
				$update_current = true;
				//var_dump('plugin file doesnt exits any more and was removed');
			endif;
			
		endif;
		
		// remove the in network plugin
		if( !empty( $old_plugin ) && $sitewide):
			$remove_network_plugin = false;
			
			foreach($network_active_plugins as $plugin => $time):
				
				if($old_plugin == $plugin)
					$remove_network_plugin = true;
			
			endforeach;
			
			if($remove_network_plugin):
				unset($network_active_plugins[$old_plugin]);
				$update_network_current = true;
			endif;
		endif; // end of remove the in network plugin
		//var_dump('plugin file doesnt exits any more and was removed');
		$old_plugin_gone = true;
	endif; // end of is file still exits check
	
	
	// var_dump( $old_plugin_gone, $network_active_plugins,$current , $update_current, "<br />");

	// only activate the plugin if the old plugin is gone and the update current is set to true
	if( $old_plugin_gone ):
		// active the new plugin 
		if ( ! validate_file( $new_plugin ) // $plugin must validate as file
				&& '.php' == substr( $new_plugin, -4 ) // $plugin must end with '.php'
				&& file_exists( WP_PLUGIN_DIR . '/' . $new_plugin ) // $plugin must exist
				// not already included as a network plugin
				&& ( ! $network_plugins || ! in_array( WP_PLUGIN_DIR . '/' . $new_plugin, $network_plugins ) )
				&& !empty( $new_plugin ) // plugin exists as a string
				&&  !in_array( $new_plugin, $current )  // is not enavled already
				&& !$sitewide
			): // plugin not active
	        $current[] = $new_plugin;
	        sort( $current );
	        
	        // var_dump($current);
	        // var_dump('activated the plugin:'. $new_plugin);
	        // do_action( 'activate_plugin', trim( $new_plugin_name ) );
	        $update_current = true;
	        //do_action( 'activate_' . trim( $new_plugin_name ) );
	        // do_action( 'activated_plugin', trim( $new_plugin_name ) );
	    
	    // add the plugin network wide  
	    elseif( ! validate_file( $new_plugin ) // $plugin must validate as file
				&& '.php' == substr( $new_plugin, -4 ) // $plugin must end with '.php'
				&& file_exists( WP_PLUGIN_DIR . '/' . $new_plugin ) // $plugin must exist
				// not already included as a network plugin
				&& ( ! $network_plugins || ! in_array( WP_PLUGIN_DIR . '/' . $new_plugin, $network_plugins ) )
				&& !empty( $new_plugin ) // plugin exists as a string
				&& $sitewide ):
	    		
	    		$network_active_plugins[$new_plugin] = time();
	    		$update_network_current = true;
	    endif; 
	else:
		// var_dump('Nothing happends');
    endif; // end of old plugin gone is gone  
    
	
    if( $update_current ):
    	update_option( 'active_plugins', $current );
    	// var_dump($current);
	endif;
	
	if( $update_network_current ):
		update_site_option( 'active_sitewide_plugins', $network_active_plugins );
		// var_dump($network_active_plugins);
	endif;
	
    return null;
}
/* not tested yet */
function olt_add_plugin($new_plugin){
	
	olt_rename_plugin( null , $old_plugin );
}
/* not tested yet */
function olt_remove_plugin( $new_plugin, $sitewide=false ){

	olt_rename_plugin( $old_plugin, null,  $sitewide );
}


// === how to rename the plugin ===
// 1. edit this file and add the rule for renaming save the changes 
// olt_rename_plugin( 'tabs-shortcode/tabs-shotcode.php', 'tabs-shortcode/tabs-shortcode.php', true  );
// olt_rename_plugin( 'tabs-shortcode/tabs-shotcode.php', 'tabs-shortcode/tabs-shortcode.php' );

// 2. update the plugin file
// - upload the new plugin 
// - delete the old plugin file 
// the rules