Update all the servers located in a "Parent directory" (Need custom "src/" folder method for accessing PocketMine API)

ServerUpdater.php

<?php

/**
 * @name ServerUpdater
 * @main ServerUpdater\Loader
 * @version 1.0.0
 * @api 1.12.0
 * @description Updates all server's PHAR file
 * @author iksaku
 */
 
namespace ServerUpdater{
    use pocketmine\command\Command;
    use pocketmine\command\CommandSender;
    use pocketmine\command\PluginIdentifiableCommand;
    use pocketmine\plugin\PluginBase;
    use pocketmine\scheduler\AsyncTask;
    use pocketmine\Server;
    use pocketmine\utils\TextFormat;
    use pocketmine\utils\Utils;

    class Loader extends PluginBase{
        public function onEnable(){
            /** Just register the new command ;) */
            $this->getServer()->getCommandMap()->register("ServersUpdater", new UpdateCommand($this));
        }

        /** @var AsyncTask|null */
        private $updating;

        /**
         * @return bool
         */
        public function callAsyncUpdater(){
            if($this->updating !== null && $this->updating->isRunning()){
                $this->getLogger()->notice(TextFormat::RED . "\"Updating Script\" is already in process... Please be patient ;)");
                return false;
            }
            $this->getServer()->getLogger()->alert(TextFormat::YELLOW . "Starting \"Updater Script\"...");
            $this->getServer()->getScheduler()->scheduleAsyncTask($this->updating = new Updater($this));
            return true;
        }
    }

    class UpdateCommand extends Command implements PluginIdentifiableCommand{
        /**
         * Update command...
         * Call a new "Update Async Task" when executed!
         */

        /** @var Loader */
        private $plugin;

        public function __construct(Loader $plugin){
            parent::__construct("update", "Update all the servers", "/update");
            $this->plugin = $plugin;
        }

        /**
         * @return Loader
         */
        public function getPlugin(){
            return $this->plugin;
        }

        /**
         * @param CommandSender $sender
         * @param string $alias
         * @param array $args
         * @return bool
         */
        public function execute(CommandSender $sender, $alias, array $args){
            if(!$this->getPlugin()->callAsyncUpdater()){
                return false;
            }
            return true;
        }
    }

    class Updater extends AsyncTask{
        /** @var string */
        private $parent;

        public function __construct(Loader $plugin){
            $this->parent = dirname($plugin->getServer()->getDataPath()) . DIRECTORY_SEPARATOR;
        }

        public function onRun(){
            // Remove any piece of old files... If present...
            if(file_exists($file = $this->parent . "archive.zip")){
                unlink($file);
            }
            if(is_dir($dir = $this->parent . "archive" . DIRECTORY_SEPARATOR)){
                rmdir($dir);
            }

            // Create a new file called "archive.zip" that will contain the zipped update...
            $file = fopen($this->parent . "archive.zip", "w+");
            // Download the zipped update from Jenkins...
            fwrite($file, Utils::getURL("http://jenkins.pocketmine.net/job/PocketMine-MP/Development/artifact/*zip*/archive.zip"));
            // After download is complete, close the file...
            fclose($file);

            // Open the zipped update...
            $zip = new \ZipArchive();
            $zip->open($this->parent . "archive.zip");
            // Extract the update from the zip to the parent directory (The directory where all servers are located)...
            $zip->extractTo($this->parent);
            // Close the zip file...
            $zip->close();

            // Remove the zip file...
            if(file_exists($file = $this->parent . "archive.zip")){
                unlink($file);
            }

            /*
             * Scan the extracted zip directory to find the update file (This is because the name changes each time there's an update),
             * rename the update file to "PocketMine-MP" and move it to the parent directory for faster reference in next steps...
             */
            foreach(scandir($dir = $this->parent . "archive" . DIRECTORY_SEPARATOR) as $f){
                if(substr($f, -5) === ".phar"){
                    rename($dir . $f, $this->parent . "PocketMine-MP.phar");
                }
            }
            // Remove the (now) unnecessary extracted (From the zip) directory...
            if(is_dir($dir = $this->parent . "archive" . DIRECTORY_SEPARATOR)){
                rmdir($dir);
            }
            // Scan all the directories and validate that they're servers and copy the update file...
            foreach(scandir($this->parent) as $dir){
                if(is_dir($d = $this->parent . $dir . DIRECTORY_SEPARATOR)){
                    if(is_dir($d . "src" . DIRECTORY_SEPARATOR)){
                        // Copy to root folder of the server, allowing another trick at server's initialization
                        copy($this->parent . "PocketMine-MP.phar", $d . "update.phar");
                    }
                }
            }
            // Remove the now unnecessary update file from the parent directory...
            if(file_exists($file = $this->parent . "PocketMine-MP.phar")){
                unlink($file);
            }
        }

        public function onCompletion(Server $server){
            $server->getLogger()->alert(TextFormat::GREEN . "All servers have been updated! Please restart your servers...");
        }
    }
}

start.cmd

@echo off
TITLE PocketMine-MP server software for Minecraft: Pocket Edition
cd /d %~dp0

if exist bin\php\php.exe (
	set PHP_BINARY=bin\php\php.exe
) else (
	set PHP_BINARY=php
)

if exist src\PocketMine-MP.phar (
	set POCKETMINE_FILE=src\PocketMine-MP.phar
) else (
	if exist PocketMine-MP.phar (
		set POCKETMINE_FILE=PocketMine-MP.phar
	) else (
		if exist src\pocketmine\PocketMine.php (
			set POCKETMINE_FILE=src\pocketmine\PocketMine.php
		) else (
			echo "Couldn't find a valid PocketMine-MP installation"
        		pause
        		exit 1
		)
	)
)

if exist update.phar (
    move /y update.phar %POCKETMINE_FILE%
)

REM if exist bin\php\php_wxwidgets.dll (
REM 	%PHP_BINARY% %POCKETMINE_FILE% --enable-gui %*
REM ) else (
	if exist bin\mintty.exe (
		start "" bin\mintty.exe -o Columns=88 -o Rows=32 -o AllowBlinking=0 -o FontQuality=3 -o Font="DejaVu Sans Mono" -o FontHeight=10 -o CursorType=0 -o CursorBlinks=1 -h error -t "PocketMine-MP" -i bin/pocketmine.ico -w max %PHP_BINARY% %POCKETMINE_FILE% --enable-ansi %*
	) else (
		%PHP_BINARY% -c bin\php %POCKETMINE_FILE% %*
	)
REM )

start.sh

#!/bin/bash
DIR="$(cd -P "$( dirname "${BASH_SOURCE[0]}" )" && pwd)"
cd "$DIR"

DO_LOOP="no"

while getopts "p:f:l" OPTION 2> /dev/null; do
	case ${OPTION} in
		p)
			PHP_BINARY="$OPTARG"
			;;
		f)
			POCKETMINE_FILE="$OPTARG"
			;;
		l)
			DO_LOOP="yes"
			;;
		\?)
			break
			;;
	esac
done

if [ "$PHP_BINARY" == "" ]; then
	if [ -f ./bin/php5/bin/php ]; then
		export PHPRC=""
		PHP_BINARY="./bin/php5/bin/php"
	elif [ type php 2>/dev/null ]; then
		PHP_BINARY=$(type -p php)
	else
		echo "Couldn't find a working PHP binary, please use the installer."
		exit 1
	fi
fi

if [ "$POCKETMINE_FILE" == "" ]; then
	if [ -f ./src/PocketMine-MP.phar ]; then
		POCKETMINE_FILE="./src/PocketMine-MP.phar"
	elif [ -f ./PocketMine-MP.phar ]; then
		POCKETMINE_FILE="./PocketMine-MP.phar"
	elif [ -f ./src/pocketmine/PocketMine.php ]; then
		POCKETMINE_FILE="./src/pocketmine/PocketMine.php"
	else
		echo "Couldn't find a valid PocketMine-MP installation"
		exit 1
	fi
fi

if [ -f ./update.phar ]; then
	mv -f ./update.phar "$POCKETMINE_FILE"
fi

LOOPS=0

set +e
while [ "$LOOPS" -eq 0 ] || [ "$DO_LOOP" == "yes" ]; do
	if [ "$DO_LOOP" == "yes" ]; then
		"$PHP_BINARY" "$POCKETMINE_FILE" $@
	else
		exec "$PHP_BINARY" "$POCKETMINE_FILE" $@
	fi
	((LOOPS++))
done

if [ ${LOOPS} -gt 1 ]; then
	echo "Restarted $LOOPS times"
fi