Here is a very simple program for creating phar files with CLI. Note that it requires phar.readonly in php.ini  set to false (Off).

<?php
$filename = "default";
$dir = "./";
$regex = "/^(?!.*build\\.php)(?:.*)$/";
$main = "main.php";
$shebang = "#!/usr/bin/env php";
$chmod = true;

for ($i = 0; $i < $argc; $i++) {
    switch ($argv[$i]) {
        case "-o":
            $i++;
            if ($i >= $argc) {
                echo "Missing output file name" . PHP_EOL;
                exit(1);
            }
            $filename = $argv[$i];
            break;
        case "-i":
            $i++;
            if ($i >= $argc) {
                echo "Missing input directory name" . PHP_EOL;
                exit(1);
            }
            $dir = $argv[$i];
            break;
        case "-p":
            $i++;
            if ($i >= $argc) {
                echo "Missing regular expression pattern" . PHP_EOL;
                exit(1);
            }
            $regex = $argv[$i];
            break;
        case "-m":
            $i++;
            if ($i >= $argc) {
                echo "Missing main file" . PHP_EOL;
                exit(1);
            }
            $main = $argv[$i];
            break;
        case "-b":
            $i++;
            if ($i >= $argc) {
                echo "Missing shebang of file" . PHP_EOL;
                exit(1);
            }
            $shebang = $argv[$i];
            break;
        case "--no-chmod":
            $chmod = false;
            break;
    }
}
if (file_exists($filename)) unlink($filename);
$phar = new Phar($filename);
$phar->buildFromDirectory($dir, $regex);
$phar->setStub(($shebang ? $shebang . PHP_EOL : "") . $phar->createDefaultStub($main));
if ($chmod) {
    chmod($filename, fileperms($phar) | 0700);
}