Thanks.
I figured out how to do it again.
The step that threw me off is contingent on which version of PHP you're using. So if you've upgraded PHP since the last time you tried to phar a directory you'll have to edit php.ini again:
phar.readonly = Off
After that it is super simple:
php -r '$phar = new Phar("plugin.phar"); $phar->buildFromDirectory("./plugin_dir");'