As you’re using a VPS with SSH access, give WP-CLI a try http://wp-cli.org/
can work wonderfully http://centminmod.com/nginx_configure_wordpress_ffpc_plugin.html#installwp
for example to install limit login attempts plugin just run this command from SSH within your wordpress install directory
wp plugin install limit-login-attempts --activate --allow-root
full list of command line options at http://wp-cli.org/commands/
updating plugins http://wp-cli.org/commands/plugin/ & http://wp-cli.org/commands/plugin/update/
wp plugin update limit-login-attempts --allow-root
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