The best way is to use git on your server
On the command line, you'd run:
git clone https://nshahzad@github.com/nshahzad/phpVMS.git [FOLDER]
Where [FOLDER] is . to plce it in the current folder, or 'phpvms' to place it in a phpvms folder:
git clone https://nshahzad@github.com/nshahzad/phpVMS.git phpvms
It will then create a local repository. Then where there's an update, you go into that folder:
git pull
http://help.github.com/remotes/ Scroll down to fetching.
Or, if you don't want to use git, you can do something like this:
wget http://downloads.phpvms.net/phpvms_beta.tar.gz
tar -xzvf phpvms_beta.tar.gz
cp -R phpvms/** .
rm phpvms_beta.tar.gz
That's off the top of my head, and I'm not sure if you need the cp, I don't remember if it extracts into a "phpvms" directory, if it does, then the cp copies all the files into the local directory
Git is the best option, though