I'm sure I remember seeing some documentation somewhere that had a way to save the port number ember-cli uses in a config file, but it doesn't seem to say anything in the documentation.
I have to use
ember server --port 9999
but i would love to save that port number in a file.
You can use a .ember-cli config file to change the port. discussion
So in your root folder, have a .ember-cli file with the following:
{
"port": 9999
}
Edit: the .ember-cli file is now documented on the ember-cli website.