command not found: bundleYou need to setup your server correctly getting started, then install bundler.
gem install bundler
my_program not found, but is already installedMina is running in a non-interactive ssh mode. That means that your full profile will not be loaded:  
There is a line at the top in most .bashrc files:
# If not running interactively, don't do anything
case $- in
    *i*) ;;
      *) return;;
esac
this means that all lines below this will not be executed when using mina.
The easiest way to fix this is to move all your export and source lines to the top of your .bashrc file.
More info at: http://stackoverflow.com/a/216204/1339894
Mina assumes that you have set up the communication with your server through the public/private keys, not password. If you want to use the password you will have to change the execution mode:
set :execution_mode, :system