From what I have seen it looks like bluetooth-agent is in fact not available in Jessie. However, this might work to automate bluetoothctl:
#!/bin/bash
# enable bluetooth
sudo systemctl start bluetooth
sleep 1
# run the program bluez
echo -e 'power on\nconnect \t \nquit' | bluetoothctl
Quoting from the site linked above, "You have to pass with echo (with option -e) the commands you want to execute. Every command you have to terminate it with a new line (\n). When I do connect I use the tab (\t) so that I do not need to update the script with the MAC of my keyboard."
The options for bluetoothctl are:
Available commands:
  list                       List available controllers
  show [ctrl]                Controller information
  select <ctrl>              Select default controller
  devices                    List available devices
  paired-devices             List paired devices
  power <on/off>             Set controller power
  pairable <on/off>          Set controller pairable mode
  discoverable <on/off>      Set controller discoverable mode
  agent <on/off/capability>  Enable/disable agent with given capability
  default-agent              Set agent as the default one
  set-scan-filter-uuids [uuid1 uuid2 ...] Set scan filter uuids
  set-scan-filter-rssi [rssi] Set scan filter rssi, and clears pathloss
  set-scan-filter-pathloss [pathloss] Set scan filter pathloss, and clears rssi
  set-scan-filter-transport [transport] Set scan filter transport
  set-scan-filter-clear      Clears discovery filter.
  scan <on/off>              Scan for devices
  info [dev]                 Device information
  pair [dev]                 Pair with device
  trust [dev]                Trust device
  untrust [dev]              Untrust device
  block [dev]                Block device
  unblock [dev]              Unblock device
  remove <dev>               Remove device
  connect <dev>              Connect device
  disconnect [dev]           Disconnect device
  list-attributes [dev]      List attributes
  select-attribute <attribute> Select attribute
  attribute-info [attribute] Select attribute
  read                       Read attribute value
  write <data=[xx xx ...]>   Write attribute value
  notify <on/off>            Notify attribute value
  register-profile <UUID ...> Register profile to connect
  unregister-profile         Unregister profile
  version                    Display version
  quit                       Quit program
You could use discoverable on and pairable on. I have never done much with bluetooth but I don't believe you need much more to get a basic connection.
To get this running at boot, put the line with the path to the script in /etc/rc.local with a & to fork it to the background, e.g 
sudo /home/pi/Desktop/StartServer.sh &
You might also be able to use the tool hciconfig instead of bluetoothctl. This might be a more streamlined approach.