Using sshfs you can mount the SD card to a directory on your Linux machine:
sshfs firstname.lastname@example.org:/mnt/sda1/arduino /home/<your user name>/Yun
You first need to install openssh-sftp-server on the arduino Yun:
opkg update opkg install openssh-sftp-server
Obviously you can mount any directory like this, it does not need to be a directory on the SD card.
Note: how to create partitions and format them on the SD card (to be done prior to what is described above is explained at http://myyafa.blogspot.be/2014/05/create-and-format-partitions-on-yun-sd.html