OK, good news - 2341:0001 is an arduino uno or mega2560, so the flash has worked
Now the 8u2 based arduini use the USB modem driver, not the FTDI serial. Run dmesg just after you plug in the uno, and you should see something like
usb 3-1.2: new full speed USB device using uhci_hcd and address 18
cdc_acm 3-1.2:1.0: ttyACM0: USB ACM device
and /dev/ttyACM0 should now exist. If the acm line is missing, run lsmod and look for cdc_acm (the modem driver). If it's not present, you need to build the USB modem driver in your kernel. Try
modprobe -v cdc_acm
anyway, just to check if you have the modules.
One other possibility is the java serial library not looking for ttyACM devices. See reply #56 to make /dev/ttyS7 a symlink to /dev/ttyACM0
In the IDE, with the uno plugged in, what serial ports does it offer you?
I had failures due to a run-away avrdude. Shut down the IDE, and run
ps -ax | fgrep avrdude
Kill all the avrdudes you see, and restart the IDE. Now check the serial ports, and that you've set the board type to Uno. Upload might now work