flat battery

Completely my fault! Due to not using my '04 TD4 for a while, the battery has gone completely flat. For some strange reason it has popped the drivers door lock which is very useful, I can open the bonnet!
Before I pull the battery out and charge it is there anything specific I should know? I know I'll have to reset the rear window once it goes back in but I assume it's the alarm is the same as on my Triumph motorbike and will scream it's head off once the battery is reconnected? I have the full set of handbooks to follow but they are currently locked in the boot...

I haven't had the alarm go off when reconnecting the battery and its just worked as normal afterwards - mine's an older '99 though.

All that will happen when the battery is reconnected is the tail door window will drop and require calibration and the radio code will need to be entered. Otherwise it'll all work just fine. Keep the drivers door open when reconnecting the battery, to avoid the doors locking.