right, first thing to do is to try and pull the outer skin of the door back out. best way is to get a nice strong (thick) piece of rope, loop one end through the spare wheel carrier, and secure the other end to something sturdy, like a telegraph pole, so the rope is a continuous loop. then using a sturdy piece of timber, start to twist the loop over on itself, round and round until it is tight. (might be best to have an assistant) once it is tight, carry on turning slowly until the door begins to move back out.
(look under "Spanish windlass" on internet for more details of how this works)
DO NOT UNDER ANY CIRCUMSTANCES BE TEMPTED TO USE THE ENGINE TO MOVE THE CAR FORWARD.
Once you have done that, open the door, remove the rear trim and look inside with a torch and see where the runners are catching. Using a suitable wooden drift and a big hammer, beat the areas which are catching back out so the glass can move freely.
Once you have done that, you can begin to deal with the issue of the window working under its own power.
The window won't power up or down while the door is open, but you can fool the ecu by closing the latch on the door with a screwdriver, it needs to be turned for two clicks.
Once this is done, try to power the window up using the dash switch. if this doesn't work, get an assistant to operate the switch whilst you help the glass back up. Good tip to wear rubber gloves as it makes it easier to push the glass up. Chances are the runners are only catching at one bit, and once over that, it should go all the way to the top.
Once nearly at the top of its run, release the button on the dash. "Open" the door (release the latch) by operating the door handle on the outside, then close the door normally.
Once again, raise the glass by the button on the dash, and hopefully it should remain closed.
The bleeps mean it needs recalibrating, unless it slides up and down freely, don't do this as it will try to drive the glass down under power.
As a last resort, undo the two clamps holding the glass, then wedge in the almost up position using anything which comes to hand, like a small piece of wood or a piece of plastic mini trunking. Note the glass cannot go all the way up, as it needs to stay clear of the small plastic lip on the roof.
Naturally, this is only a suggestion, and you should take necessary precautions to avoid smaking yourself in the face with a piece of wood wedged in a spanish windlass. I merely give suggestions, the execution of the plan is down to you. No liability etc etc.
Good Luck.