1st, just to rule this out...have your wife push the clutch pedal in and out multipe times with the car off, while you are standing in front of it...looking to the left of the air box, just below on the front of the gear box, you should see a little arm extension pressed into a cup like flange sticking out of the boxes bell housing...This should move when the clutch is pressed in, and move back when the clutch is let out...If that isn't happening, its ALL a clutch issue, and you mostly likely simply have air in the clutch cyilnder/lines...
if that checks out, moving on: can you have the car running...and move through the gears WITHOUT pushing the clutch pedal? and is there any gates? Like does the shifter still go into the right 'gear' positions, if that makes sense? That will help to start narrowing it down...
If you can simply select any gear without using the pedal...the clutch failed in some way, probably something to do with the pressure plate...as this can happen in the other direction if the throwout bearing or release fork fail (clutch is permanently engaged)...yours could be stuck not engaging...
if you can select gears without pushing in the clutch pedal, but the car doesn't move when in gear...probably not the clutch, and probably not the layshaft/input shaft or gear shafts...most likely the differential or an axle...
If you have a stock protege diff (as in, not an LSD)...just a failed axle will prevent the car from moving...What you'll need to do is to see under the car as SAFELY as possible. Use a jack and some stands, get the front tires off the ground, block the rear tires, use the e-brake, etc...don't get fully under the car, but get in a low enough position to try and see the driver's side axle shaft, as well as the intermediate shaft traveling towards the passenger side front wheel...While looking as best as possible, have your wife select first gear and let the clutch out and give a very small amount of throttle...
An number of different things could happen with this...if neither axle turns...its inside the box, and probably a problem with the diff's spider gears (i doubt the ring gear, as you'll notice a lot of crunching and grinding with that)...if the axle cups at the gear box spin, but one or both axles aren't turning...the inner CV joint failed...if the axles turn, but still no wheel movement...the outer CV joints failed, or the spline axle stub/hub input failed at that wheel...
an open diff will send power to the wheel with the least resistance...if any of the above outer parts have failed, or are improperly installed, the car won't move...But usually if anything goes in the gear box, you'll know it by grinding sounds and other noises coming from it...if you are getting engine power into that box (as the clutch is working properly), not hearing anything completely obviously wrong, i'm guessing outside of it are where your problems lie...