To Shadowtrap at the end? Did he sacrifice himself for Claptrap, or…?
It sure looked like it. I mean, if Clappy goes, he goes too since he’s in Clappy’s mind. I’ll go way out on a limb here and even suggest Shadowtrap figured keeping Clappy alive was his best bet at revenge on Jack - which, as it turns out, is sort of correct…
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But how can a subroutine sacrifice its life for a Robot’s life?
It’s only a subroutine and Claptrap is a robot.
Details, details! It wouldn’t be a Borderlands DLC without at least one plot-hole 
Edit: since everything in Clappy’s mind was some sort of personification of code sub-routines and memory stores (the ultimate in visual programming interfaces?) you can simply interpret the visuals as equivalent to running EMERGENCY_RESTORE.EXE
Makes sense.
Remember, according to some random sign in Concordia, plot holes are non canon.
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I kinda got the feeling that all Claptraps have a Shadow-TP inside them.
No.
Shadowtrap was made when Jack installed Vaulthunter.EXE.
Remember the holographic memory thingy?
Then Shadowtrap becomes captured and Claptrap returns again.
Sure looked like that was “a” Shadow-Tp waking-up deep inside Claptraps circuits.
But Shadowtrap was born from the Vaulthunter.exe.
I’m gonna have to watch that little cutscene a few more times.
Was it born or did Jack just add/remove filters?
Still, even if it was added, it looked like it was still in there and woke up.
Jack boots the VH.exe, and Shadowtrap says:
“Experimental FRAGTRAP ready for duty, Jack sir!”
Suddenly a small explosion appears and Claptrap returns again.
which is funny to me when you listen to clappy’s starting echo…
Plot holes aren’t canon.
Fragtrap himself has dialogue saying he was what fragtrap was supposed to be, but he was captured mere millicycles into his life by insecurity forces, and without him, claptrap’s combat subroutines were bound to be erratic. It explains why clappy is the last of his line, only he had a shadow-trap inside him.
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does it explain why Clappy lives? or “how” Shadow “saves” him? i remember the lines of which you speak but i didnt get that conclusion in your last sentence. i got the impression that it was Shadow who woke in the end scene but that didnt make sense to me.
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It’s not explained, as @VaultHunter101 said, we see a visual cutscene, but what that means in terms of code depends on how much you know about experimental far future AI 