Plagiarism of code by other PhD student
This is a tricky one. It probably sounds like academic plagiarism, but your licensing concerns are probably not going to resolve the problem at the core of this. There's two sides to this, the academic (plagiarism) side and the commercial (licensing) side. They're almost entirely separate, so I'm going to break them up.



Academic/Plagiarism Claim


  The code in the repo is over 97% direct copy of code that I had produced while working in my previous employment...


Without attribution, this is plagiarism, and may be grounds to have the PhD rescinded, but this would be a serious procedure as it's likely to have life-altering affects on the PhD student in question. You'd need to be 100% sure of what you're doing and the validity of your claims going into this. Even if the case was black and white (which I don't think this one necessarily is), the student's University isn't going to take rescinding a PhD lightly as it reflects badly on them.

Additionally, it sounds like there is a some attribution within the work:


  The indirect mention of my name is as a maintainer not the sole developer


...which might well be sufficient for the University to write this off as a referencing error, maybe requiring the student to make a small addendum to their thesis.


  The code is just part of the story, since the person also claimed that in addition to writing the code they used the code to produce the results in that chapter. They didn't - since I know that I ran the batches in question (this was around 2 years of work). 


If you can prove it, the experiments that they claim to have run, that you performed while under the employ of their department are probably your strongest leg to stand on here. But you'd have to have good evidence, and be able to show they haven't run the experiments themselves. If yours were not published previously, and they've generated the data themselves using your code, this may well be null and void.



Commercial/Licensing Claim

The licensing perspective of this is completely separate to the plagiarism side - if the work was published as GPL, they can basically do what they like with it, without attribution, provided that any code based upon it remains GPL. This bit is important, as it's probably where you have a leg to stand on, based on this comment: 


  although the person has also removed the GPL from the repo, which I thought was against the license terms


That is absolutely in breach of the terms, which is why most industrial entities won't touch GPL code with a bargepole (due to what's commonly called "license bleed"). 

Based on this, you might have a valid claim to get their repo pulled, but that's not going to solve your actual problem.

Again, from the comments:


  ...I feel that the supervisor (who used to be my boss)...


I understand this to mean that the PhD student in question is supervised by your old boss, which means you had a contract with their institution. Depending on the contract you had with them, they could therefore own all the rights to it regardless, making your initial GPL license in breach of your contract with them without prior stated agreement. This wouldn't affect the legitimacy of your plagiarism complaint, as that's a genuine academic concern, but might affect how the department deals with your request.