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@JeffE recommends in a comment:

Discuss your situation with the department chair and your previous instructor, and keep careful documentation of everything.

At this point, you should treat the situation as if you were sued for committing a crime. The stakes are very high: at worst you risk being expelled from the university, which would leave a permanent scar on your CV and significantly mess up your life on the short term. You might think that I am exaggerating, but in your situation, you cannot be too careful. Some people, perhaps on this website too, will try to convince you that if you appear defensive, or uncooperative, then you are going to garner ill will. But ill will is immaterial, while being convicted of academic fraud is very real.

You should of course refrain from talking (especially orally) with your accuser. You should be extremely cautious in what you say to the authorities (the representatives from the department or the university). You should restrict yourself to denying the allegations, and only answer questions submitted in writing. You should seek help, at the very least from your friends/family (this is a stressful time), from your student union, from a trusted advisor at your university if you have one; perhaps even consult a professional lawyer who is used to dealing with university matters if you think the situation deserves it.

If you are afraid of how your department's chair / former instructor will react because of these actions, you can send them a letter/email explaining your motivations: a formal disciplinary process was launched against you, and while you are innocent, you are also afraid of what might happen if you do not take this seriously.

If you have not left anything out of your question, then your chances are good. People are not convicted based on lack of proof, in your case, lack of proof that you are good enough to have coded the web app that you have submitted. If this is all the other prof has against you, then he will be laughed out of the disciplinary process... unless you do something wrong.

I would strongly advise that you do not follow the advice given in Michael Kay's answer. You should obviously not admit that you do not master such and such fundamental notion, or that you had "good luck" when coding your webapp. This can only hurt you and introduce doubt about your abilities. You submitted your work, there is no material evidence that you cheated, and you got an A for it: this means that your instructor thinks that you actually master what was required for the class. Stick to this.

I'm really guessing here, so I might be completely way out, but my guess would be that you wrote the code and got it working despite not understanding some fundamental concept of WHY it worked; and the Prof, having a more theoretical mind-set than yours, can't imagine the possibility that people can get code working without understanding the theory.

It would help to know exactly what the question was.

So my answer to your question would be: try to engage in dialogue. Ask why the Prof thinks it would be impossible to get the code working when lacking the relevant knowledge; explain how you got it working despite not knowing the answer to the question. Perhaps be prepared to concede that there was an element of "good luck" in the process, and that the reason you asked the question was because you were seeking a deeper understanding of why your solution worked.

I have to say that after years of answering coding questions on SO, I am amazed how many programmers seem to operate quite successfully without having any real knowledge of the theory of what they are doing: you can get a long way by trial and error, and perhaps your Prof doesn't realise that.

Your Github commit history is sufficient to demonstrate that you did not cheat. Show that to the appropriate authorities and they should decide in your favor.

However, I guess you have misunderstood the situation (assuming you have stated the facts accurately). I suspect there is a conflict between Prof. X and the professor who gave you an A. Prof. X is attempting to make the other professor look bad in front of his colleagues by presenting evidence that his teaching is not good.

Most likely the end result will be harm to Prof. X's reputation, if he has one.

In addition the other answers,

document every interaction you have with Prof X.

• 
  keep communications to a minimum, your discussions will not convince him of anything and he will be looking for ways of incriminating you. The more you talk, the more opportunities you have to put your foot in your mouth (e.g. telling him you got an A in a subject which you don't 100% understand, which started this whole thing)


• communicate with Prof X through email, rather than orally. This is probably the best method to keep record of who said what.


• write down your oral conversations after they happen (remain factual)


• record the lectures, many apps on your phone can do this.


• make extra sure that nothing you submit for this class could be suspected of being plagiarized

Additionally, in regard to your academic performance overall rather than to the accusations in the other class

look at ways of getting out of Prof. X's class. He will most likely not be a fair grader.

• Look at whether or not it's possible to take this class with a different professor, either by switching section or taking it at another university and getting the credit transferred. Given your username and your mention that the web course you just finished had 5 students, I would imagine this might not be possible... but worth looking into


• If the course is not a prerequisite for upcoming courses in your program (and if you think that next year's instructor will not be Prof. X), look at the deadline to drop the course, and take it in the future with another professor who will most likely be fairer towards you.

If you can't find a way to get out of Prof X's class that won't affect your GPA (such as dropping a class after the deadline would) or delaying your graduation (if it's a prerequisite) make sure to do everything you can to be the "perfect student".

This week I found out that Prof X is starting a formal university
disciplinary process against me.

You were asked in comments how you were notified about this, and I haven't seen an answer.

Unless you have heard about this in some official capacity, my advice would be to

• make sure your process in the web-development course is as well-documented as it can be


• Think about how best you can present your github history in a manner that a hearing panel can understand it


• check your code against plagiarism detection tools to make sure there isn't a real problem


• simply forget about the whole thing until you have an official notification.

The reason why I suggest this is because it feels like you're missing something. It is pretty unlikely that Prof X would launch an academic honesty case for a course he did not teach. He may well be encouraging the other prof to do so, or he may even be filing a case FOR THE SUMMER COURSE YOU'RE IN RIGHT NOW -- in which case you should consider whether all of the work you're claiming credit for is your own.

When (and if!!!) you get notification of an accusation of academic dishonesty, you'll be presented with what substantiates the accusation. Deny it and request a hearing. At the hearing, (assuming you're right about it being about the earlier course) explain that you are having a disagreeable misunderstanding with X, that you don't know what he's talking about, and walk the panel through your github record and show that your code passes plagiarism detection software (assuming that it does). The standard such boards use is usually not unreasonable doubt. My instructions, serving on such a board, is "halfway plus a hair" -- so if plagiarism detection software shows a problem, there is high likelihood of penalty -- assuming the board will even hear a case from one prof about another prof's class. That feels highly irregular.

Of course, the standard caveat is that I've only heard your side of the story. The prof may have a perfectly reasonable case against you.

If you're presented with some plagiarism detection output that shows copied code, and it does go to hearing, you will likely be found responsible. If this is the case, you might consider waiving the hearing and accepting the offered penalty, if you find it reasonable. It sounds like prof X might have a hair up his butt about you, and you might get a more just penalty from a hearing board.

If you do get a responsible finding, it's not the end of the world, and likely not even something that anybody important will ever find out about down the road, if this is a first offense. Try to learn whatever lesson is there to be learned, and move on.