Should I be using rebase?

You should never use rebase unless you are working on a new branch that you created. As I didn’t show you how to do that, I don’t expect you to be doing that. Rebase can potentially change the repository history which is bad. If you are new to git, stick to the following: add, commit, push, pull. I would also recommend sticking with command line git in the terminal as opposed to using a git client to learn it a little better.

I know that in the first code assignment we submitted you had asked for our names to be written in the main c file, for this one does it matter whether it goes in the c or the llvm file?

You should put it in the README.md file at the top. So, for example, mine would be like this:
# Assignment 3 - Justin LaPre
See here for an example.

Assignment 3: for transpose, are we using the same definition of “transpose” that we used in Assignment 1 (swapping the 1st and 3rd columns, 2nd and 4th, etc.) or are we doing an actual transposition (swapping the rows and columns)?

For Assignment 3, you should be using the actual transpose and NOT the fake one we used in Assignment 1.

So I’m having a small problem with calling a function in LLVM for assignment 3. How do you correctly call a function that isn’t in the LLVM code, but is in the C code. When I compile it, I get an error that says, error: use of undefined value '@mm_alloc'.

You can use declare just like define but without a function body. This will let the compiler know that, say, mm_alloc() exists but not in this particular file. See here for an example.

How should we output stuff to the console in LLVM for the mm_print method? Should we just use printf(), or is there a better command to use (especially if we don’t want to deal with fancy format strings but just printing a single char or int at a time)?

You can generate some code from a similar “test” program that prints strings to the console using printf().