[josephdviviano]

^ this! your repo should have script(s) in it that re-generate, entirely, all of the binary results files that can be fed into some notebook to automatically generate the figures you put directly into your overleaf. Ditto for tables saved as text outputs. Also, write tests. No one will force you to, but it will save you from finding a bug a month before a conference deadline or during the review process, which can cost you way way more time than just writing the test.

For lit reviews, I just do it in overleaf + bibtex. I wasted a lot of time with reference managers that I never seemed to use when I was actually writing my papers. When you read a paper you think you will need to cite, write two sentences describing the result and put a reference in an overleaf. That will serve as a great cognitive map when you're trying to find "that thing you read last year" but can't remember the names.

Best part of this is your toolchain is light and flexible (these days I just use git, vscode, conda, and overleaf), and you will have clean github repos to show off when you're looking for the next step post-PhD.