I wouldn’t overthink the tools. I found a mostly minimal toolset was sufficient when I did my PhD: actively used repositories to make sure I never lost my work (private repos so I didn’t have to care what I put in them), plain old emacs for editing, and a mix of Mathematica, Matlab, and Python for my numerical and plotting needs. Used physical sticky notes and cheap legal pads for notes and keeping on top of todo lists. I printed papers to read since I never found a digital method to maintain the deep focus I needed to fully read the papers. I generally discourage students from worrying much about tools: at the end of the day if you’re thinking more about a tool or workflow process than your research work, you’re not making progress towards the degree. Use whatever tools and methods allow you to be productive without thinking about the tools or methods.