I believe having some good guide books at hand, is like having having good mentors. These help me gain some clarity and navigate through my PhD journey. I will share some of them, that are useful for different stages and aspects of PhD, and hope it could help other people who are also in this journey. This is not a comprehensive list, only the ones I have read myself and found helpful.
Before starting a PhD
Navigating through the PhD and the academia
Writing
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Handbook of Writing for the Mathematical Sciences by Nicholas J. Higham