Mood.
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And thesis.tex is basically just a preamble followed by input{chapters/chapter1} and all the other chapters.
input{chapters/chapter1}
No, a single super-document, easier to "back up" which is why in the same folder there are also "thesis_final.tex", "thesis_final_revised.tex", "thesis_final_revised_v2.tex", "thesis_final_revised_v2_final.tex"
Just use git... One of the huge advantages of latex over docx is its easy diffability
How about thesis.typ?
True.