This question could be divided into (at least) two sub-questions:
(1) How do you organize the files?
Reference management software is frequently recommended but I still wonder the most efficient way to organize papers. For example, do you create a reference folder for each project, or do you organize references by topic? Or other suggestions?
(2) How do you organize the thoughts/takeaways?
Would you write down the key messages for each paper and organize them in a document? How do you organize those thoughts/takeaways instead of leaving it in a document that is getting larger and larger (and messier)?
In some sense the two sub-questions are linked -- well-organized thoughts could be reflected in the organization of files, and well-organized folders may stimulate well-organized thoughts. As a graduate student who has not been familiar with the literature, I'm always wondering how people start to get the big picture of the literature and how people effectively organized the papers they've read.