I use various cloud-based services.
I've always wanted to write and publish a paper using my hometown as a case study. Sadly, a reviewer asked me to cut it from one of my papers so it'll have to wait yet another year. I do have a few projects on it.
To be clear: this is EXACTLY how I organized my files when I wrote my undergrad, Masters and Doctoral theses. My method has not changed even now that I am a professor.
(some call this a tree diagram)
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But I seriously haven't even had the time to do that (I may just do that right now).
Some articles I've downloaded I want to read are there too.
I set time aside every weekend to reorganize my files, but because I already have a system, it takes me SUBSTANTIALLY less time to do it nowadays.
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Dr. Robert A. Karl @RAKarl has developed an amazing set of techniques to organize and process materials and files if you do archival work across different sites. This thread is gold if you're a comparativist, a historian or do archival work
This thread in handy blog post form, with additional text.