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Help me devise an efficient workflow for online study

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Please give me your tips for completing online study, particularly how you keep track of all the readings you did working from PDFs, highlighting / note-taking strategies, and any tools that helped you. My Master's degree is 90% online and many of the readings are available in pdf fromat from various online journals.

What windows based, desktop / laptop tools have you found useful in reading the material comfortably, keeping notes, keeping track of citations - and anything else I might not yet have considered?

The tools I currently have at my disposal are:
An old, but usable ipad 2, with Dropbox and Goodreader
A laptop - decent size, with a subscription to Office365 and a new install of Adobe Digital editions which I need for some library ebooks (I haven't poked around in ADE yet, but it seems pretty clunky and horrible...)

I also have Linux Mint installed on VirtualBox, if there happens to be a good Linux solution to this...

I can't really afford software licences, so please be mindful of that - however, if there is an excellent 1 stop solution for all of this I'd be interested in hearing about it. I could always consider selling a kidney on the black market.

Technology hadn't come very far comparatively when I did my BA, so I have no idea about what the best practices are. Thanks for your help.

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