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Currently, I'm writing a paper in Microsoft Word 2007. I use Endnote to organise my references and bibliography and hold electronic copies of papers I've found where possible. I have stacks of books by my desk and a fairly disorganised (physical) folder of papers. I currently use Diigo (in conjunction with the bookmarklet for Chrome) to store, highlight, annotate and tag online articles of interest.

I am partly interested to know if there is a system out there that combines all these things but I'm guessing that's more of a question for the SuperUser Exchange. Ideally, I would like to write in a tool like Google Docs/Drive so that I have a revision history of what I've written but I think I will have to move everything to Microsoft Word for submission eventually anyway.

What I really want to know is if there exists a productivity method for rationalising the bookmarking and citation side of things. I've heard Zotero and Mendeley are both services to explore and I've started using Evernote to store ideas on the go but without some kind of framework I fear I'm at a loss as to decide which tool is the best fit. I'm interested generally in what services people use for recording ideas (their own or others') when writing or doing research, how they find these affect their productivity, and how they link these services up with a method to facilitate a better articulation and presentation of ideas. As someone fairly new to the idea of productivity methods, do they affect which tools one decides to use?

If anyone knows of a way to link up the services I have or move easily to a more efficient system, I'd welcome those kinds of suggestions too.

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This might be complete overkill for you, but I use LaTeX with a git repository - this serves this purpose perfectly (as well as keeping backups nicely off my machine). I mainly like how ridiculously easy citations are with LaTeX - I use Mendeley - and how nicely formatted the resulting PDFs are. Unfortunately not the best with Word documents... –  enderland Feb 24 '13 at 18:50
    
Another option to consider is something by the way of OneNote and the use of Google Book Search/G‌​oogle Scholar –  dmcgill50 Mar 4 '13 at 16:00

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I don't have a complete answer for you, but some snippets around Evernote may be of some use.

Evernote keeps a revision history, although you can't get at it unless you're a paid subscriber. It works very well.

There is an add-on for Evernote that allows you to design templates for your notes. I've only read about it, I have no experience with it, but it might be useful for bibliography work.

Evernote web clipper allows you to save things from the web directly to your Evernote notebooks. It plugs in to your browser (all major browsers supported) and allows you to select a full web page, a highlighted section, or just the URL to add to Evernote.

With a planned tagging approach using a limited vocabulary for tags, I think you ought to be able to get your reference material all into Evernote. Of course, that limited vocabulary for tagging might be the hard part to come up with.

I'm finding that the more I use Evernote, the more I find uses for Evernote. It may not be as clean a repository as a purpose-built application for something like a bibliography, but the ability to use tags to link disparate data is terrific.

For an example, I have a project under way developing a performance of 12th Century music. In Evernote, I have stored a jpg of the original manuscript, jpgs of details of the manuscript, links to web pages about the culture of the time and place, PDF files of modern editions of the music downloaded from the web, my notes about each of the tunes, links to mp3 files and YouTube performances by other people, and the outline of the presentation I'll make about the performance preparations. Lots of different kinds of data, all in once place.

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Thanks, I'd read that Evernote has a revision history if you pay. I'm not yet sure if it's worth me committing to! But hearing how you've been using it is helpful. I have the Clipper too but am still getting used to it. Thanks also for the outline of your project, which sounds fascinating by the way, as well as organised! (Are you focusing on 12C music in a particular culture/country?) –  guypursey Feb 22 '13 at 19:17
    
This particular project is working with the Cantigas d'Amico by Martin Codax, en.wikipedia.org/wiki/Mart%C3%ADn_Codax for a quick intro. (Typo above, actually 13C). I make my living as a software developer, so I can indulge my interest in music pre-1650. :-) –  Dennis S. Feb 22 '13 at 21:57

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