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There have already been many questions about this in the past, here for example. But I feel like many of them are probably somewhat outdated, after all, 2018 is getting closer rapidly.

I'm only in third semester, but I already remark, that I'm about to gather tons of pdf's, a good amount of them such, that I'd like to keep for later reading. I'm looking for a PDF tool that gives me the following features:

  • Fluent organizing of documents. I want to have folders/subfolders. If I want to move documents from one to another folder this must go very quickly without too much hacking. The structure should be independent of the actual file structure on my hard drive.

  • A stable in-program PDF viewer, or the possibility to set a default one that opens Documents. Highlighting. I like highlighting, in different colors, and I want to select the color without having to go through a bunch of select options to switch the highlight color. For me different colors have different meaning, so this must go quickly too. The same with notes. The option to add text box with a shortcut would be highly appreciated.

  • Speed. I downloaded Mendeley. If Skim is able to fluently display a PDF I explect the same for a PDF organizing tool. I don't want to wait 0.8s for a page to load if I'm rapidly scrolling through a document. The same with zooming. I want to use my trackpad to zoom, or to press ctrl while using the mouse is fine too. But having to click on +/- zoom option is certainly not an option.

  • Search options. On first look, I very much liked how Mendeley displays so many informations about the PDF's and I can only imagine how desirable it becomes to search documents for exmaple based on authors.

  • The ability to form groups/folders, that I can share with others.

  • Must be available on macOS, support for Ubuntu would be a plus.

  • I remarked, that many questions were about Bibtex stuff too. I have very few experience with references using Latex, but I guess sooner or later I'll reach the point where I need those things.

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    How many is "many" for you? 100, 10.000, one million? – Federico Poloni Dec 12 '17 at 19:45
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    I've perhaps 200 up to now, but the rate of new documents piling up is increasing fast. Meaning I remark that I already (want to) save way more PDF than for example at the beginning of the semester. – Felix Crazzolara Dec 12 '17 at 19:49
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    You might have underestimated portabilty. After moving to a new (Mac or whatever) machine, to a new operating system, or after moving to a new version of the organizer 5 years later, your old organization system could be irreversibly gone. – Leon Meier Dec 12 '17 at 19:58
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    Not specific to academia? – Leon Meier Dec 12 '17 at 19:58
  • Whenever my brain parses "organize" it returns "syntax error"! – Massimo Ortolano Dec 12 '17 at 20:02
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One tool that seems to meet your requirements is Zotero. I recommend it highly. In particular, I've had good experience with it across multiple platforms and web browsers, including Ubuntu with Chrome and Firefox.

Zotero lets you organize your collection of papers into folders and can store the same item in multiple folders (collections in Zotero terminology.). You can attach a .pdf of a paper to the bibliographic data for that paper and Zotero can search within the content of your .pdf files. Zotero integrates well with Bibles and Latex.

screenshot
Zotero (source: Wikipedia; click image for larger variant)

Zotero uses the AGPLv3 license. You can find more details e.g. at Wikipedia.

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    It also has good export features with plugins, so it won't lock you in a particular software/workflow. And it's FLOSS. – henning Dec 12 '17 at 20:46
  • Please include license information, details about zooming and highlithing, and a screenshot, thanks! – Nicolas Raoul Dec 15 '17 at 6:53
  • Could you also please describe how Zotero can be used for document management, as OP requested? It is described as "reference management software", mainly dealing with quotations (though one can attach PDFs). – Izzy Mar 13 '18 at 13:16
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I use a tool called TheBrain.

You can download a trial. It's not free, but if your professional or academic life depends on tools, you'd want the most appropriate aid.

You can view a tutorial at tutorials and, in particular, you may want to view the webinar at Using TheBrain for Visual File Management

They usually demo it on Windows boxes, but I use it on macOS (Mac Mini, High Sierra)

See also This table of comparisons that show characteristics of programs like Zotero (but not TheBrain).

Best wishes ... cheers, drl

0

Write a literature review in LaTeX using BibTeX to manage your references.

Make sure each BibTeX entry has enough information for you to access the corresponding manuscript. I generally don't include any information: I can search Google Scholar using the title and that gives me access to the manuscript. Sometimes a manuscript is incredible difficult to access, in such cases I include a URL in my BibTeX entry. In hindsight, I should have been including the DOI of each manuscript, where available.

I believe this method achieves your objectives and the literature review provides a rich resource of information. Moreover, the review will most likely be publishable at some point.

Organisation vs. Viewing. This answer deals only with the organisation aspect of the question. Albeit, adopting this answer will likely change the viewing needs. (E.g., notes will appear in the literature review rather than as annotations in research papers.) The viewing aspect simply requires choosing the right PDF viewer. Options for Linux include Foxit Linux PDF Reader, GNU GV, Mupdf, Okular, Qpdfview, & XPDF.

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