True. I missed the date. Springer acquired Papers in 2013 and Readcube got it from Springer in 2016.
And they are working on a new version.
I haven’t tried Papers yet. Will test drive BookEnds first. But I did try ReadCube.
On the positive side it indexes your PDF library without dupicating any files, and considering that I have about 167 GB of PDFs in my DropBox that would be a lot of duplcation. However I found out that it will choke if you give it too much at once. I tried to just have it index part of my JSTOR collection. That was not a good idea as it basically stopped working and hogged the CPU while trying to digest everything. Best to do something like that before going to bed. Or to just feed it smaller bites.
But the deal breaker for now with ReadCube is that it can not read any annotations in PDFs that you have made with Acrobat Pro. Nor will Acrobat Pro read any anntations you make with ReadCube. Their tech support told me that “It is just now coming” as they say in India. Apparently they are getting a lot of complaints about this incompatibility. Like they didn’t think their users would like to read and use all their previous annotation? Duhh.
I previously wrote:
If anyone has a few/many books they would like to scan and turn into PDFs you can take a look over here diybookscanner.org.
I made the mistake of getting some engineering friends to help me and they took a perfectly working plan and “improved” it to the point that it didn’t work. Money and time wasted. Better to follow a plan or buy a kit. There current best model costs about as much as the yearly maintanence fee for the Bookeye scanner bookeye.us/index.html
With a two camera setup you can scan at a rate of 600-800 pages/hour. Half that with one camera.
I now have only a few items to scan since the project is over and I will just use the cardboard box method. Cheap and best. instructables.com/id/Bargain … board-Box/
My library that previously took up several rooms now fits into a flash drive. I can take my library with me where ever I go. 
And it is also on DropBox.
My one and only concern is that it works well with Scrivener. Currently that is not Zotero. We’ll shall soon see if BookEnds lives up to its press.
I feel exactly the same way. I want to write, just not write code.
The salient point is not whether it is open source or commercial, it is actually the support provided to make it a working tool. Some open source projects like FireFox go to a lot of effort to make it work. While some commercial products seem like they find customers to be a nuisance. One commercial product that gets rave reviews from its customers is this creator of Dreamweaver extentions projectseven.com. I am one of their very satisfied customers.
Anyway, now to test drive BookEnds.
Installed Bookends. Created a test page with dummy text to place footnotes in. Command Y worked in both programs. I was able to compile it with Scrivener (wrong font came out but that is different problem), and Bookends scanned it quickely but there is absolutely no difference between the original text and the scanned text. All the footnotes are in the footer in curly brackets looking like this:
{Bādarāyaṇa and Baladevavidyābhūṣaṇa, 1979, #53964}
{Bādarāyaṇa and Baladevavidyābhūṣaṇa, 1979, #53964@78-81}
{Valens, 1993, #44863@pp 34-37}
{Valens, 1993, #44863}
{West, 1971, #24995@pp 3-5}
{West, 1971, #24995}
{West, 1971, #24995@9-12}
{Copleston, 1993, #3540}
{Zeller, 1881, #21665}
So is this a problem with Scrivener, or Bookends or MS Word? 
What must I do to make it a flawless experience?
Problem solved. When all else fails, read the manual. I was probably making the same mistake in Zotero. 
Well, the bookends manual is > 400pages so reading it for a quick solution may not always be, um, quick! 
The Bookends forum is fairly efficient (but low traffic), and Jon often replies within a day.
I can recommend you have a look at some of the Applescripts shared on the forum there, they can provide a really nice addition to the UI. If you use Alfred there are some nice Bookends workflows too. In fact I’ve been asked by a friend to convert my Applescripts into a workflow which I’ll do on her machine sometime soon (I prefer Quicksilver to Alfred), and can share it back.
It was the 58 page tutorial, considerably smaller. It works but it doesn’t have the Citation style I want. It has 4 different versions of Chicago but not the version I want, Chicago 16th edition (note) 
Zotero has it but not Bookends.
Instead of getting this as a footnote
Copleston, A History of Philosophy, Vol. 1.
I get this
Frederick Copleston, A History of Philosophy, Vol. 1: Greece and Rome From the Pre-Socratics to Plotinus (New York: Image, 1993).
And there doesn’t seem to be a way of importing styles, at least I haven’t found it yet. Will look in documentation to see if I can find anything. Though it does say I can make a custom style based on an existing style. So maybe that would work. But would prefer to just import a working style.
Thank you for that. Once I get the basic workflow going in both programs (having problems with Compile in Scrivener) then I can explore the more powerful aspects of BookEnds.
In Biblio > Formats Manager… — isn’t Chicago 16th A the one?
It differentiates between the first and subsequent footnote cite. As far as I can see this is correct according to Chicago 16th documentation on the notes style:
chicagomanualofstyle.org/too … guide.html
Nevertheless if you want them to be the same just copy the from “Subsequent” back to “Field order”, then you get the simpler citation everywhere. You can easily customise the formats, and the Format Manager is one of the most powerful I’ve used. As I use Pandoc with Scrivener, I actually don’t use Bookends formats any more, but the CSL files that Zotero, Papers and many others use. They are more difficult to edit (mendeley has a clunk editor, otherwise you are hand editing obtuse XML!), and have a different set of limitations. But in my field of study, we don’t have difficult bibliographic formatting to worry about…
Seems there are more citethisforme.com/guides/chi … ite-a-book
What I did is make a new format based on Chicago 16th A and just deleted the unnecessary items. Seems to work so far. Now if I can only figure out how to get ibid to work. I have registered on the Bookends forum just waiting for approval and will hopefully find out what to do there.
I’m not constricted so I can choose what I like. This format gives the essentials without making a mess at the bottom of the page. Why use Pandoc if you are already using BookEnds? What is the advantage?
Pandoc is a first and foremost a very powerful markdown conversion system with bibliographic support. The trivial answer to your question is that I don’t have to manually scan anything, I compile to markdown in Scrivener, and automagically get a fully referenced document in the style of my choice output, no manual fiddling involved. But that only scratches the surface. Say I have a manuscript and one copy is to go to LaTeX and Nature style citations, the other to DOCX and APA. I can specify a front matter document that lets Pandoc generate both documents simultaneously from the same compile. No manual fussing. For Word, Pandoc generate a proper outlined document, with fully styled output and I can give Pandoc a word template with my preferred document/paragraph/character styles and it will use this as the basis to generate the DOCX. And so on, and so forth!
Bookends is still essential to my workflow. It is my second brain where I store and keyword, and manage, and discover the references that are the lifeblood of any academic! It makes it easy to search for, annotate, and clean up my references (standardise author and journal names for example is really great in BE).
Are there any videos that teach how to use Pandoc + Scrivener?
I intend to make my scrivener+pandoc tutorial much more comprehensive soon, but I’m waiting for Scrivener 3 to go fully public first.
I don’t really like video tutorials, but did find this: youtube.com/watch?v=BrZRIU8IHaI
Here are some older written workflows and tutorials:
larryullman.com/2013/04/10/m … -yii-book/
davidsmith.name/2014/05/23/ … umanities/
parkerderrington.com/scriven … t-writing/
Thank you for that information I went through it all; the first one on Github looked interesting. However, on further consideration it would be over kill for my needs. I think that at least for now BookEnds and Scrivener should do just fine if I can just figure out why Scrivener is sending out the wrong version of Baskerville to MS Word as I mention here Compile is changing body fonts
However, if my needs ever change I now know where to look. Again, than you for taking the time to point out the possibilities and tools available, it’s very much appreciated.
Been using BookEnds and so far it works flawlessly as advertised, unlike Zotero. Thank you for pointing me in the right direction. I am a lot more productive now.
If you want to be even more productive, you may find my recently released Bookends Tools for Alfred useful:
github.com/iandol/bookends-tools
For Scrivener, they package methods to search texts selection in Scrivener directly in Bookends, a tool to create OPML files from selected references you can import into Scrivener Binder and some quick author search interfaces to directly add a citation without switching to Bookends at all.
BookEnds on Steriods
I found that BookEnds works well with PDFs. You have the option to import a PDF into BookEnds or BookEnds can just link to a PDF in an existing folder no matter how deep it gets into sub-directories. I prefer the latter option. I suppose the former is ok if you only have a small number of documents or you don’t mind duplicating. But I have a large number of files that I have organized into topic folders and I prefer to just link to a file in an already existing structure that I understand. I will only link BE’s to PDFs on an as-needed basis, not the whole collection.
So it looks like BookEnds is going to be my citation tool of choice to work with Scrivener. Again, that you for pointing me in the right direction and out of the wilderness.