Just a heads up that the latest version of Zotero switches to a proprietary pdf highlight and annotation method. They did this to facilitate annotating of pdfs held in group libraries without fights among group users, or so they say. But I think it’s a terrible idea, because you’re reliant on Zotero working well to take your annotations with you, should you ever want to leave. Bookends, on the other hand, uses standard pdf annotations which you can edit on any other standard pdf app.
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Source for confirmation? Didn’t see it in the linked article but might have just missed it. This is a pretty important issue for me.
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Having just ported over a bunch of bookends refs and PDFs I can confirm — none of my highlights recognized. Woah… definitely a deal breaker
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I think I’ll stay with Bookends, subscription and all. 
I can’t replicate this.
All my files with highlights added via PDF Expert on the iPad have the highlights showing and are showing in Zotero.
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From the article (which has further details):
Why does Zotero store PDF annotations in its database instead of in the PDF file?
The new PDF reader in Zotero 6 makes PDF reading and annotation a first-class part of the Zotero experience.
To enable this tight integration, Zotero stores annotations in the Zotero database, not in the PDF file. This allows for fast, conflict-free syncing, including in groups, and enables advanced functionality that wouldn’t be possible otherwise.
Zotero 6 also offers various ways to export its PDFs with the annotations included in the PDF.
While I understand users desiring annotations being stored in the PDF, as an app developer I can fully sympathize with the decision for Zotero 6 to store annotations in the database. Storing them in the PDF severely limits your options to develop advanced features, and can make things like sync hard to impossible.
Having good sharing & (scriptable) export options to output PDFs with annotations included can help to satisfy the different needs.
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Likewise and agreed. This is not enough to make me instantly drop Zotero, but it is something that I need to test out and keep an eye on. It seems that PDFs I annotated before this update using Preview have had their highlights retained in the new Zotero version. If they provide easy-to-use and officially supported export methods it is fine with me but it is definitely something to be wary of in this day and age.
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@Bmosbacker I would not describe Bookends as having a subscription. In my mind a subscription is a product that when you stop paying for it (monthly or annual) it stops working. On the other hand Bookends comes with 2 years of free updates. If, after 2 years, you no longer want to update (or want to update later on), that’s fine. The app will still work perfectly fine.
Overall I think I update my Bookends about every 4 years … until there’s enough changes in the app that I really wan the upgrade, or a huge Mac OS update has forced it.
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It looks like you bought via the App Store. I bought directly. I honestly didn’t even know they sold on App Store. I believe with that version there’s no choice for the developer: one time purchase or subscription. Here’s the page for purchasing directly and see the details. Before next Jan you can switch over:
https://www.sonnysoftware.com/orders/order.html
I have no idea how much it is on App Store, but $60 for first time purchase, $40 for upgrade (which would be your case)
My mistake - total zotero neophyte 
. The highlights are there, but not “extracted” to the note fields. I guess this has to be done manually or via zotfile, or something else? Clearly the comments above are referring to the annotations done within Zotero. I do worry about ease of getting annotations out.
Here’s what I ended up with:
Yes, a switch back to Zotero. Because the iOS version doesn’t play well with synced files, I still need to use Zotfile to automatically save PDFs to a folder in my iCloud Drive (Google Drive or Dropbox would work just as well). That puts the PDFs in a place that I can access from PDFExpert, no matter what device I’m on. I can still add notes to a source in Zotero, and those notes will sync just fine. (Thankfully this means I don’t need to use Zotfile for directly managing PDFs on the iPad, which was the part I always found fiddly and annoying.)
Using linked files + PDFExpert means I don’t get Zotero’s new annotation features, but the upside is that I get reliable sync without having to buy additional storage from Zotero. (Their prices aren’t unreasonable, but I already have +/- 25 GB in Dropbox thanks to referrals from the early days, and I’ve got 2 TB in iCloud. I might as well use what I have.)
If I need to extract annotations from a PDF, PDFExpert lets me export those to Markdown fairly easily.
@Bmosbacker and @Mathew_T_Mitchell, the Mac app for Bookends is a paid update about every two years if you want new features; what you already have keeps working. At least, that’s how it is for me. I bought directly from the developer. The subscription I’ve been paying for ($9.99/year, if memory serves) is for syncing between macOS and iOS.
Sorry, the source is that I asked Dan Stillman and that’s what he told me!
Interesting to see people’s reactions here.
I personally want my annotations to be in the pdf because I like them to be editable from different apps. I got burned by the demise of Sente and I have learnt my lesson. On the other hand, I’m in the minority maybe in that I couldn’t care less about the “advanced features” enabled by proprietary systems. Simple features, well implemented, are usually enough for me.
I’m also surprised to see such a pushback against Bookend’s modest subscription fee. I like to pay for the software I use, I don’t see why people’s labor shouldn’t be compensated. Even when I use open source software, like Zettlr, I send them $10 a month, which seems fair for an app I use every working day.
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My sense is that, at least in this forum, there’s not an objection to subscriptions in the abstract, for the reasons you mention.
As a practical matter, though, there are limits to the number of subscriptions a person can reasonably maintain. The thread on annual subscription totals was an eye opener.
Sorry, yes, I believe the extraction of the notes from the PDF’s to the note field has always been a manual process, though from memory, Zotfile add on does automate that when importing in files that have been highlighted using it to sync between devices.
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I think this is exactly the point. I doubt anyone begrudges developers a proper return for their labor. The issue is the proliferation of subscriptions, which is in effect “renting” the application. Each individual has to decide what represents good and wise stewardship of his or her finances, including a reasonable budget for app subscriptions and/or purchases.
When deciding whether or not to pay a subscription I start by asking “do I NEED the features this app offers?” If I don’t NEED those features, though I may prefer them, I usually opt for the “good enough” non-subscription app. An example is an app like Carrot Weather. It is a great app., I like it but I don’t NEED the customizations. What I NEED is accurate weather data and forecast. The stock weather app provides that so I don’t pay a subscription for my weather app. Fantastical is another example. It is a beautiful app, the natural language parsing is, well, fantastic, and the feature set robust. But, I don’t NEED those features. I just need to add and see events on my calendar. I could add a host of other apps where I’ve made a similar assessment–Ulysses, TextExpander, perhaps 1Password (still reviewing), MindNode, and more.
As to Bookends, now that I realize there is a non-subscription version available directly from the developer I’ll probably go that route.
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Thanks!
20 characters…
If you are interested in using the webdav syncing, there is an offer on stacksocial for 100GB of lifetime storage for $30 with Koofr. That should be more than sufficient for most PDF libraries, but there are also offers for 250gb and 1tb as well. Then you can configure Zotero using Koofr’s webdav setup. I’ve been using this setup for a few months and it’s been working well. Also I prefer the one-time payment without subscription.
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That depends, though. There are apps where the updates only unlock new features (like Bookends). There are also apps where your data is accessible across multiple apps, so the subscription may come and go but your data is your data. I don’t dislike that model and I don’t see a problem with “renting” the app when I need it in that case. It’s like the app is an expensive power tool that you’re renting when you need to do a job (or, say, for your years of working professionally on X), but what you make with the tool is independent of the rental.
And then there are apps where everything about them is ephemeral (I assume that that’s what carrot weather is like). It may be harder to wrap one’s head around a subscription in those cases.
So yeah – lots of nuance to consider.
I had a look at the thread linked by @acavender about subscription totals. I think I don’t go anywhere near those amounts, primarily because I really only pay for a handful of things at this point: Bookends, Highlights (which of course is relevant to this thread because it does automatic extraction of standard PDF annotations…), Zettlr (via Patreon) and Taio. Hardly a huge sum. And none of those apps locks me into anything (in the case of Bookends, the synced .bib file is de facto an automatic export that you can open in BibDesk and other apps, and the PDFs, unlike Zotero are annotated in standard form so you don’t need any special export operation to be in control of your annotations…).
Here in New York City, a bitter, salty espresso comes easily to $3.50. It tastes nothing like the real thing (I’m from Italy…) and it’s gone in a minute. It’s hard not to feel hypocritical complaining about $10/month, say, for an app I work with 5hr/day when I’m sipping the aforementioned disappointing beverage for $3.50…
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Zotero still looks like a Windows 98 app - bad font & typographical spacing, no interface with Mac standard right-click etc. If they could port the iOS version back to the Mac with Swift UI, they might be getting somewhere.
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