Setting up workflow with DTPro, Bookends, & Scrivener

Hi Cassady,

My apologies for resurrecting this old thread. I’m considering integrating bookends into my research and workflow, but I’m not entirely sure how to start. I am familiar with several different strategies for integrating Devonthink and Bookends from this point forward (I like your process, for example). However, I’m unsure of how to import my existing pdf libraries from DTPO into Bookends, without disrupting their filing structure in DTPO. Am I missing something obvious here?


I use Bookends, Scriviner, and DT3. I too keep my PDFs in Bookends and store them all in iCloud Drive. As you know, the advantage to that is that if I annotate a PDF on one device, the annotation is on all devices (they share the same PDF).

I index that Bookends folder in DT3 (I don’t import the PDFs, just index the folder). What I love about this is that I can do a search in DT3 across all my PDFs. I do this a lot in my research. Newly added PDFs added through Bookends are automatically indexed the next time I open the that database in DT3.

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Trouble is , if there is no pdf in iCloud BE library , it won’t appear in the DTO index , and easy to miss

  • any solution found ?

I would also like to know if there’s a solution to this…!

I’m an academic and also own these three tools. I’ve just not ‘gotten going’ with them into a workflow, although I believe they can offer me a lot for a powerful workflow. I read various posts, but it often seems that examples shared throw in yet one more tool, or talk about scripts or such, which just feels overwhelming to me.

  • When I’ve tried working with DTPro I like what I see but feel like I’m probably missing a lot. I
  • Bookends looks sensible enough and posts here suggest it is the best reference manager to integrate w DTPro. I currently have all my tagging of relevant articles in Mendeley and am loath to lose all that data.
  • I wrote my last article in Scrivener and liked it a lot, but end up cutting and pasting all the sections back and forth between a Google doc to get input from collaborators.

I am wondering if anyone who is a part of this community is expert at using these three tools together AND consults with others to create customized tweaks. I’m happy to compensate for this expertise. It would just be so much more efficient it seems to hear about some options, and to ask questions and then devise my set up with access to someone who knows the settings, etc.

I can explain more if anyone is interested in such a gig. I guess part of the issue is that I like learning through interaction and have a limit for technical prowess (no programming/ scripting know how).

@sdexter – being new to DT myself, I don’t have anything to say about most of this, except on one point:

It seems like one point of friction here for an integrated workflow is that AFAIK Mendeley doesn’t offer much possibility of integrating with DT (or anything else). I have no experience with BookEnds, but I recently switched from Mendely to Zotero (b/c I didn’t like what seemed to me the increasing lock-in that Mendeley is pushing). I believe I was able to preserve all my tags.

And then, it appears that Zotero can be made to integrate with DT. Again, I have no experience with this, but here’s a thread that seems to suggest that Zotero+DTmay work about as well as BookEnds+DT:

If you are interested in looking more into Mendeley → Zotero, I can probably dig up some links and maybe some of my notes on the transition, if that would help. BTW I only ever annotated PDFs outside Mendely (and now Zotero) – if you’ve been annotating inside Mendely, I’m not sure how the Mendeley → Zotero migration wold go.

I have three Macs syncing DEVONthink through Dropbox. I have Bookends store the PDF attachments in the iCloud Folder for iOS Sync (/Users/user/Library/Mobile Documents/iCloud~com~sonnysoftware~bot/Documents). I then have DEVONthink index that folder. The problem is that, whenever I add a new record with an attachment to Bookends, the file is listed twice in the Bookends indexed folder in the other two computers when I open DEVONthink in them. Is this being caused by using the iCloud folder to store the Bookends attachments? Should I store the Bookends attachments in a directory in my drive, and then index THAT folder? Thanks for any insights about this.

I haven’t had much success using iCloud sync with bookends. I have never used iCloud sync for anything else, but have used Dropbox for years. The errors I got with iCloud and bookends sync (newly added bookends items just not showing up on other devices) were ones I have never had with dropbox. So I switched to putting the bookends PDFs in dropbox. Then I indexed dropbox folder in DEVONthink. That has been working for me. I think I’ve seen others on these forums opine that iCloud sync is not particularly robust. HTH!

Thank you for your response. I am wondering if others are indexing the Bookends iCloud attachment folder in DEVONthink without incident.

  • Do you happen to be using a VPN?
    • If so, which one?

Thanks for the thought @BLUEFROG – but no, no VPN.

I should probably clarify my issue. I had the problem when adding a PDF on an iPad into Bookends for iOS – which of course requires the use of iCloud sync. The newly added PDF then did not show up on my Macs (I think perhaps the reference did). Things seemed to work when adding a PDF on Bookends for Mac – everything showed up correctly on iPad, at least the one time I tried it.

When I hit the issue on iPad, I did do some troubleshooting (disable/re-enable the sync; rebooted things) but couldn’t get it to work. As I have never used iCloud sync for any other kinds of file sync (I don’t trust the reliability of Apple cloud anything for anything important), but have used Dropbox for years without ever having a file not sync, I decided I was going to give up on Bookends for iOS, and just use Bookends for Mac with PDFs in Dropbox and indexed in DT3, and thus also showing up in DTTG.

I can think of a few loci for the issue I encountered: (1) how Bookends works with iCloud sync (2) how Bookends for iOS works with iCloud sync (3) iCloud sync itself (4) something on my end. So I suppose the issue is not necessarily iCloud sync itself. But given that things have just worked with Dropbox for over ten years, I was not willing to spend any further time on troubleshooting.

Hope that made sense.

This is happening to me as well. Same set up.

I did an experiment to try to identify the problem. I added a record with an attachment to Bookends. I then checked on all three computers to ensure that the new attachment was showing exactly the same in each computer’s iCloud directory—which they were. I then opened DEVONthink in my base computer, and it showed the new file in the Bookends indexed directory. So far, so good. However, when I went to my second computer, it synced with the Dropbox store, and then showed the file twice, with both files having different timestamps for Added (with the timestamp being the moment I opened DEVONthink). I then went to the third computer, and the file was now in triplicate, with its timestamp for Added also the time when DEVONthink was opened. I have attached a screenshot that shows the triple listing of the same file. I hope this helps to isolate the issue.

No VPNs are being used.

Are you using Dropbox’s Smart Sync feature to keep the file online until you download it on demand?


But the Apps directory in Dropbox, which I believe is where the DEVONthink store is, is not listed as one of those on-demand.

Ahh… your Bookends attachments are in iCloud but you’re syncing to Dropbox.

Are the files in iCloud being stored locally or being downloaded on demand?

When one activates iCloud Drive, a directory with that name appears in the Finder that shows the contents of iCloud Drive. I did not know that one could choose not to have the files in iCloud Drive downloaded.

That is why I use Paperpile. PDFs are maintained in Google Drive. I índex them in DT3 and have the best of two worlds. An excellent reference manager and a wonderful document manager.