[jaster]

It definitely does not solve all the issues listed in the article, but for me Zotero https://www.zotero.org has been absolutely brilliant as a "digital content organizer".

While it is "marketed" for scientists, it is a very general tool, that allows me to archive, tag, organize and search any webpage (with the option of taking a snapshot) or digital item.

I started using it for research articles, but it quickly expanded as a general bookmark organizer, then to books and even some podcast and movies archival. I use specific folders as reading/watching/listening queues.

Best of all it is FLOSS software, which is an absolute requirement for me to future-proof my use, and has an API that can be used to interact with external software. I use it for example as a document "backend" for my emacs org-mode journal (via the zotxt-emacs package).

There is an online sync service offered at a very reasonable cost (including a free tier). This is one of the very rare online services I'm paying money for. My understanding is that the sync server is open-source, but not production ready for self-hosting yet. The devs are supposedly working on it.

I strongly recommend you at least take a look.

[lbotos]

Not OP, I considered zotero, but for me, I used mobile too much and it seemed that it was a bit of the "wild west". I settled on Joplin which has a mobile app and has been great for me over the past 6 months. I'm working on a FF <-> Joplin bookmarks mirroring browser extension, which would get all of my bookmarks into Joplin as a SSOT.

[jaster]

Good point. I don't use it on mobile (I sync things between my personal and professional computer mostly) so I can't comment much on this aspect.

Joplin seems very nice indeed! But it seems to be more oriented for personal notes no? I mostly use Zotero for archiving webpages and various digital media (Zotero allows e.g. to embedded an epub as an item, or to add a link to a file stored locally).

[lbotos]

Joplin has a bookmarklet that lets you screenshot or copy html if you want webpages: https://joplinapp.org/clipper/ I haven't gotten too deep into the "media" aspects -- but it's been great to act as a "digital note hub" that encompasses writing, research, and tagging.

[FlashBlaze]

Have you given Zettlr https://www.zettlr.com/ a try?

[ta988]

Yes a Zotero app for mobile is something unfortunately missing. Ot doesnt seem too hard to talk to their API though.

[newfromblammo]

There has been a Zotero mobile app in the worka for awhile. The API is brilliant, if you’re an iOS user you can use Shortcuts to build with it.

[petemir]

Papership exists for iOS. It's not perfect, but it is good enough. I principally use it to search through the tree structure of documents, and then open them with other apps.

[ta988]

I discovered today "Zoo for Zotero", an android app that is Free. Seems to work well.

[mStreamTeam]

I'd like to agree and say joplin is great. I use synching to make sure my jolin notes are automatically synced between my phone, home computer, and work laptop

[kitotik]

Curious why you don’t use the sync that ships with Joplin?

[petemir]

Joplin does not offer any original synchronization system. It just offers NextCloud, Dropbox, Onedrive, Webdav or the local filesystem. If you don't use any of those services, or you do not have a server where to setup Webdav, Local filesystem + Syncthing seems like the best choice.

[porpoise]

To add to the point about "very general tool", it's even possible to hack Zotero so as to give Word/GoogleDoc some rudimentary dynamic content or Roam-like features. Just define a custom citation format (but mentally pretend citations as Roam-like [[links]]), and in Word/GoogleDoc invoke the Zotero add-on for insertion citation. The autocomplete search is fuzzy and fast, and Zotero inserts a field code with unique id that makes it easy to keep track of all references to the same idea/thesis/concept even under different aliases. Better still, if you alter the dynamic content inside Zotero it can automatically update the displayed value of the field code next time you invoke the add-on.

[atombender]

Another great app is DEVONthink [1]. It's not as good (if at all) at scientific citation management, but it's a brilliant app for saving a database of information.

Devon supports PDFs, Markdown, images, bookmarks (which can be viewed in the app), and more. The PDF handling is superb. The search is excellent, and it has extensive support for tags and metadata. Sync is very good. I also like that it stores each collection as a separate database file that you can keep in different places.

Among other things, I use it to collect and categorize images, which works really well because you can view any collection/folder as a "gallery".

My only complaint is that the databases are local, and you only sync between devices. I can't share notes with other people for real-time collaboration.

[1] https://devontechnologies.com/apps/devonthink

[walterbell]

Their iOS app is a lifesaver, because it will sync robustly across iOS/Mac devices, via WebDAV on FreeNAS, and includes a built-in web scraper for public pages, PDF and even audio files. With censorship increasing, it's valuable to have a local cache alongside the tagged bookmark.

[SomeHacker44]

Agree on DevonThink. Unfortunately I have recently left the Apple ecosystem and have not found a good replacement for this for Windows 10. Almost everything else has been replaced or was cross platform.

(The other thing is Foreflight, which may keep me as an iPad owner solely for that. Sigh.)

[newfromblammo]

You can share a whole database for collaboration, I have been doing this for years.

[atombender]

You can of course share for syncing, but real-time collaboration like Google Docs, or Apple's Notes?

I believe Devon has zero support for conflict resolution. It can only overwrite or duplicate on conflict.

[prepend]

I use zotero to manage literature reviews and citations. But it is frustrating how the web version (I won’t install the desktop version) sucks at importing content. The magic add works for many sites and papers, but not all. The fact that it can’t import a citation is so annoying that I’ll probably drop the tool and use endnote that sucks so much more, but at least works consistently.

[ta988]

You are really missing the magic if you don't use the desktop app. It syncs across devices and web as well (through their servers or yours with webdav)

[prepend]

I use it in an environment where I can’t install desktop software.

I would like to install, but my annoyance is that I think they aren’t implementing to try to drive more installs.

[newfromblammo]

It’s FOSS, they don’t have deliverables so I doubt that is their motivation.

[sbr464]

I thought it was odd that it opened the system pdf viewer to view documents. I could be wrong, I’m not sure if it was possible to configure. It seemed to slow down the experience when clicking around to preview documents/links.

[abdullahkhalids]

> Write programs that do one thing and do it well.

> Write programs to work together.

https://en.wikipedia.org/wiki/Unix_philosophy

[smnrchrds]

I used Zotero when it had the web capture and highlight tool and stopped using it when it was removed. Have they added such a tool back in or are there any alternative or plugins to recover this functionality?

[jaster]

Not sure if that is what you are asking, but Zotero has plugins for saving web page directly from the browser: https://www.zotero.org/download/connectors

I use it extensively with FFox.

Regarding highlight tool I can't say, I did not look for the feature (I usually take my notes in a separate Note item attached to the article)

[fudged71]

Is a link saved as an offline web format with fulltext, or just as a link?

[gildas]

It uses SingleFile under the hood so it saves a full offline page in HTML.