Obsidian is vault-centric and has some harsh limitations in what workflows it allows because of this. It doesn't matter whether vaults are folders, because there is more to this than just the folder. This is really annoying, because Obsidian is a one of the best markdown-editors at the moment, with a good plugin-community, unlike others.
I like Obsidian, but I really dislike the annoying design-philosophy which restricts my usage.
For example, it's not possible to open any random folder with it, you need to first register the folder as a vault, and then can open the vault. It also doesn't handle file links under Linux correctly. For whatever reason, any link pointing to a file inside the vault, disappears. Probably some flaw in their file system-abstraction, but that made several workflows for me impossible. And then there is the problem with every vault having its own isolated configuration. Basically, every vault has a folder ".obsidian" which contains all installed plugins, configurations and whatever. For any new vault, you need to link this folder, and for whatever reason they are still unable to let obsidian handle this automatically.
Overall, Obsidian is designed to have mainly one, or at least just a very low number of vaults. But considering how poor obsidian scales with file numbers, this is not working well for every one. For me, this removed any motivation to use Obsidian for everything.
Interesting that you have so few vaults. I have dozens of them, each for a different project, or for different aspects of the same project. The way folders work in Obsidian is quite bad, when I am creating a new note it insists in putting it into the top folder instead of in the folder where I am currently in, so I prefer to keep it flat. I am just using the default setup and cannot be bothered much with plugins. There is no proper API documentation either.
It is a great editor. Your points are spot on. The vault-centric use of Obsidian is limiting, and has stopped me from using it as my main editor. I use it only for a single synced vault. All other md files are edited using other tools.
Obsidian is really nice, and quite powerful, especially thanks to plugins. It's also moving fast, the developers are very active. I used it for a while to move on from org-mode, but kinda lost interesst because of certain excentrics it has.
One specific problem that killed it for me temporary is the lack of support for multiple vaults, to the point that there is not even a truely centralized global configuation. Everything is saved in the vault itself, including plugins. Vault is the name of the data-directory, basically your workspace. For someone using multiple vaults (work, and private stuff) on multiple systems, this really kills any motivation to use it. Did this change in the meanwhile? I losly follow the changelog and haven't seen anything yet regarding this things, but maybe I just missed it.
Other than thoise specific problems, it's awesome how activate and vibrant the community itself is. There is a very active forum and discord-server, and many awesome plugins coming from the community are available. Obsidian has really the potential to leave org-mode behind and become a serious alternative for the rest of the world.
I tried using the URI-scheme and vault-parameter some time ago on linux, to open specific vaults via script. Surprisingly, this did not worked at all. Even worse, the whole scripting of obsidian is horrible even on the fundamental levels, and it failed on pretty much any normal job. Though, this is not such a surprise, considering that it's complete foreign to linux any kind of integration. At the end, it's a closed space, not like an editor, open to the rest of the system.
I think that's because Obsidian is designed for individuals over teams. It uses a local folder structure for organizing MD files and keeping them portable, although the backlinks mean everything can stay in sync. They aren't set up as a SaaS in the way Notion are, and that has a big impact on the design and intended audience for it.
Happy Obsidian user here. I love that the "vault" concept it uses is literally just a folder of markdown files, meaning I'm still in full control of my data. I don't use their proprietary sync service, I just drop it into a regular folder and let syncthing take care of cloning it to every device I own and a few extras for backup.
Obsidian itself has got to be the nicest markdown editor I have ever used, hands down. It gets so many of the little details absolutely right, down to tiny things like a quick shortcut to turn a list item into a checkbox (Ctrl+L) and then into a checked box (Ctrl+L again), without needing to even think about the underlying syntax. But you totally can, if you need that control. It's great.
You can also use Foam, a FOSS VSCode extension that is compatible with the basic markdown files from Obsidian. You can just open your vault in it and it will probably work if you're not using the fancy features in Obsidian.
If you'll allow me to rant a bit about Obsidian, its never going to be a mainstream competitor to Notion because it's file-based. For modern tools like Notion, Airtable, etc the filesystem is just a fallback option for piping data around when other more direct methods do not exist. Modern tools are database-driven, supporting multiple data types (images, text, tables, etc), different editing UIs for different content, multi-user support with comments, and instantaneous pointer updates when content is renamed/deleted/moved.
I've seen several products now including Obsidian that seem to take markdown support quite literally, centering themselves around .md files and markdown presentation (### Heading 3), rather than simply markdown keyboard shortcuts and ability to export as markdown. Markdown has its place but its primarily for easy diffing in text-only content like code editors, or a human readable option for backing up content. Tools like Obsidian are essentially lightly tweaked code editors, not modern project-based editors the whole company can use.
Probably referring to the limitations of Markdown? Not sure what Markdown flavor Obsidian supports, some extensions (e.g. tables) are quite powerful...
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