Is it possible and practical to incorporate the Obsidian folder structure into my general Windows folder structure?
The idea here is twofold:
I would prefer not to have to copy files I want to reference from Obsidian notes into the Obsidian folder structure and have two versions of the file.
Rather than replicating my general Windows folder structure in a separate Obsidian structure, they would be one and the same.
Would this work? Are there negative implications?
All your folders in Obsidian?
That sounds as if it could slow things down.
Another thing you can do, but it is a little more job, is to create symlinks in your root vault to the folder structure
I just created a template note in obsidian that contains the full URL to the Documents folder on my Mac. Something like “file:///users//Documents/”.
As I do know the structure of the Documents folder very well I can link easily to a local file by adding the template I created above (CMD-ALT-T hotkey in my configuration) and then add the folders and files I want after it.
To have autocomplete would be extremely cool but I expect it not to happen on a short notice.
Regards,
Jeroen
Maybe that’s kind of an edge case for a PKM and also Windows’fault and not Obsidian’s? 
Obsidian works best with markdown files, and embeds best images or PDFs. That keeps your vault light and agile. Embedding a whole directory structure does not seem ideal. It seems you’re looking for a document manager, for which Obsidian isn’t ideally suited.
Do you actually know if this is not ideal? I am very much with @StoltHD here, I have (and had) a project folder which I now use as the vault. I keep everything I do in there, each project gets a folder and they do contain various types of files. I like to comment on what I do using markdown files or also have some pure note taking projects such that this set-up works perfectly for me.
On a side note, what’s the current state on getting a .obsidianignore? This would help very much with this set up.
Well, you should know that in Mac territory, what you both want is alien. There are a million ways to do deep linking throughout the system without having to resort to this (through URL schemes). You can link to pretty much anything even to parts of other apps without symlinks, which is why this looks like an OS specific request and very possibly outside Obsidian’s scope.
Quite a lot of posts about symlinks are from Mac users who ran into issues trying to use them
And I really don’t get the use case when we have DEVONthink, Hook and so on.
Anyway. Do what thou wilt.
People are drawn to Obsidian because of it relying on the open format of raw text files, in particular. Why would they use something like Hook?
To link to other parts of the system, not to Obsidian itself since it has an URL scheme.
(Note that I am not using Hook, I’m using native deep linking in the software I use everywhere – URL schemes support is a major selling point for me.)
I am absolutely not talking about aliases and React linking. But it doesn’t look like we will get anywhere, so I’m exiting this conversation and wishing you all a good day
I’m interested in this as well.
I’ve outlined my idea here: