Copy the vault-sjabloon folder to wherever you want to work and give it a name of your own. This folder is your Cowork working folder and, if you like, your Obsidian vault at the same time. Connecting it to Cowork happens in step 4.
Once the folder hangs off a project, Cowork automatically reads the CLAUDE.md in it on opening and follows the instructions inside it. That is layer 2, so the vault itself only: how the folders are organised and when Claude should load what. The numbered folders from 00-INBOX to 10-SYSTEEM each have a fixed purpose, explained in a README per folder.
Inside 10-SYSTEEM, the templates/ folder has a role of its own. It holds the shape of a document that keeps coming back without a process of its own, the halfway house between a loose project file and a skill. The README in that folder gives the criterion, plus the rule that a template becomes a candidate for a skill the third time you use it.
You have two memories, each with its own job. Claude's memory holds the facts about you: who you are, what you do, for whom and what you are working on. It lives in your account and is there in every chat, even when your computer is off. Fill it using memory-intake.md. tasks/MEMORY.md is the signpost of your vault: paths, the state of running projects and references to project notes, under 120 lines. Rules belong in neither; they go in your global settings and your skills. Personal data of clients does not belong there either.
Finally, fill the routing map in CLAUDE.md with your own workstations. If you work for several clients or on several projects, create an HQ folder per project inside tasks/. That is layer 4.
Obsidian, optional but worth it. Cowork works with ordinary folders and files, so you need nothing extra. If you also want to read those files comfortably and link them together, Obsidian is the logical companion. It is free, stores everything locally as plain markdown files and changes nothing about your folder. Download it at obsidian.md/download.
The combination works because both look at the same files. Claude writes a note and you see it appear in Obsidian straight away; the other way round, Claude reads whatever you type there. When you open Obsidian, choose the option for an existing folder and point it at your vault.
Two settings are worth getting right immediately, both under Settings in the Files and links pane. Set the default location for new notes to 00-INBOX, otherwise loose notes land in the root of your vault. And switch on automatic updating of internal links, so a renamed file leaves no dead links behind.
Done when Cowork knows your structure on opening the folder, your memory holds the facts from memory-intake.md and MEMORY.md points to your running projects.