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. That surprises people, and without a division of labour the same facts drift apart in two places. tasks/MEMORY.md is the memory you edit yourself: running projects, decisions made and names that keep coming back. Keep each line short and hold to the ceiling of 150 lines, otherwise the file slows everything down. Cowork's own memory fills itself while you work and you leave that one alone. If you spot something there you want to manage yourself, move it to MEMORY.md.
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 and MEMORY.md holds three or four facts you refer to often.