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Folder Structure Guide

How to organise your Cowork folder for governance that actually holds.

Structure is not overhead. It is the difference between a Claude that knows which file is authoritative and one that is silently working from the wrong version.

The single most common recoverable failure in long-horizon collaboration is file divergence: two versions of the same document exist, Claude references the wrong one, and work compounds on a broken foundation. This folder structure prevents it.

The Recommended Structure

📁 Claude/                          ← Your main Cowork folder
│
├── 📁 00-governance/               ← Control layer. Read-first every session.
│   ├── RUNNING-DOCUMENT.md         ← Claude's memory (read at session start)
│   ├── PARTNERSHIP-AGREEMENT.md    ← Operating agreement
│   ├── TRUTH-PROTOCOL.md          ← Anti-sycophancy rules
│   ├── SESSION-START-PROTOCOL.md  ← How to begin every session
│   ├── FAILURE-RECOVERY.md        ← What to do when things break
│   └── CANONICAL-NUMBERS.md       ← Single source of numeric truth
│
├── 📁 01-inputs/                   ← Raw materials. Claude reads, never writes here.
│   ├── papers/                     ← Research, reference documents
│   ├── data/                       ← Source data, raw files
│   └── uploads/                    ← Files you've provided
│
├── 📁 02-working/                  ← Active work in progress
│   ├── [Project Name]/             ← One folder per project
│   │   ├── RUNNING-DOCUMENT.md     ← Project-specific running doc (if needed)
│   │   └── [working files]
│   └── scratch/                    ← Temporary working files (safe to delete)
│
├── 📁 03-outputs/                  ← Finished work
│   ├── drafts/                     ← In review
│   └── final/                      ← Approved and complete
│
├── 📁 04-archive/                  ← Deprecated files. Never delete — rollback needs history.
│   ├── [DEPRECATED-filename]
│   └── [OLD-VERSION-filename]
│
└── Claude_Session_Updates.md       ← Companion file for scheduled tasks (Cowork-specific)

The Governance Folder (00-governance)

This folder is the control layer. Everything Claude needs to operate properly lives here.

Rule: Claude reads this folder at the start of every session before doing anything else.

Never put working files here. Governance documents are stable. Working files change constantly. Mixing them creates confusion about what is authoritative.

If you have project-specific rules, create a project-level RUNNING-DOCUMENT.md inside the project's 02-working/ folder. Reference the main governance docs from it — don't duplicate them.

The Inputs Folder (01-inputs)

Read-only for Claude. This is where source material lives: research papers, reference documents, data files, anything Claude reads but does not modify.

Why separate? Keeping inputs immutable means you always have the original. Claude's edits and outputs go elsewhere. The source material is never corrupted.

The Working Folder (02-working)

One subfolder per project. Claude works here.

Each project folder can have its own RUNNING-DOCUMENT.md if the project is large enough to need one. For smaller work, the main governance Running Document is sufficient.

The scratch/ subfolder is for temporary files — notes, drafts, experiments — that do not need to be preserved. Clean it out periodically.

The Outputs Folder (03-outputs)

Work you've completed. Separated into drafts/ (in review, may change) and final/ (approved, should not change without deliberate decision).

When a file moves from drafts/ to final/, update the Files In Play section of RUNNING-DOCUMENT.md.

The Archive Folder (04-archive)

Never delete old files. Archive them.

This is the rollback requirement. When something goes wrong and you need to return to a previous version, you need the history. Deleted files cannot be restored.

Naming convention for archived files:

DEPRECATED-[original-filename]
OLD-v1-[original-filename]
SUPERSEDED-[YYYY-MM-DD]-[original-filename]

The date in the filename tells you when it was archived.

File Naming Conventions

For active files:

[ProjectName]-[Description]-[Status].md
[ProjectName]-[Description]-v[N].[status].docx

Status suffixes:

  • -DRAFT — Work in progress
  • -REVIEW — Waiting for your input
  • -FINAL — Approved and complete
  • -CANONICAL — Single authoritative source for this domain

For archive:

DEPRECATED-[original-filename]
SUPERSEDED-[YYYY-MM-DD]-[original-filename]

Examples:

GovernanceProject-RunningDoc-v2.FINAL.docx
Claudishi-CurriculumMap-CANONICAL.md
DEPRECATED-GovernanceProject-RunningDoc-v1.docx

The Single Canonical Version Rule

For every domain — every topic, every project, every data type — there must be exactly one authoritative file.

Not one main file and one recent version. Not one file Claude should usually use. One file. Period.

When you create a new version:

  1. Rename the old file with the DEPRECATED- prefix
  2. Move it to 04-archive/
  3. Update the Files In Play section of RUNNING-DOCUMENT.md
  4. Tell Claude the new canonical file

This takes two minutes. It prevents hours of untangling.

The Companion Update File (Cowork-Specific)

If you're using Cowork's scheduled tasks (automated Monday/Wednesday/Friday sessions), add a Claude_Session_Updates.md file to your main Claude folder.

Scheduled tasks append updates to this file between your live sessions. At the start of each live session:

"Check Claude_Session_Updates.md for automated updates since our last session.
Summarise what happened and flag anything that needs my attention."

This connects your automated background work to your live collaboration — nothing runs in parallel without being integrated.

Common Mistakes

Too many folders More structure is not better structure. If you're spending time organising rather than working, simplify. The five-folder system above is the maximum most people need.

Deleting instead of archiving The moment you delete an old file is the moment you lose the ability to roll back. Archive everything.

Two canonical versions "I'll keep both just in case" creates version divergence. Pick one. Archive the other. This is not negotiable.

Working directly in governance documents The 00-governance/ folder contains stable operating documents. Do not use it as scratch space. Working files go in 02-working/.

Not updating RUNNING-DOCUMENT.md when files move If Claude doesn't know a file changed, it will reference the old one. Every time a file moves or gets a new canonical version, update the Files In Play section.

Starting From Scratch

If you're setting up for the first time:

  1. Create the five folders (00-governance/ through 04-archive/)
  2. Copy all governance templates into 00-governance/
  3. Fill in RUNNING-DOCUMENT.md with your details
  4. Fill in PARTNERSHIP-AGREEMENT.md
  5. Create your first project folder in 02-working/

Everything else can wait until the problem it solves becomes real for you.

The goal is not a perfect folder structure. The goal is a structure Claude can navigate without guessing.