Folder Structure

Every AI Business OS workspace has the same layout, so Claude always knows where to look and where to put things.

The Top Level

your-workspace/
├── .claude/              The engine and your configuration
├── .vscode/              VS Code settings and recommended extensions
├── Archive/              Completed projects
├── Documentation/        Templates and reports for the whole workspace
├── Domains/              All business work, filed by function
├── Infrastructure/       Engine scripts
│   └── Scripts/
└── Scripts/              Scripts that keep the project register safe

The workspace root also holds AGENTS.md, README.md, CHANGELOG.md, ROADMAP.md, PHILOSOPHY.md and LICENSE. Claude does not create new files at the root, so everything you produce goes into one of the folders.

.claude/

This folder holds the engine and your configuration, and Claude Code reads it automatically when you open the workspace.

.claude/
├── CLAUDE.md             Master instructions for Claude
├── agents/               Agent definitions
├── commands/             Slash commands such as /day and /night
├── company/              Your organisation's context files
├── config/               Integration settings
├── docs/                 Guides and reference documents
├── rules/                Behaviour rules, loaded automatically
├── skills/               Reusable workflows
└── state/                The project register and its schema

Some of these files are yours and some belong to the engine. .claude/CLAUDE.md, the files in company/, config/integrations.json and state/state.json are yours, and updates never change them. The engine manifest at .claude/engine-manifest.json lists the engine files that /update maintains. Ask Claude before you change anything else in .claude/, because Claude can tell you what an update would do to the change.

These pages describe the parts of .claude/ in detail.

• CLAUDE.md and AGENTS.md Files
• Company Context Files
• How Rules Work
• State Files and Validation
• Configuration

Domains/

All business work lives in Domains/, filed by the function of the business it belongs to. There are seventeen domains, numbered 01 to 16 plus 99. Each one holds numbered reference subfolders for standing material and tracked project folders for time-bound work. A new workspace starts with this tree, including three sample projects and three sample clients that you can delete.

Domains/
├── 01 Clients/
│   ├── Client-A/                           Sample client
│   │   ├── Communications/
│   │   ├── Projects/
│   │   └── Reference/
│   ├── Client-B/                           Sample client
│   │   ├── Communications/
│   │   ├── Projects/
│   │   └── Reference/
│   ├── Client-C/                           Sample client
│   │   ├── Communications/
│   │   ├── Projects/
│   │   └── Reference/
│   └── _Templates/                         Empty, for your client templates
├── 02 Finance/
│   ├── 02.1 Accounts Payable/
│   ├── 02.2 Accounts Receivable/
│   ├── 02.3 Budgets/
│   ├── 02.4 Reports/
│   └── 02.5 Tax & Compliance/
├── 03 Human Resources/
│   ├── 03.1 Employee Records/
│   ├── 03.2 Onboarding/
│   ├── 03.3 Policies/
│   ├── 03.4 Recruitment/
│   ├── 03.5 Training/
│   └── P003 Staff Training Programme/      Sample project
│       └── Docs/
├── 04 Information Technology/
│   ├── 04.1 Architecture/
│   ├── 04.2 Runbooks/
│   ├── 04.3 Security/
│   ├── 04.4 Software Development/
│   ├── 04.5 Systems/
│   └── P001 Website Redesign/              Sample project
│       ├── Design/
│       └── Development/
├── 05 Strategy & Leadership/
│   ├── 05.1 Board/
│   ├── 05.2 Decisions/
│   ├── 05.3 OKRs/
│   └── 05.4 Strategy/
├── 06 Sales/
│   ├── 06.1 Contracts/
│   ├── 06.2 Pipeline/
│   └── 06.3 Proposals/
├── 07 Marketing/
│   ├── 07.1 Analytics/
│   ├── 07.2 Brand Assets/
│   ├── 07.3 Campaigns/
│   ├── 07.4 Content/
│   ├── 07.5 Social Media/
│   └── P002 Q2 Marketing Campaign/         Sample project
│       ├── Assets/
│       └── Campaigns/
├── 08 Communications/
│   ├── 08.1 Crisis Playbooks/
│   ├── 08.2 Internal Comms/
│   ├── 08.3 Press/
│   └── 08.4 Stakeholders/
├── 09 Customer Service/
│   ├── 09.1 Customer Success/
│   ├── 09.2 Knowledge Base/
│   ├── 09.3 Service Levels/
│   └── 09.4 Tickets/
├── 10 Operations/
│   ├── 10.1 Logistics/
│   ├── 10.2 Processes/
│   ├── 10.3 Quality/
│   └── 10.4 Vendors & Suppliers/
├── 11 Procurement/
│   ├── 11.1 Agreements/
│   ├── 11.2 Policies/
│   ├── 11.3 RFQs/
│   └── 11.4 Suppliers/
├── 12 Property & Facilities/
│   ├── 12.1 Assets/
│   ├── 12.2 Insurance/
│   ├── 12.3 Leases/
│   └── 12.4 Maintenance/
├── 13 Products/
│   ├── 13.1 Catalogue/
│   ├── 13.2 Development/
│   └── 13.3 Pricing/
├── 14 Research & Development/
│   ├── 14.1 Market Scans/
│   ├── 14.2 Patents/
│   ├── 14.3 Prototypes/
│   └── 14.4 Research Archive/
├── 15 Education & Training/
│   ├── 15.1 Assessments/
│   ├── 15.2 Courses/
│   ├── 15.3 Curriculum/
│   └── 15.4 Learners/
├── 16 Legal & Compliance/
│   ├── 16.1 Audits/
│   ├── 16.2 Certifications/
│   ├── 16.3 Contracts/
│   ├── 16.4 Controls/
│   ├── 16.5 Data Protection/
│   ├── 16.6 Intellectual Property/
│   └── 16.7 Risk Register/
└── 99 Cross-Domain/                        Projects shared by three or more domains

Every domain folder also holds a CLAUDE.md and an AGENTS.md, which tell Claude what the domain is for, and each sample project holds its own CLAUDE.md, AGENTS.md and PRD.md. The Domains page explains each domain, how to add or remove reference subfolders and what to do with domains you do not need.

Archive/

Completed projects move here from their domain. The folder keeps its name, so P004 Year-End Audit stays P004 Year-End Audit, and the project’s path in the register changes to the new location. Nothing is deleted. Archiving a project from /status moves the folder for you.

Documentation/

This folder holds material for the whole workspace that does not belong to one domain or project.

Subfolder	Holds
Templates/	Documents you reuse as starting points, such as the PRD template that /newproject uses. See Templates
Reports/	Generated reports and analyses, including the page that /dashboard builds

If something belongs to a project, it goes in that project’s folder. If it belongs to a business function, it goes in that domain.

Infrastructure/ and Scripts/

Infrastructure/Scripts/ holds the scripts the engine runs, such as the update script, the two safety hooks and the backup and validation scripts for the project register. Scripts/ holds a second copy of the backup and validation scripts, which some commands call by that path. You do not need to open either folder in normal use. If you write your own automation scripts, keep them in Infrastructure/Scripts/.

Where Things Go

Content	Location
Active project work	Domains/NN Domain/{ID} {Project Name}/
Standing material for a business function	Domains/NN Domain/NN.M Subfolder/
Client work	Domains/01 Clients/[Client-Name]/
Projects shared equally by three or more domains	Domains/99 Cross-Domain/{ID} {Project Name}/
Completed projects	Archive/{ID} {Project Name}/
Reusable templates	Documentation/Templates/
Reports and analyses	Documentation/Reports/
Your own scripts	Infrastructure/Scripts/
Session checkpoints and agent outputs	~/Documents/Agent Outputs/[project-id]/, outside the workspace

The last row sits outside the workspace on purpose. /save writes checkpoint files there, and the folder can hold outputs from more than one workspace.

File Names

Kind of file	Pattern	Example
Structural files	Upper case, no date	CLAUDE.md, README.md, PRD.md
Your working files	Date first, then a Title Case name with hyphens	2026-10-14-Workshop-Agenda.md
Project folders	ID, a space, then the name in Title Case	P012 Spring Workshop
Client folders	Title Case with hyphens	Harbour-Dental

The date in a working file name is the date you created it. File names use hyphens in place of spaces. Claude applies these patterns to new files only and does not rename files you already have, because renaming can break links between files.

What Stays Out of Git

Large files stay on your cloud storage and out of the workspace. The .gitignore file stops git from committing them, so they never reach your remote repository.

• Office documents, such as .docx, .xlsx and .pptx files.
• PDFs.
• Images, audio and video.
• CAD files, archives and spreadsheets in CSV or TSV format.
• Secrets, such as .env files, keys and credential files.

Keep these on your cloud storage and give Claude the path when you want it to work with one. /setup records your cloud storage location in .claude/CLAUDE.md.

Caution

Do not keep the workspace inside a folder that a sync app copies to the cloud, such as the Dropbox, OneDrive, Google Drive or iCloud Drive folder on your computer. The Git documentation warns against syncing any part of a Git repository this way. These apps copy files one at a time as they change and do not understand how a repository fits together, so a copy taken while git is writing can leave missing objects, broken branches and lost work. Keep the workspace in a normal folder, such as ~/Documents/, and use git to sync it between machines.

If your workspace is already inside a cloud folder, follow these steps.

1. Copy the workspace folder to a location outside cloud sync, such as ~/Documents/.
2. Open the copy in VS Code from its new location.
3. Remove the old copy from cloud sync once you have checked the new one works.

Your git history and remote repository are unaffected by the move.

Cloud Storage Connectors

A connector is a different thing from a sync app. Claude has connectors for Dropbox, Google Drive and Microsoft 365, which you add at claude.ai/customize/connectors. If you sign in to Claude Code with your Claude account, the connectors you have added there are also available in Claude Code. On Team and Enterprise plans an administrator adds them for the organisation.

A connector does not sync any folder on your computer. Claude reaches your cloud storage through the provider’s online service, finds and reads the files you ask about, and can create or change files there when the connector allows it. Nothing it does touches the workspace’s .git folder, so a connector is a safe way to work with documents that live in your cloud storage while the workspace stays in a normal folder.

Connector	Made by	What Claude can do with your files
Dropbox	Dropbox	Search, read, create, move, copy and delete files and folders, and create sharing links
Google Drive	Google	Search, read, create, update, copy and share files, and move files to the bin
Microsoft 365	Anthropic	Search and read OneDrive and SharePoint files. Creating and updating files works only once an administrator in your organisation turns on the write tools. Work and school accounts only

Claude asks before it uses a connector’s tools unless you have chosen to allow them. You can set each tool to always allow, needs approval or blocked on the connector’s page at claude.ai.

The caution above still applies if you also run the provider’s sync app. Keep the workspace out of the folder that app syncs, and use the connector to reach the files in your cloud storage.