The Problem with One System
Most people start with one tool. Everything goes into Obsidian, or everything goes into Google Drive, or everything lives in a folder on your desktop. It works until it does not.
PDFs, contracts, and tax documents are not the same thing as the knowledge you extract from them. And neither of those are the scripts, configs, and agent workspaces that operate on the knowledge. When they all live together, you end up with a vault full of binary files Obsidian cannot index, a Drive full of markdown nobody reads, and a workspace cluttered with documents that should be somewhere searchable.
The solution is not picking the right tool. It is defining what each tool is for, and then being disciplined about the boundary.
What Goes Where
The way I think about it: if I received it or downloaded it, it goes in Drive. If I wrote it or extracted it from something, it goes in Obsidian. If it runs or builds something, it goes in the workspace.
| File Type | Layer | Why |
|---|---|---|
| Tax return PDF | Drive | Source document; Obsidian cannot render PDFs usefully |
| Employment contract | Drive | Legal original; needs to be accessible from any device |
| Property appraisal | Drive | Third-party document with images and formatting |
| Spreadsheet (financial model) | Drive | Needs Google Sheets or Excel; markdown cannot replace it |
| Tax analysis (your notes) | Obsidian | Knowledge you extracted; needs links, tags, frontmatter |
| Immigration timeline | Obsidian | Your synthesis; references source docs in Drive |
| Research on a topic | Obsidian | AI-generated or manual; needs freshness metadata |
| Daily journal entry | Obsidian | Personal notes; benefits from Calendar plugin and Dataview |
| Deploy script | Workspace | Executable; does not belong in a knowledge base |
| Agent config | Workspace | Operational; changes frequently, versioned differently |
| API keys / secrets | Workspace | Security-sensitive; never in Drive or a synced vault |
| Contacts database | Both | Source in workspace; knowledge summary in Obsidian |
The "both" cases are rare but real. A contacts database might live as a JSON or CSV in the workspace (for scripts to read), with a human-readable summary in Obsidian (for you to browse). The workspace version is the source of truth; the Obsidian version is a view into it.
Mirror the Folder Structure
If your Drive has a folder called 00_Spain and your vault has a folder called 00_Spain, you never have to think about where something is. The numbering system keeps both sorted identically. When you are looking at a tax analysis in Obsidian and need the source PDF, you know it is in the same-numbered folder in Drive.
The subfolders differ because they serve different purposes. Drive subfolders organize by file type (contracts, tax-forms, PDFs). Obsidian subfolders organize by topic (Beckham Law, Relocation, Immigration). But the top-level numbers match, so context-switching between tools is instant.
The Flow Between Layers
Information moves in one direction: from source to knowledge to operations. A tax document arrives as a PDF in Drive. You (or your AI) read it and extract the relevant facts into an Obsidian note. A script in your workspace might then read that Obsidian note to generate a report or update a dashboard.
In practice, information moves in one direction. I've never had a reason for scripts to write PDFs back to Drive, or for knowledge notes to become operational configs. If you find yourself copying a markdown file from Obsidian into your workspace so a script can read it, the script should probably just read the vault directly.
How AI Agents Read All Three
If you use an AI assistant (Claude, ChatGPT, a local model, anything), the three-layer structure determines how it accesses information.
The separation has a security benefit too. My AI agent can read the vault and workspace, but it doesn't have access to Drive (which has sensitive legal documents and financial records). That boundary exists because the layers are separate, not because I configured a complex permission system.
Setting This Up
1. Create the Drive structure
Create a shared folder in Google Drive with numbered top-level folders matching your domains. I use a folder called 00_AIProjects as the root, with project-specific subfolders inside it. The numbering does not need to be identical to your vault, but the domain names should match.
2. Create the Obsidian vault
Mirror the top-level folder numbers from Drive. Add the vault-specific folders that Drive does not need: Archive, System, Research, Journal. See the Knowledge Vault guide for the full vault setup including plugins, templates, and freshness metadata.
3. Set up the workspace
Your workspace is wherever your AI assistant or scripts live. Keep it separate from the vault and Drive. It should contain operational files only: scripts, configs, agent memory, build outputs, secrets. Nothing that a human needs to browse or search belongs here; that goes in the vault.
4. Define the boundaries
Write these rules down somewhere your AI can read them (AGENTS.md, a workspace config, or the vault itself). The boundaries are:
Drive = source documents. Files you received, downloaded, or were given. PDFs, contracts, spreadsheets, photos. Binary files and anything that needs its original formatting. Shared and accessible from any device.
Vault = extracted knowledge. Your notes, analyses, research, journal entries. Always markdown. Always with frontmatter. Always searchable. The vault is the single source of truth for "what do I know about X."
Workspace = operations. Scripts, configs, agent memory, secrets, templates, build artifacts. Things that do work, not things that store knowledge. If you would not want it showing up in an Obsidian search, it belongs here.
Why This Works
Three properties make this system durable. First, each layer uses the tool best suited to its content: Drive handles binary files and sharing, Obsidian handles linked markdown and queries, the filesystem handles executable code. Second, the mirrored numbering means you never lose context when switching tools. Third, the clear boundaries mean new files have an obvious home; you do not have to decide where something goes because the type of file determines the answer.
The system also degrades gracefully. If you stop using Obsidian, the knowledge is still plain markdown on disk. If you stop using Drive, the source documents are still local files. If you stop using AI agents, the folder structure and metadata still work for a human browsing manually. No single tool is a dependency.
For the full Obsidian setup (plugins, templates, freshness metadata, canonical promotion, Dataview dashboard), see the Knowledge Vault guide. For how AI agents maintain session memory across restarts, see How My AI Remembers.
Three Layers Setup Guide
The full three-layer architecture in a single markdown file. Folder structure, what-goes-where rules, agent access patterns, and boundary definitions. Hand it to your AI or follow it yourself.
Download .md