If you're following our full second-brain walkthrough (or building your own version some other way), this is the quick reference for what each file and folder is actually for — bookmark it and come back whenever a term trips you up.
The core three
Vault
The top-level folder that holds everything. Usually managed in Obsidian (free, and you own the plain-text files directly), but any folder your AI assistant can read and write to works.
raw/
Your inbox. Unprocessed material lands here exactly as saved — an article, a transcript, a meeting export. Nothing here has been synthesized yet; it's the source material, kept untouched.
wiki/
What your AI assistant builds from what's in raw/ — organized, synthesized pages by topic, person, or project. This is the part that actually gets smarter over time as more goes into raw/.
If you only set up three things, make it these. Everything else on this page is a refinement you add once these three are working.
The identity files
user.md
Who you are — your role, how you communicate, the frameworks or principles you operate by. This is what stops the AI from giving you generic advice that ignores your actual situation.
soul.md
How the AI should act — tone, values, personality. Some setups fold this into user.md; splitting it out just makes it easier to tweak the AI's voice without touching your own description.
identity.md
Optional, but a nice touch — a name and a role for the assistant itself ("part chief-of-staff, part research partner"). Purely cosmetic, but it changes how the interactions feel.
Our AI Prompt Builder is built for exactly this shape of file — role, tone, always/never rules, one example. The second-brain walkthrough uses it to draft user.md step by step.
Files that keep it honest
index.md
A running catalog of everything in the wiki. Without this, both you and the AI end up re-discovering the same notes repeatedly instead of building on them.
log.md
A plain record of what changed and when. This is what lets you trust an automated system — you can always check exactly what it touched and why.
Category folders
Add these once you notice the same kind of thing keeps needing somewhere to live — not before. Common ones:
people/
One file per person — how you met, contact details, things you know about them, past conversations. Useful the moment you have to ask "wait, where did I meet this person again?"
projects/
What you're tracking, timestamped, with context on status and blockers.
decisions/
What you decided, why, and what the alternatives were — genuinely useful when a similar decision comes up again months later.
meetings/
Notes and outcomes from calls and conversations — a natural fit if you already use a meeting-transcription tool that can export notes straight into this folder.
daily/
A short daily dump — a few lines on what happened. Low effort, and it becomes the raw material your nightly compounding pass works from.
One advanced pattern: MOCs
MOC (Map of Content)
A single file that pulls together everything on one sprawling topic — think of it as a consolidated index for one subject instead of the whole vault. Not needed on day one; add one when a specific topic starts feeling scattered across too many separate notes.
The two habits that keep it alive
Ingest
The instruction that tells your AI to read what's new in raw/, update the wiki, and log what changed. Say this once clearly and you can re-run it — manually or on a schedule — indefinitely.
Compounding pass
A nightly or periodic review where the assistant connects related notes, cleans up duplicates, and flags anything worth your attention. This is what separates "a folder I can search" from a system that actually improves without you managing it by hand.
Frequently asked questions
No — start with a vault, a raw folder, a wiki folder, and one identity file. Add index.md, log.md, and category folders as the vault grows large enough to need them.
user.md is about you — your role, priorities, and how you communicate. soul.md is about the assistant — the tone and values it should adopt when it talks to you. Some setups combine both into one file.
raw is untouched source material — articles, transcripts, meeting notes, exactly as saved. wiki is what your AI assistant generates from that material — organized, synthesized pages by topic, person, or project.
No. Manually asking your assistant to process the raw folder works fine at first. Automation is worth adding once feeding the vault becomes a daily habit.