Turns your existing notes, project folders, and Claude Code memory into an Obsidian vault that Claude Code uses as long-term memory.
It is not a template. It reads what you already have and builds the vault out of that, so it is useful on the first day instead of being a folder of blanks you have to fill in.
You run it once and then delete it.
Read this before deciding whether to use it.
The installer is a set of instructions that Claude Code follows. It ships with a test suite of 24 structural checks and a reference build, and those pass. But the installer itself has not been executed start to finish. The checks verify that the target is correct and internally consistent. They do not verify that following the instructions arrives there.
What that means in practice:
- It has never moved, renamed, or deleted anything, because it is not written to. But that property has been reviewed, not observed.
- On Windows, the launchers are the best-proven part: setup writes
.cmdfiles and never edits your PowerShell profile. That is deliberate — the profile approach failed on a clean Windows account, because a default account's execution policy resolves toRestrictedand PowerShell refuses to load any profile script at all. The line goes in correctly and simply never runs. - On macOS and Linux the shell-profile line is still the least proven step, and the one with the most annoying failure mode.
- If something goes wrong, UNDO.md reverses every change it makes. Reversing it by hand takes about a minute.
If you want to try it safely, run it against a folder of copies rather than your real notes. If you want to wait until someone has run it, that is a reasonable call and this section will change when that happens.
Read this part before anything else.
It reads: your Claude Code memory files, and any project folders or note folders you point it at. Nothing else. It never goes looking anywhere you did not name.
It copies. Your original files are never moved, renamed, or deleted. If setup fails halfway, everything you had is exactly where it was.
It writes:
- A vault, at a folder you choose.
- A working folder next to it, holding the configuration file, a set of background helpers, and a viewer that draws your notes as a link graph. Everything lands inside that one folder — nothing is installed system-wide, nothing is registered, and deleting the folder removes all of it.
- A shortcut on your Desktop, and a small file that makes a word you choose work in a terminal. Both open the same thing. On Windows your PowerShell profile is never touched and no security setting is changed. On macOS and Linux, one line is added to your shell profile; you are told which file and which line before it happens, and if it cannot be done you get the line to paste in yourself.
It skips anything that looks like a password or a key — .env files,
credentials, tokens. They are listed as skipped so you know they were seen and
deliberately passed over, and their contents are never read out.
Nothing is written until you say yes, twice. Once before it starts, and once after it shows you the full list of what it found and where each thing would go. You can strike anything off that list.
- Claude Code. You are running the installer inside it.
- Obsidian is optional. The vault is plain Markdown and works without it.
- git is optional. See below.
With git:
git clone https://github.com/matthewmernaugh/brain-setup.git
cd brain-setup
Without git: click the green Code button on this page, choose Download ZIP, and unzip it anywhere. That works exactly as well.
Then open Claude Code in that folder and type:
/setup
Five questions. Everything else is either detected from your machine or read out of your own files.
- What should I call you?
- What do you want to call me?
- What do you spend your time on? (pick as many as apply)
- Where should this live?
- What do you want to type to start it?
That is the whole interview. You also point it at your projects and notes, and you approve a list before anything is written.
- A vault organized around what you actually do, with your existing notes sorted into it and given consistent frontmatter.
- A note for each project it found, with its stack, status, and decisions.
- A list of open items pulled out of your own notes, so the vault starts with real work in it.
- A configuration file that tells Claude Code how to use all of it, in every future session.
- A set of background helpers, in that same folder: one that writes your notes up without interrupting you, one that checks the vault for broken links and missing index entries, one that reads your reference notes so the whole library does not have to be opened, and — if you do the kind of work that needs it — a research pair that gathers from multiple sources and then audits its own output.
- A link graph you can run locally to see how your notes actually connect.
- Optionally, a Linear workspace with a project per project and issues for the open items.
No opinions ship. No design rules, no writing style, no productivity system. The configuration carries only the mechanics that make the vault work. What you think about how to build things stays yours to write.
You start future sessions by double-clicking the Desktop shortcut, or by typing the word you chose in question 5. Both open Claude Code in the working folder, which is where it needs to be — not in the vault, and not in this repo.
Then delete this folder. It has done its job.
Windows is the reference platform and is the only one this has been verified on end to end.
macOS and Linux are supported but unverified. Almost everything is plain
Markdown and identical across platforms. Two things are not: the launchers,
where macOS and Linux still use a shell-profile alias rather than the .cmd
files Windows gets, and the link-graph viewer, which needs Node. Both are
written to fail loudly rather than half-apply — if a step cannot be done safely,
it prints exactly what to add and where, and carries on.
If something breaks on your platform, the vault still gets built. Open an issue.
- How it works — what happens in each of the nine phases, and what it writes.
- Undoing it — reversing every change, by hand, in about a minute.
- Troubleshooting — what to do when a step fails.
- Security — what it reads, what it refuses to touch, and how to report a problem.
MIT. See LICENSE.