NeuroStack

Not a note-taking app. A memory layer for the notes you already have.

Your AI assistant forgets everything when the conversation ends. You ask it about the paper you summarised last week — it has no idea. You ask it to continue the chapter outline you built together — it starts from scratch.

And even when it does find your notes, it might find the wrong version. The thesis argument you reversed, the runbook endpoint you deprecated, the decision you made in April that you overturned in June. It cites these confidently. It has no idea they're wrong.

NeuroStack reads your existing Markdown notes — from Obsidian, Logseq, Notion exports, or any folder of .md files — indexes them into a searchable knowledge graph, and connects that graph to your AI. It detects when notes have gone stale before your AI cites them. Indexing never modifies your files; optional MCP write tools let an AI client author or edit notes through your git history when you want it to.

npm install -g neurostack && neurostack init

Works with Claude, Cursor, Windsurf, Gemini CLI, VS Code, and Codex — anything that supports MCP.

Your notes, in your control

By default, NeuroStack is a read-only indexing layer:

• Indexing, search, summaries, and graph analysis never modify your Markdown files

• All index data lives in NeuroStack's own separate database

• To remove it completely: neurostack uninstall — your notes are untouched

• Nothing ever leaves your machine, unless you configure a third-party LLM provider for summaries and embeddings

If your vault is a git repo, four opt-in MCP write tools let an AI client author and edit notes for you: vault_write_file, vault_delete_file, plus vault_read_file / vault_list_files. Every write commits and pushes to your git remote with a descriptive message — so every change is visible in git log, revertable with git revert, and serialised under a per-vault lock. Writes hard-reject invalid frontmatter, paths outside the vault, and hidden directories (.git, .obsidian, …). Because the tools are exposed to any client talking to neurostack serve, gate them at the transport (auth, tunnel, LAN only) if you put the MCP endpoint on the public internet.

Related MCP server: brain-mcp

Who this is for

You do not need to be a developer. If you take notes in Markdown — or can export your notes as Markdown from Obsidian, Notion, Bear, or Roam — NeuroStack works for you.

Get started in three steps

You will need Node.js installed (most computers already have it). The npm package handles the Python setup for you.

Step 1 — Install

npm install -g neurostack

Step 2 — Set up (takes about two minutes)

neurostack init

The setup wizard asks which vault folder to index, which mode to run (Lite or Full), and which profession pack to apply. It does everything else automatically.

Step 3 — Connect to your AI

For Claude Desktop:

neurostack setup-desktop

For Claude Code:

claude mcp add neurostack -- neurostack serve

For Cursor, Windsurf, Gemini CLI, or VS Code:

neurostack setup-client cursor      # or: windsurf, gemini, vscode

Done. Open a new conversation and ask your AI about something from your notes.

Everything runs on your machine. Choose a tier during neurostack init:

• Lite (~130 MB) — keyword search, link-based connections between notes, stale detection, MCP server. No GPU or Ollama required.

• Full (~560 MB) — adds semantic search (finds notes by meaning, not just keywords), AI-generated summaries, connections between notes, and topic clustering via local Ollama. GPU or 6+ core CPU recommended.

Non-interactive setup:

neurostack init --mode lite ~/my-notes    # lite mode
neurostack init --mode full ~/my-notes    # full mode

# PyPI
pipx install neurostack
pip install neurostack        # inside a venv
uv tool install neurostack

# One-line script
curl -fsSL https://raw.githubusercontent.com/raphasouthall/neurostack/main/install.sh | bash

# Lite mode (no ML deps)
curl -fsSL https://raw.githubusercontent.com/raphasouthall/neurostack/main/install.sh | NEUROSTACK_MODE=lite bash

On Ubuntu 23.04+, Debian 12+, and Fedora 38+, bare pip install outside a virtual environment is blocked by the operating system. Use npm, pipx, or uv tool install instead.

To uninstall: neurostack uninstall

What it actually feels like

The researcher. You ask Claude to help write the methodology section. Instead of starting from scratch, it already knows you've read 50 papers on complementary learning systems, that you settled on a particular framing in January, and that the meta-analysis you were relying on has been flagged as stale — it keeps appearing in searches where it no longer fits. You check it, update the note, and the AI's next answer reflects where your thinking actually is.

The writer. You ask Cursor to help with chapter eleven. It knows Elena's backstory from chapter two, the decision you made in your world-building notes to keep magic systems implicit, and that you changed her last name in a revision three weeks ago. No contradictions.

The DevOps engineer. You ask about the deployment runbook for the auth service. NeuroStack surfaces it — but also flags it as stale. You check it. The endpoint was renamed six weeks ago. You fix the note. The next time anyone asks, they get the right answer.

The student. You're revising three weeks before exams. You ask your AI what's on the syllabus for Module 4. It searches your notes — and stale detection tells you two of the topics were in last year's module structure, which you replaced when the course was restructured. You know what to revise. You don't waste time on dropped content.

The data scientist. You ask about the hyperparameters from your best experiment. NeuroStack returns the results from the rerun, not the original — because you updated that note, and the update is reflected in the index.

What makes it different

NeuroStack is not a replacement for Obsidian, Notion, or any note-taking app. It sits on top of what you already use and adds what they don't have.

Stale detection is the feature no other tool offers. When a note keeps appearing in contexts where it no longer fits — a deprecated API, a reversed decision, a superseded paper — NeuroStack flags it and demotes it in future results. Without this, your AI confidently cites information that is no longer true.

Profession packs

When you run neurostack init, you choose a profession pack. Each one configures NeuroStack with templates, folder structures, and AI guidance suited to how your profession actually uses notes.

Apply a pack to an existing vault without losing any notes:

neurostack scaffold researcher ~/my-notes    # or: writer, student, developer, devops, data-scientist

You can also import an existing Markdown directory:

neurostack onboard ~/my-notes

How retrieval works

Most memory tools give your AI a wall of text and let it figure out what's relevant. NeuroStack is tiered. It starts with the cheapest retrieval that answers the question and escalates only when it needs to.

Simple factual questions resolve at ~15 tokens. Deep dives get full context. Your AI spends its attention budget where it matters.

Your AI remembers decisions

Across sessions, your AI can save and retrieve typed memories: observations, decisions, conventions, learnings, bugs. When you start a new session, those memories are surfaced automatically.

"We decided to keep authentication stateless." "The thesis framing shifted from consolidation to complementary learning systems." "Elena's surname changed from Vasquez to Reyes in the chapter 7 revision."

These aren't just notes. They're things your AI remembers you decided together. They survive /clear. They survive closing the terminal. They survive switching machines.

neurostack memories add "revised thesis framing to CLS, not just consolidation" --type decision --tags "thesis,neuroscience"
neurostack memories search "thesis direction"

Learns from your AI sessions

NeuroStack can scan your past AI conversations, extract the key decisions, observations, and learnings, and save them as memories — automatically. No manual work.

neurostack harvest --sessions 5          # extract insights from last 5 sessions
neurostack hooks install                 # set up hourly auto-harvest

Supports Claude Code, VS Code, Codex CLI, Aider, and Gemini CLI session formats.

Keeps itself current

Your vault changes. NeuroStack watches it.

neurostack watch     # auto-index on vault changes

The index updates as you write. Stale detection runs continuously. You don't maintain it — it maintains itself.

What changes day-to-day

How your vault is stored

~/your-vault/                           # your Markdown files (not modified by indexing; AI clients can edit via opt-in MCP write tools)
~/.config/neurostack/config.toml        # configuration
~/.local/share/neurostack/
    neurostack.db                       # SQLite + FTS5 knowledge graph
    sessions.db                         # session transcript index

NeuroStack reads your vault. By default, it writes nothing back — all index data lives in its own SQLite databases. The opt-in MCP write tools (vault_write_file / vault_delete_file) are the one exception: they create or edit .md files in the vault and commit + push the change to your git remote on the spot.

Memory write-back (opt-in)

Memories live in SQLite by default, so they're invisible in Obsidian and vanish if the database is lost. Turn on write-back to persist qualifying memories as markdown files you own:

[writeback]
enabled = true                 # opt-in; default false
path = ".neurostack"           # quarantine dir, relative to vault_root
include_observations = false   # also write the noisier observation/context types

• Files land under {vault_root}/.neurostack/memories/<type>/<YYYY-MM>/<uuid>.md. NeuroStack only ever writes inside that one directory — your notes are never touched.

• Only persistent (no-TTL) decision / convention / learning / bug memories are written; ephemeral (TTL) memories never are.

• The database stays the source of truth; files are readable exports. vault_remember / vault_update_memory / vault_forget / vault_merge keep the files in step automatically.

• The directory self-ignores via its own .gitignore so memories stay out of git until you opt in (delete that file to version them). NeuroStack never commits on your behalf.

• neurostack migrate write-back [--dry-run] exports existing memories; neurostack sync reconciles files against the DB (the DB wins on conflict).

Search & retrieval

Context & insights

Memories

Sessions

Vault files (opt-in write surface — git-backed)

# Setup
neurostack init                          # one-command setup: deps, vault, index
neurostack init --mode full ~/brain      # non-interactive full mode
neurostack onboard ~/my-notes            # import existing Markdown notes
neurostack scaffold researcher           # apply a profession pack
neurostack scaffold --list               # see all packs
neurostack update                        # pull latest source + re-sync deps
neurostack uninstall                     # complete removal

# Search & retrieval
neurostack search "query"                # hybrid search
neurostack ask "question"                # RAG Q&A with citations
neurostack tiered "query"                # tiered: triples -> summaries -> full
neurostack triples "query"               # knowledge graph triples
neurostack summary "note.md"             # AI-generated note summary
neurostack related "note.md"             # semantically similar notes
neurostack graph "note.md"               # wiki-link neighborhood
neurostack communities query "topic"     # GraphRAG across topic clusters
neurostack context "task" --budget 2000  # task-scoped context recovery
neurostack brief                         # session briefing

# Maintenance
neurostack index                         # build/rebuild knowledge graph
neurostack watch                         # auto-index on vault changes
neurostack decay                         # excitability report
neurostack prediction-errors             # stale note detection
neurostack backfill [summaries|triples|all]
neurostack communities build             # rebuild topic clusters
neurostack reembed-chunks                # re-embed all chunks
neurostack export --include triples -o dump.json  # dump index data as JSON

# Memories
neurostack memories add "text" --type observation
neurostack memories search "query"
neurostack memories list
neurostack memories update <id> --content "revised"
neurostack memories merge <target> <source>
neurostack memories forget <id>
neurostack memories prune --expired

# Sessions
neurostack harvest --sessions 5          # extract session insights
neurostack sessions search "query"       # search transcripts
neurostack hooks install                 # hourly harvest timer

# Client setup
neurostack setup-client cursor           # or: windsurf, gemini, vscode, claude-code
neurostack setup-client --list
neurostack setup-desktop                 # Claude Desktop

# Diagnostics
neurostack stats                         # index health
neurostack doctor                        # validate all subsystems
neurostack demo                          # interactive demo with sample vault

Each feature models a specific mechanism from memory neuroscience:

Full citations: docs/neuroscience-appendix.md

FAQ

Does it modify my vault files? Not by default. Indexing, search, summaries, and every read tool leave your files untouched — all index data lives in NeuroStack's own SQLite databases. Four opt-in MCP write tools (vault_write_file, vault_delete_file, plus vault_read_file / vault_list_files) let an AI client author and edit notes; every write commits and pushes to your git remote, so changes are tracked and revertable. If your vault is not a git repo, the file is still written to disk but the commit step is skipped. Separately, opt-in memory write-back persists memories as markdown, but only ever inside the quarantined .neurostack/ directory — never alongside your own notes.

Do I need a GPU? No. Lite mode has zero ML dependencies. Full mode runs on CPU but summarization is slow without a GPU.

Do I need to know Python? No. The npm package handles everything. You never touch a virtualenv.

How large a vault can it handle? Tested with ~5,000 notes. FTS5 search stays fast at any size.

Can I use it without an AI client? Yes. The CLI works standalone and pipes into any LLM.

Is my vault private? Yes. Nothing leaves your machine, unless you point Full mode at a third-party LLM provider instead of local Ollama. In that case the text you index goes to that provider under its own policy.

What AI clients does it work with? Claude Code, Claude Desktop, Cursor, Windsurf, Gemini CLI, VS Code, and Codex — anything that supports MCP.

Requirements

• Linux or macOS

• Lite mode: Node.js + Python 3.11+. No GPU or Ollama required.

• Full mode: Ollama with nomic-embed-text and a summary model. GPU or 6+ core CPU recommended.

Get started

npm install -g neurostack
neurostack init

Two minutes. One wizard. Your AI stops forgetting.

• Contributing: CONTRIBUTING.md

• GitHub: github.com/raphasouthall/neurostack

• Sponsor: GitHub Sponsors | Buy me a coffee

Apache-2.0 — see LICENSE. No GPL dependencies.