rhizome-cli 0.1.0

A rhizomatic Zettelkasten system for atomizing and connecting notes

rhizome

A rhizomatic Zettelkasten system that atomizes notes and synthesizes connections using local LLMs

Motivation

All of this is motivated by the fear that I'll write the same thing in my notes twice, miss an important connection, or impose an artificially skewed structure on my notes. Therefore, I decided to cultivate a personal knowledge management system that does the following:

passively atomizes heterogenous, unstructured notes

Why spend my time doing what I could have automated? Instead of manually defined backlinks in a PKM system, assign them using embedding similarity

actively synthesizes new connections

Again, instead of relying on manual, human-assigned connections, let embedding models make them in the background.

enables writing with a contextual foundation

Creating a rhizomatic machine that takes a given piece of context, searches through an embedding space, and returns related ideas alleviates the fear of writing the same idea again.

A note on LLMs

While this idea was something I had a few years ago, I've relied on vibe coding (specifically, Claude Sonnet 4.5 with VSCode + Copilot) to build this system. I've looked through the code enough to feel confident using this on my own device, but please check it yourself.

Quick Start

# Install Ollama and pull a model
ollama pull llama3.1
ollama serve

# Install rhizome
source .venv/bin/activate
rhizome your_notes_folder

See USAGE.md for detailed instructions.

Output Structure

output/
├── chunks/          # Atomic ideas from your notes
│   ├── chunk-1.md  # type: chunk, source: [[original-file.md]]
│   └── chunk-2.md
└── plateaus/        # Connected ideas across chunks
    └── knowledge-synthesis.md  # type: plateau, synthesized content