MonkeyLLM

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(★ 9)

Knowledge engine for AI agents: your documents become a git-versioned markdown knowledge graph the agent navigates over MCP. Curated summaries, typed edges, cited answers, SQL over your spreadsheets, no chunking. Same 12B local model: 0/11 on multi-hop questions as top-k RAG, 11/11 as a navigator. Python, Apache-2.0, self-hostable.

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- - dco.yml
  - release.yml
  - tests.yml
- CODEOWNERS
- pull_request_template.md
- - api.js
  - background.js
  - clip.js
  - editor.css
  - editor.html
  - editor.js
  - i18n.js
  - LICENSE
  - manifest.json
  - offscreen.html
  - offscreen.js
  - permission.html
  - permission.js
  - popup.css
  - popup.html
  - popup.js
  - README.md
  - region.js
- - docker-compose.yml
  - Dockerfile
  - LICENSE
  - pyproject.toml
  - README.md
- - .gitignore
  - check-ask-window.mjs
  - check-consoles.mjs
  - check-hands.mjs
  - check-skill.mjs
  - check-tags.mjs
  - check-trail.mjs
  - check-window.mjs
  - index.html
  - LICENSE
  - package-lock.json
  - package.json
  - postcss.config.js
  - tailwind.config.js
  - vite.config.js
- baselines.py
- chunks.py
- questions-locate-v1.json
- questions-locate-v1.md
- questions-v1.json
- questions-v2.json
- questions-v3.json
- questions-v4.json
- questions-wide.json
- regrade.py
- run_bench.py
- README.md
- - README.md
- banner.png
- design-troop-fork-tier.md
- extending.md
- ingest-tools.md
- linkedin-cover.png
- linkedin-page-cover-tall.png
- linkedin-page-cover.jpg
- linkedin-page-cover.png
- [email protected]
- local-inference.md
- logo-dark.png
- logo-light.png
- logo.png
- model-notes.md
- monkeyllm-arquitetura.md
- monkeyllm-roadmap.md
- monkeyllm-spec-v0.1.md
- monkeyllm-spec-v0.10.md
- monkeyllm-spec-v0.11.md
- monkeyllm-spec-v0.12.md
- monkeyllm-spec-v0.13.md
- monkeyllm-spec-v0.14.md
- monkeyllm-spec-v0.15.md
- monkeyllm-spec-v0.16.md
- monkeyllm-spec-v0.17.md
- monkeyllm-spec-v0.18.md
- monkeyllm-spec-v0.19.md
- monkeyllm-spec-v0.2.md
- monkeyllm-spec-v0.20.md
- monkeyllm-spec-v0.21.md
- monkeyllm-spec-v0.22.md
- monkeyllm-spec-v0.23.md
- monkeyllm-spec-v0.24.md
- monkeyllm-spec-v0.25.md
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- monkeyllm-spec-v0.27.md
- monkeyllm-spec-v0.28.md
- monkeyllm-spec-v0.29.md
- monkeyllm-spec-v0.3.md
- monkeyllm-spec-v0.30.md
- monkeyllm-spec-v0.31.md
- monkeyllm-spec-v0.32.md
- monkeyllm-spec-v0.33.md
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- monkeyllm-spec-v0.37.md
- monkeyllm-spec-v0.38.md
- monkeyllm-spec-v0.39.md
- monkeyllm-spec-v0.4.md
- monkeyllm-spec-v0.40.md
- monkeyllm-spec-v0.41.md
- monkeyllm-spec-v0.42.md
- monkeyllm-spec-v0.43.md
- monkeyllm-spec-v0.44.md
- monkeyllm-spec-v0.45.md
- monkeyllm-spec-v0.46.md
- monkeyllm-spec-v0.47.md
- monkeyllm-spec-v0.48.md
- monkeyllm-spec-v0.49.md
- monkeyllm-spec-v0.5.md
- monkeyllm-spec-v0.50.md
- monkeyllm-spec-v0.51.md
- monkeyllm-spec-v0.52.md
- monkeyllm-spec-v0.53.md
- monkeyllm-spec-v0.54.md
- monkeyllm-spec-v0.55.md
- monkeyllm-spec-v0.56.md
- monkeyllm-spec-v0.57.md
- monkeyllm-spec-v0.58.md
- monkeyllm-spec-v0.59.md
- monkeyllm-spec-v0.6.md
- monkeyllm-spec-v0.60.md
- monkeyllm-spec-v0.61.md
- monkeyllm-spec-v0.62.md
- monkeyllm-spec-v0.63.md
- monkeyllm-spec-v0.64.md
- monkeyllm-spec-v0.65.md
- monkeyllm-spec-v0.66.md
- monkeyllm-spec-v0.67.md
- monkeyllm-spec-v0.68.md
- monkeyllm-spec-v0.69.md
- monkeyllm-spec-v0.7.md
- monkeyllm-spec-v0.70.md
- monkeyllm-spec-v0.71.md
- monkeyllm-spec-v0.72.md
- monkeyllm-spec-v0.73.md
- monkeyllm-spec-v0.74.md
- monkeyllm-spec-v0.75.md
- monkeyllm-spec-v0.76.md
- monkeyllm-spec-v0.77.md
- monkeyllm-spec-v0.78.md
- monkeyllm-spec-v0.79.md
- monkeyllm-spec-v0.8.md
- monkeyllm-spec-v0.80.md
- monkeyllm-spec-v0.81.md
- monkeyllm-spec-v0.9.md
- social-preview.png
- studio-forest-views-design.md
- - harvest.py
  - mcp_demo.py
  - questions-buried.json
  - questions-failed.json
  - questions.json
  - resultdo_01.txt
  - run_demo.py
- - LICENSE
  - main.py
  - manifest.json
  - README.md
- - build_bench_forest.py
  - build_dump.py
  - build_fixture.py
  - build_wide_forest.py
- monkeyllm-paper.md
- bench_locate.py
- build_brand_art.py
- convergence.py
- dev-studio.sh
- i18n.py
- junit_to_html.py
- measure_curation.py
- serve_llm.py
- setup_models.py
- - __init__.py
  - canopy.py
  - catalog.py
  - cli.py
  - cli_ext.py
  - curator.py
  - dialect.py
  - errors.py
  - fetch.py
  - forest.py
  - gardener.py
  - gitops.py
  - harvest.py
  - indexer.py
  - links.py
  - lint.py
  - models.py
  - parser.py
  - ranger.py
  - server.py
  - signatures.py
  - snapshot.py
  - telemetry.py
  - tokens.py
  - trails.py
  - vine.py
  - windows.py
- README.md
- T01-phase1-helicopter-closeout.md
- T02-english-normalization.md
- T03-troop-orchestrator.md
- T04-phase2-living-bank.md
- T05-publication-readiness.md
- T06-bench-multihop-hardening.md
- T07-station-host.md
- T08-scoped-vine-policies.md
- T09-studio-ui.md
- T10-studio-forest-views.md
- T10.1-compose-review.md
- T11-answer-store.md
- T12-snapshot-travel.md
- T13-browser-clipper.md
- T14-media-in-answers.md
- T15-first-minute-and-handbook.md
- T18-extensions.md
- conftest.py
- test_answer_prompts.py
- test_bench_baselines.py
- test_body_shape.py
- test_budgets_telemetry.py
- test_canopy_vector.py
- test_containment.py
- test_content_policy.py
- test_curator.py
- test_dataset_adoption.py
- test_dataset_curation.py
- test_demo_loop.py
- test_dense_share.py
- test_derive_terms_languages.py
- test_docx_converter.py
- test_embed_clock.py
- test_fetch_snapshot.py
- test_gardener.py
- test_gardener_rollup.py
- test_gauntlet.py
- test_harvest.py
- test_infra.py
- test_init_forest.py
- test_llm_providers.py
- test_locate_terms.py
- test_mcp_demo.py
- test_media_stub.py
- test_multi_forest.py
- test_parser_models.py
- test_payload_policy.py
- test_plant_dataset.py
- test_query_budget.py
- test_query_security.py
- test_ranger.py
- test_read_ergonomics.py
- test_read_primitives.py
- test_repo_hygiene.py
- test_signatures.py
- test_skill_console.py
- test_sniff.py
- test_sniff_memo.py
- test_station_admin_scope.py
- test_station_answer_progress.py
- test_station_answer_store.py
- test_station_answer_terms.py
- test_station_api.py
- test_station_audit.py
- test_station_binding_budget_repair.py
- test_station_clipper.py
- test_station_compose_review.py
- test_station_credentials.py
- test_station_env_providers.py
- test_station_explain.py
- test_station_first_run.py
- test_station_forage.py
- test_station_jobs.py
- test_station_lifecycle.py
- test_station_maintenance.py
- test_station_map.py
- test_station_mcp.py
- test_station_models.py
- test_station_pair.py
- test_station_payload.py
- test_station_people.py
- test_station_reindex.py
- test_station_reply_budget.py
- test_station_scoping.py
- test_station_studio_routes.py
- test_station_v052_surface.py
- test_station_view.py
- test_station_vision.py
- test_station_warm.py
- test_station_webhooks.py
- test_studio_audit_console.py
- test_studio_calls.py
- test_studio_data_console.py
- test_studio_history.py
- test_studio_i18n.py
- test_studio_routes.py
- test_tend.py
- test_trail_panel.py
- test_troop.py
- test_v054_reads.py
- test_v054_wire.py
- test_v055_lock.py
- test_v056_document.py
- test_v056_prune.py
- test_v056_station.py
- test_v057_reads.py
- test_v057_station.py
- test_v058_document.py
- test_v058_station.py
- test_v059_coverage.py
- test_v059_station.py
- test_v061_surface.py
- test_v062_sniff_cold.py
- test_v075_console.py
- test_v075_lang.py
- test_v075_recurate.py
- test_v075_scent.py
- test_v075_tags.py
- test_v075_votes.py
- test_v076_window.py
- test_v077_mcp_clarity.py
- test_v078_upload_passport.py
- test_v079_walk_window.py
- test_v080_consoles.py
- test_v080_extensions.py
- test_v080_station_extensions.py
- test_v080_whisper.py
- test_v081_authoring.py
- test_version_agreement.py
- test_view.py
- test_windows.py
- test_write_primitives.py
- __init__.py
- orchestrator.py
.dockerignore
.env.example
.gitignore
CLAUDE.md
CONTRIBUTING.md
docker-compose.yml
LICENSE
LICENSING.md
NOTICE
pyproject.toml
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// repository documentation

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**A knowledge engine for AI agents: a new way to query your data.** Your
documents become a git-versioned markdown knowledge graph an agent
navigates over MCP: curated summaries, typed edges, cited answers, SQL
over your spreadsheets, nothing chunked into anonymous fragments.

This repository is **not an application**. Knowledge lives in a
**forest**: a git-versioned tree of markdown nodes, each carrying a
curated, scent-bearing passport. An AI does not get handed a retrieval
dump. It **navigates**: drops in through search, follows typed edges,
reads exactly the node it needs, and plants what it learns. Successful
hunts deposit pheromone and mint shortcut links, so the corpus itself
learns from use.

<div align="center">
  <img src="https://raw.githubusercontent.com/JimmyWesley/MonkeyLLM/main/docs/guide/assets/graph-sample.png" alt="A real knowledge forest: 1,877 nodes across 49 branches, seen in the Explore console" width="900"/>
  <br/>
  <sub>A real forest: 1,877 nodes across 49 branches. Every cluster is a
  branch, every dot a node; solid lines are curated trails, dashed ones are
  shortcuts a hunt discovered, and the glow is pheromone left by use.</sub>
</div>

The number that made us write it down: on a benchmark where **every
question needs ≥3 chained hops**, the *same* 12B local model scores
**0 / 11 as a classic top-k RAG reader** and **11 / 11 (100%) as a forest
navigator**, at **0.66×** the token cost per correct answer of an
iterative-RAG baseline, on a single consumer GPU. If your first reaction
is *"I need to test whether this actually serves my case"*, good. Every
number is reproducible from committed scripts, and the whole design is
written down in [the paper](https://github.com/JimmyWesley/MonkeyLLM/blob/main/paper/monkeyllm-paper.md).

Everything else in this repository exists *around* that engine. The
**Studio** console you see in the screenshots is not the product. It is
the **management layer**: the window where people watch, govern and teach
what the engine serves.

The spec is the truth: the latest `docs/monkeyllm-spec-v*.md` is
normative; code follows it, never the other way around.

## The engine, inside your own code

The engine is a plain Python package (**Apache-2.0**) with no host, no
server and no UI attached. Point it at a folder and you have a forest;
operate it from your own Python:

```bash
pip install monkeyllm                           # the monkeyllm package + vine CLI
vine init --forest ./brain --title "My brain"   # an empty forest, git and all
```

Straight from source, without waiting for a release:
`pip install "git+https://github.com/JimmyWesley/MonkeyLLM.git"`. Python
3.11+; the file converters of Part G are an extra
(`pip install "monkeyllm[ingest]"`), and contributors want the editable
install further down.

```python
from monkeyllm import Vine
from monkeyllm.harvest import harvest

vine = Vine("./brain")
vine.plant({"id": "inbox/_index", "type": "branch", "parent": "_index",
            "title": "Inbox", "summary": "Loose notes before they find a branch."})
vine.plant({"id": "inbox/first-note", "type": "note", "parent": "inbox/_index",
            "title": "First note", "summary": "Where this brain begins.",
            "body": "Planted from my own code."})

vine.locate("where does this brain begin?")   # ranked entry points, BM25, zero embeddings
harvest(vine, "first note")                   # one-shot retrieval: evidence + snippets, zero LLM
```

Every primitive an agent uses rides that same object (`locate`, `look`,
`move`, `pick`, `scan`, `sniff`, `query`, `plant`, `graft`, `tend`), each
token-budgeted, each truncation explicit. The Gardener (`vine adopt` /
`vine sync`) mirrors an existing document tree into a forest, and the
Ranger (`vine ranger`) keeps it healthy over time.

And the same forest speaks **MCP** to any agent, straight from the CLI:

```bash
vine serve --forest ./brain                    # stdio MCP server
vine serve --forest ./brain --transport http   # or over HTTP
```

Claude Code, or any MCP-capable runtime, then holds the forest's tools:
no host, no accounts, your machine, your ecosystem.

## Anything you feed it becomes navigable

You do not prepare your files for the engine. You hand them over and the
**Gardener** converts, summarises and commits each one, through the same
pipeline whether it runs from the command line (`vine adopt`), from the
console, or from your browser:

| What you drop in | What it becomes |
|---|---|
| `.md`, `.markdown`, `.txt` | a `note`; the text is already the body |
| `.docx` | a `document`: headings and paragraphs as markdown |
| `.pdf` | a `document`, through a one-line converter hook, using any CLI extractor you trust ([how](https://github.com/JimmyWesley/MonkeyLLM/blob/main/docs/ingest-tools.md)) |
| `.csv` | a **dataset**: a real SQLite table, queried with read-only SQL |
| `.json` | a dataset when it is a flat table, otherwise a `document` holding the JSON |
| `.xlsx`, `.xls` | a dataset **per sheet**, with types inferred |
| `.db`, `.sqlite`, `.sqlite3` | adopted whole: the database itself becomes the payload, with a generated query manual and sample rows |
| `.png`, `.jpg`, `.jpeg`, `.gif`, `.webp` | a `media` node; on a Station with a `vision` model bound, it also gets a written description that search can find |
| `.mp3`, `.wav`, `.m4a`, `.ogg`, `.flac` | a `media` node carrying its passport |
| anything else | listed as `unsupported` in the report, by name, so you can see exactly what did not land |

Tabular files stop being documents: a spreadsheet becomes a table an
agent queries in SQL, with a `## Query manual` and sample rows written
into its passport, so a model knows which tables and columns exist before
it asks. What they *mean* is the one thing a machine cannot infer, so a
person writes it in a `## Notes` section that travels with the dataset
everywhere it is read.

`.docx`, `.xlsx` and `.xls` need the optional `ingest` extra
(`pip install -e ".[ingest]"`). PDFs need a converter hook, because a good
extractor is a heavyweight (often copyleft) dependency this project will
not force on you: name the tool in `_meta/gardener.yaml` and it joins the
pipeline. Everything else in the table works out of the box.

![Sending files into a forest from the Ingest console](https://raw.githubusercontent.com/JimmyWesley/MonkeyLLM/main/docs/guide/assets/ingest.png)

Drop files, mirror a whole folder the host can read, or write a document
in place: each one arrives with a curated passport, and a batch is a job
you can watch. Nothing is chunked and forgotten. Every document becomes a
node with a name, a summary and edges.

### And from the browser

The **Clipper** (`apps/clipper/`) is a Chrome/Edge/Brave extension that
turns the page you are reading into a forest: the readable article or just
your selection as markdown, a screenshot or a dragged region as a `media`
node. Drag the region, adjust it by its handles, mark it up (arrow, box,
pen, text label) and leave a note for the Gardener, typed or dictated. The
clip lands with the page's address attached, so it can always be traced
back.

<div align="center">
  <table>
    <tr>
      <td align="center" width="30%">
        <img src="https://raw.githubusercontent.com/JimmyWesley/MonkeyLLM/main/docs/guide/assets/clipper.png" width="250" alt="The Clipper popup: clip, capture, write or ask"/>
      </td>
      <td align="center" width="70%">
        <img src="https://raw.githubusercontent.com/JimmyWesley/MonkeyLLM/main/docs/guide/assets/sample-clipper.png" width="620" alt="Capturing and annotating a region of a page, with a note for the Gardener"/>
      </td>
    </tr>
    <tr>
      <td align="center"><sub>One click: clip, capture, write, or ask the forest.</sub></td>
      <td align="center"><sub>Drag a region, annotate it, leave a note, then capture.</sub></td>
    </tr>
  </table>
</div>

It holds a paired key of its own, never your password, and the Station
serves the build at `/clipper.zip`, offered on the console's own rail: a
key that can only narrow your access is self-service, so getting the
extension is too.

## Quick start (development)

```bash
pip install -e ".[dev]" && pip install -e apps/station
python -m pytest -q
python forests/scripts/build_fixture.py
python -m monkeyllm.cli validate --forest forests/forest-fixture
```

## The management layer (Station + Studio)

When a forest must be a **shared, governed asset** instead of a personal
directory, the **Station** (spec Part J) wraps the untouched engine with
identity, per-forest policy, audit and model bindings, serving REST under
`/v1` and MCP under `/mcp`. It also serves the **Studio**, the web console:

Ask questions that arrive with their sources, walk the tree as a living
graph, query datasets in SQL, feed the forest from uploads and the browser
Clipper, grant scoped access, and hand your own AI the skill that makes
the forest its persistent memory. The console is where the engine's
possibilities become visible, but whatever it shows, an API client holding
the same key could fetch: there is no privileged path.

## Documentation

**[The MonkeyLLM Handbook](https://github.com/JimmyWesley/MonkeyLLM/blob/main/docs/guide/README.md)**: install it, sign in
for the first time, use and feed the forest, connect your own AI over MCP
(including the Claude Code skill the Studio generates), and govern the
deployment. English, Português and Español, with screenshots.

## The paper

**[MonkeyLLM: Stigmergic Navigation of Knowledge Forests](https://github.com/JimmyWesley/MonkeyLLM/blob/main/paper/monkeyllm-paper.md)**,
replacing retrieval-augmented generation with agentic foraging by small
language models. The forest, the scent contract, the ten budgeted
primitives, the pheromone economy, and the **Forest Principle** (*spend
intelligence on the environment so you can spend less on the model*), with
every benchmark number reproducible from this repository.

## Roadmap

The engine, the Station, the Studio and the Clipper are built and
measured; the phases below are what comes next. The full plan, with exit
criteria per phase, is [`docs/monkeyllm-roadmap.md`](https://github.com/JimmyWesley/MonkeyLLM/blob/main/docs/monkeyllm-roadmap.md);
the working backlog is [`tasks/`](https://github.com/JimmyWesley/MonkeyLLM/blob/main/tasks/README.md).

| Next | What it means | Where it stands |
|---|---|---|
| **Monkey Bench, officially** | The full benchmark run published with its traces, against top-k and iterative RAG baselines | 3 of 4 exit criteria met; the fourth re-measured as tokens-per-correct (0.66×) |
| **Convergence curve** | Proving hops-to-answer *drops* as a forest is used: the pheromone economy paying off, and the paper's signature chart | measured once; the criterion is not met yet, and the findings (floor effect, pheromone cross-talk) are themselves results |
| **The Troop** | Parallel foragers with a judge: today an accuracy amplifier, not yet a speed one | 8/8 accuracy on both arms; the wall-clock criterion needs a deeper corpus |
| **Entities and typed edges at ingest** | The Gardener extracting people, places and relations, beyond today's summaries and `related-to` proposals | designed (Part G), needs a spec bump |
| **Station hardening** | OIDC sign-in, per-principal quotas | the rest of Part J ships today |
| **Publication** | The paper deposited with a DOI (Zenodo / arXiv) | written; deposit pending |
| **Phase 3: a faster core** (conditional) | Rust for Catalog + Canopy behind the same contracts, **only if** telemetry proves the bottleneck | deliberately not started; the SLM dominates the cost today |

The rule the project holds itself to: **no phase starts before the
previous one passes its exit criteria, and no optimization happens
without a measurement that justifies it.** The benchmark is the judge,
not intuition, which is why a criterion that did not pass is written down
above instead of quietly dropped.

## Layout

| Path | What lives there |
|---|---|
| `src/monkeyllm/` | **the engine**: `vine` CLI, 10 primitives, harvest, Gardener (ingest), Ranger (maintenance), catalog, Canopy |
| `apps/station/` | the deployable host: REST `/v1`, MCP `/mcp`, serves the Studio |
| `apps/studio/` | the web console (React/Vite, built into the Station image) |
| `apps/clipper/` | the browser extension: clip the page you are reading into a forest |
| `paper/` | the paper: design, vocabulary, benchmarks, authorship |
| `forests/` | generated forests (gitignored except `forests/scripts/`); rebuild, never edit |
| `bench/` | Monkey Bench: chunker, RAG baselines, runner |
| `scripts/` | infra + measurement (local models, bench, curation metrics) |
| `docs/` | the spec, the handbook (`docs/guide/`) and design notes |
| `tasks/` | backlog, one file per task |

## Run the whole environment (Docker)

One container serves frontend and backend; data persists in named volumes:

```bash
cp .env.example .env   # fill in what you use
docker compose up --build -d
```

See [deploy/README.md](https://github.com/JimmyWesley/MonkeyLLM/blob/main/deploy/README.md) for the full walkthrough,
including Dokploy and optional local llama.cpp inference.

## License

Two licenses, split along the line the architecture already draws:

- **Engine** (`src/monkeyllm/`, the spec, the benchmark, the tooling):
  [Apache-2.0](https://github.com/JimmyWesley/MonkeyLLM/blob/main/LICENSE). The MCP contract is meant to spread.
- **Host** (`apps/station/`, `apps/studio/`, `apps/clipper/`):
  [AGPL-3.0-only](https://github.com/JimmyWesley/MonkeyLLM/blob/main/apps/station/LICENSE). Self-hosting is free and
  unrestricted; offering it as a managed service means opening your stack.

See [LICENSING.md](https://github.com/JimmyWesley/MonkeyLLM/blob/main/LICENSING.md) for the full map, the commercial option and
the DCO requirement for contributions.

MonkeyLLM

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