Metadata-Version: 2.4
Name: matryca-plumber
Version: 1.9.1
Summary: Enterprise-grade, local-first autonomous background AI daemon and headless mutation plane for Logseq OG.
License: Apache-2.0
Project-URL: Homepage, https://github.com/MarcoPorcellato/matryca-plumber
Project-URL: Repository, https://github.com/MarcoPorcellato/matryca-plumber
Project-URL: Issues, https://github.com/MarcoPorcellato/matryca-plumber/issues
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: NOTICE
Requires-Dist: logseq-matryca-parser<2.0.0,>=1.1.1
Requires-Dist: pydantic<3.0.0,>=2.0.0
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Dynamic: license-file

# Matryca Plumber

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[![Platform](https://img.shields.io/badge/platform-macOS%20%7C%20Linux%20%7C%20Windows-lightgrey)](#-key-features--differentiators)
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[![Security](https://img.shields.io/badge/security-policy-important)](SECURITY.md)
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**Developed by [Marco Porcellato](https://github.com/MarcoPorcellato) · [Matryca.ai](https://matryca.ai)** — open-source local-first maintenance daemon for Logseq OG. The product name is **Matryca Plumber** (not “Matryca” alone). See [`docs/BRANDING.md`](docs/BRANDING.md).

> **v1.9 — Structural graph hygiene + agent DX.** Agentic Knowledge Management for Logseq OG: **enterprise-grade, local-first background AI** with Sovereign UI, typed CLI, and direct Markdown AST mutation (no Logseq HTTP API). **v1.9** adds **zero-LLM link rot checks** (`dead-link::` / `missing-asset::`), **Journey Log** on today's journal, CLI **`--json`**, **`matryca context load`**, and **`read subtree`** for token-efficient agent reads — on top of v1.8 **Zero-Prefill** prompts, bounded RAM, and cooperative bootstrap I/O for **16 GB CPU-only laptops**. Optional FastMCP stdio reuses the same `graph_dispatch` contract. Inspired by [Andrej Karpathy's LLM-Wiki vision](https://karpathy.ai/blog). **100% native Logseq AST parity**, OCC, versioned AI authorship stamping.

![Matryca Plumber — Agentic Knowledge Management for Logseq OG](images/matryca-plumber-1-5-10-demo.gif)

> "Logseq is building the best local outliner database. But AI Agent memory is at the very bottom of their roadmap. Matryca Plumber gives you that future today, safely bridging your local agents to your Logseq graph without waiting years." - Marco Porcellato - Matryca.ai chief architect and co-founder

Matryca Plumber is a **100% headless, sandboxed** **standalone daemon + CLI** that turns your local Logseq graph into a high token-density agentic workspace — **no network APIs and no Logseq desktop JSON-RPC**. It treats your vault as a **tree of blocks**, not a flat document store. Logseq OG remains optional: humans and the daemon co-edit the **same** `.md` trees on disk.

**Matryca Plumber** is not a one-shot script — it is an **enterprise-grade, local-first background AI daemon for Logseq**. It polls your graph on a duty cycle, calls a local LLM (LM Studio or Ollama), appends semantic indexes, runs optional cognitive lint modules, and logs every token transaction — **while you edit the same `.md` files in Logseq or leave the vault idle**. Optional **MCP-attached** sessions reuse the identical mutation plane for interactive queries; they are **not** required for background operation. Every write path mirrors Logseq's on-disk AST contract: page frontmatter at line 0, block properties contiguous to their parent bullet, namespace filenames encoded exactly like Logseq's Clojure Datalog layer, and **optimistic concurrency control** that aborts stale writes when you type during inference.

**Matryca Plumber** turns your local graph into a high token-density agentic workspace by continuously polling your notes, running local LLMs (like LM Studio or Ollama), appending semantic indexes, and healing broken links—all completely offline, while you work or sleep.

**Zero Cloud. Zero Data Leaks. 100% Native Logseq AST.**

---

## ⚠️ Important: Clone Your Graph First

Matryca Plumber edits your local `.md` files directly. While it features safe Optimistic Concurrency Control (OCC) to prevent data loss, **we strongly recommend testing it on a clone of your graph first**. This allows you to see the AI in action and explore its capabilities without affecting your primary notes.

**How to safely clone your graph (crucial if you use Logseq Sync):**
1. Make a copy of your entire Logseq graph folder on your computer (e.g., duplicate your `MyGraph` folder and rename it to `MyGraph_Test`).
2. Open Logseq, click on your graph name in the top left, and select **Add new graph**.
3. Choose the new `MyGraph_Test` directory.
4. **If you use Logseq Sync:** Do *not* enable Sync on this test graph. This ensures the AI's test edits remain strictly local and do not propagate to your other devices.
5. Alternatively, for a minimal test graph:
  a. Create an empty folder and add it as a new graph in Logseq.
  b. Close Logseq; copy only pages/, journals/, assets/ from production.
  c. Reopen and Re-index.
6. Point Matryca Plumber's `.env` configuration (`LOGSEQ_GRAPH_PATH`) to this test folder.

Once you are comfortable with how Matryca Plumber behaves and have tuned the safety tiers, you can point it to your main graph.

---

## 🚀 Quick Install & Getting Started

The fastest way to get started is using [uv](https://docs.astral.sh/uv/), the blazing-fast Python package manager.

### 1. Try it instantly (Zero-install)
Run the CLI directly without polluting your system. This **only opens the Sovereign UI** at [http://127.0.0.1:8500](http://127.0.0.1:8500) — it does **not** start graph maintenance until you complete the pre-flight checklist and click **Start Engine** (or run `matryca plumber start` separately).
```bash
uvx --from matryca-plumber matryca-plumber status
```
(`matryca-plumber status` is shorthand for `matryca plumber status`.)

### 2. Global Installation (Recommended)
Install the binary to use the `matryca` command anywhere:
```bash
uv tool install matryca-plumber
```

### 3. Open the control room (recommended first step)
```bash
matryca plumber status
# same as: matryca-plumber status
```
The browser opens the **Sovereign UI**. On **every** fresh visit, a **Pre-flight checklist** modal appears first (even if you already ran `matryca plumber start` in a terminal). Dismiss it with **Continue to dashboard** once the live checks are green, then click **Start Engine** in the header to launch the maintenance daemon from the UI.

**Optional — headless daemon before opening the UI:**
```bash
matryca plumber start    # background worker only; no browser
matryca plumber status   # UI still shows pre-flight; engine may already show IDLE/RUNNING
```

### 4. Set it and forget it (Background Service)
Install it as a LaunchAgent/systemd service so it wakes up with your OS:
```bash
matryca service install
```

### 5. Agent-native CLI (v1.9 — optional, no MCP required)

Same headless contract as MCP tools; add **`--json`** for structured stdout:

```bash
export LOGSEQ_GRAPH_PATH=/path/to/your/graph

matryca --json read page "My Project"
matryca context load "My Project"
matryca context load "My Project|aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa"
matryca --json read subtree '{"page":"My Project","block_uuid":"…","heading":"Implementation"}'
```

Full spec: [`docs/openspec/agent-dx.md`](docs/openspec/agent-dx.md). Background link checks: [`docs/openspec/link-verification.md`](docs/openspec/link-verification.md).

---

## 🧠 What does it actually do?

Unlike generic scripts, Matryca Plumber is a continuous background engine. When paired with a local LLM (**Gemma 4-E4b Instruct** via LM Studio or Ollama), it provides:

- **Semantic Indexing**: Automatically generates summaries, suggested tags, and cross-references for your pages.
- **Dangling Link Healing**: Finds broken `[[WikiLinks]]` and creates isolated seed pages for them.
- **Entity Consolidation**: Suggests `alias::` properties for overlapping concepts.
- **Auto-Split Dense Blocks**: Extracts oversized subtrees into new pages to keep your graph fast and readable.
- **Claude Desktop Integration (FastMCP)**: Seven MCP tools (five mega-tools + **`store_fact`** + **`ingest_document`**) query and mutate your graph headlessly. Set `MATRYCA_MCP_ENABLED=true` in `.env` only on machines where you trust the MCP host (stdio MCP is off by default; the host has full graph read/write with no separate authentication).
- **Telos & Identity (in-graph persona)**: Optional `pages/matryca___config.md` or `pages/matryca-config.md` with `- # Telos` and `- # AI Constraints` headings — injected into daemon LLM prompts and MCP output; **`store_fact`** appends durable preferences under Constraints ([`docs/openspec/identity-config.md`](docs/openspec/identity-config.md)).
- **Atomic document ingestion**: **`ingest_document`** parses external Markdown via an OS temp file (never under `pages/`), stamps fresh `id::` UUIDs, and appends to daily `Ingest/YYYY-MM-DD` or `MATRYCA_INGEST_PAGE`, with optional `LOG` / `GLOSSARY` ledgers ([`docs/openspec/ingest.md`](docs/openspec/ingest.md)).
- **Structural link verification (v1.9)**: Passive harvest of URLs and `assets/` paths into `.matryca_link_registry.json`; async HTTP HEAD + filesystem checks; OCC-safe **`dead-link::`** / **`missing-asset::`** block properties ([`docs/openspec/link-verification.md`](docs/openspec/link-verification.md)).
- **Agent-centric DX (v1.9)**: Global CLI **`--json`**, **`matryca context load`**, **`read subtree`**, and **Journey Log** (`## 🤖 Matryca Activity` on today's journal) ([`docs/openspec/agent-dx.md`](docs/openspec/agent-dx.md)).

---

## 🖥️ The Sovereign UI

Matryca Plumber is 100% headless, but it ships with a **Sovereign UI Cockpit** (`matryca plumber status` or `uvx … matryca-plumber status`). 
It's a local React dashboard running on `http://127.0.0.1:8500` that provides:
- **Pre-flight checklist** (modal on each UI open): operator guidance plus automated readiness checks before **Start Engine** is enabled.
- **Live Graph Telemetry**: See exactly what the AI is indexing in real-time.
- **Dynamic Impact**: Mathematically separates *Organic Human Mind* (your notes) from *Agent Cognition* (AI enhancements).
- **Zero-Trust Security**: Every REST call requires a Bearer token (`X-Matryca-Token`). Set `MATRYCA_UI_TOKEN` on shared hosts (or `MATRYCA_UI_REQUIRE_EXPLICIT_TOKEN=true`); session bootstrap is loopback-only; split rate limits for authenticated vs anonymous API traffic.
- **Trust & Safety Drawer**: Visually toggle what the AI is allowed to edit (Safe Mode, Augmented Mode, Surgeon Mode).

See [`SECURITY.md`](SECURITY.md) for the full operator hardening matrix (`MATRYCA_MCP_ENABLED`, graph path allowlist, shared LLM SSRF policy, log redaction).

### Pre-flight checklist (what you see in the app)

Matryca Plumber provisions missing runtime files automatically where possible (repo `.env` from `.env.example`, `matryca-l1/`, cache dirs, `matryca-wiki.yml`). The modal still walks you through setup so nothing surprises you on first run. It is developed by **Marco Porcellato** at **[Matryca.ai](https://matryca.ai)** — the same attribution shown in the Sovereign UI pre-flight wizard.

**Operator steps (same text as the UI wizard):**

1. **Control room connection** — If you can read this dashboard, the local API on port `8500` is up. Keep the window open while the engine runs.

2. **Logseq graph (test vault first)** — Point `LOGSEQ_GRAPH_PATH` at the **root** of a Logseq OG vault (the folder that contains `pages/`). Use a **clone** for your first run; do not enable Logseq Sync on test graphs. In the UI: **Settings** (gear) → **Logseq Graph Path** → absolute path → Save.

3. **Local LLM** — Start an OpenAI-compatible server (LM Studio, Ollama, etc.). In Settings set the base URL (e.g. `http://localhost:1234/v1`) and the **exact** model id, then **Refresh models** to confirm discovery.

   **Matryca Plumber** (by Marco Porcellato · Matryca.ai) is built for **offline, CPU-only** use on a typical **16 GB RAM** machine — no cloud subscription or discrete GPU required. The **recommended and tested** model is **Gemma 4-E4b Instruct** — set the exact id `gemma-4-e4b-it` in Settings, then **Refresh models**. For CPU inference, prefer **GGUF** weights at **`Q4_K_M`** or **`Q5_K_M`**. We are actively testing additional open models to improve CPU-only, 16 GB setups; Gemma 4-E4b Instruct is our current default. Avoid large **MoE** models (e.g. Llama 4 Scout): full weights still require 60GB+ RAM.

4. **First-run expectations** — **Phase 1** catalogs the entire graph (can take a long time on large vaults; v1.8 yields to the OS periodically during harvest). **Phase 2** processes roughly one LLM-heavy page per poll interval by default. After Phase 1, the daemon releases heavy in-memory indexes to keep RAM stable for long runs.

**Live checks** (re-run anytime with **Re-run checks**):

| Check | What it validates |
|-------|-------------------|
| Environment file | Repository `.env` exists (created from `.env.example` on first boot when possible). |
| Logseq graph path | `LOGSEQ_GRAPH_PATH` is set and points at a valid vault root. |
| L1 session memory | Sibling `matryca-l1/` (or configured `MATRYCA_L1_PATH` / wiki `memory_path`) is ready. |
| Local LLM endpoint | `LLM_BASE_URL` passes SSRF policy and `GET /v1/models` responds; warns if the configured model id is not listed. |

**Start Engine** stays disabled until every live check is green. If you started the daemon earlier with `matryca plumber start`, the UI may already show **IDLE** or **RUNNING** and **Start Engine** may be disabled — the pre-flight modal still opens so you can review settings; use **Pre-flight** in the header to reopen it later.

---

## ✨ Key Features & Differentiators

* 🤖 **100% Local-First & Headless:** No Logseq HTTP API required. It edits the `.md` files directly using atomic file I/O.
* 📐 **Exact Logseq AST Compliance:** True line-0 page frontmatter, block properties at +2 indent, and exact namespace encoding. Other tools break your graph; Matryca Plumber keeps it pristine.
* 🔐 **Optimistic Concurrency Control:** It snapshots `st_mtime` before inference and acquires the page lock **only for the write**. If you edited in Logseq while the model was thinking, the commit aborts. **No silent data loss** — and Logseq can still save during long local runs.
* 🪟 **Windows, macOS & Linux Support:** Runs safely in the background everywhere using a robust cross-platform lock (`.matryca_plumber_daemon.lock`).
* ⚡ **Context Acceleration Shield:** Shrinks megabyte-class pages to Phase 1 summaries or semantic skeletons before they reach the local LLM — essential on CPU-only hardware.
* 🛡️ **TRIZ-governed LLM resilience:** Caps completion tokens, balanced-brace JSON extraction, prose sanitization on compression/history paths, stateless ontology reports, and an 8k block-catalog cap on semantic index prompts — see [`docs/resilience-llm-json-triz.md`](docs/resilience-llm-json-triz.md).
* 🖥️ **Edge computing profile (v1.8):** KV-cache-aligned prompts (`PagePromptSession`), bounded RAM (BM25 postings-lite, semantic cache LRU, post-bootstrap teardown), and cooperative bootstrap I/O — tuned for **16 GB laptops** and vaults up to **~10,000** pages. See [docs/v1.8-OPTIMIZATION-PLAN.md](docs/v1.8-OPTIMIZATION-PLAN.md).
* 🔗 **Structural hygiene (v1.9):** Background link rot and missing-asset detection without LLM tokens; visible duty-cycle summaries in your daily journal.
* 🤖 **Agent-native CLI (v1.9):** `matryca --json …` for machine-readable stdout; `matryca context load` and `read subtree` to shrink context windows.

---

## 🛡️ Trust & Safety Risk Tiers

You are in control. Nothing mutates your prose unless you explicitly enable it in the UI.

| Mode | Risk | What it allows |
|------|------|----------------|
| 🟢 **Safe Mode** | Read-only | Semantic routing cache, entity consolidation (`alias::`), property hygiene — **never edits your bullet text**. |
| 🟠 **Augmented Mode** | Side-blocks | **Heal Dangling Links**, **Backpropagate Links** (appends foldable context sections) — your original bullets stay intact. |
| 🔴 **Surgeon Mode** | Inline edits | **Inline Semantic Corrections** (wraps concepts in `[[WikiLinks]]`), **Auto-Split Dense Blocks** — **strictly opt-in**. |

---

## ⚙️ Configuration Quickstart

Copy `.env.example` to `.env`. The only **required** variable is your graph path:

```env
LOGSEQ_GRAPH_PATH=/absolute/path/to/your/Logseq/graph
MATRYCA_LM_BASE_URL=http://localhost:1234/v1   # LM Studio or Ollama endpoint
MATRYCA_LM_MODEL=gemma-4-e4b-it                # Gemma 4-E4b Instruct — tested default

# Optional: Claude Desktop / Cursor MCP (off by default)
MATRYCA_MCP_ENABLED=true
```

On first start (daemon, CLI, MCP, or UI), Matryca Plumber **automatically creates** anything missing for a healthy runtime:

- **`logs/`** (or paths from `MATRYCA_PLUMBER_LOG_PATH` / `MATRYCA_LOGURU_LOG_PATH`)
- **`<parent-of-your-vault>/matryca-l1/`** — session rules beside the vault (not inside `pages/`); optional override via `MATRYCA_L1_PATH`
- **`<vault>/.matryca_semantic_cache/`**, **`templates/`**, and **`matryca-wiki.yml`** (from `matryca-wiki.example.yml` when absent)
- **In-memory graph index** at startup (AST cache); **identity** loaded when a Telos/Constraints config page exists

The **identity config page** is not auto-created (use Logseq or `store_fact`). **Ingest / LOG / GLOSSARY** pages are created on first `ingest_document` call. Optional `MATRYCA_INGEST_PAGE` pins a fixed inbox (e.g. `AI_Inbox`). See [`docs/openspec/identity-config.md`](docs/openspec/identity-config.md) and [`docs/openspec/ingest.md`](docs/openspec/ingest.md).

See [`docs/openspec/runtime-bootstrap.md`](docs/openspec/runtime-bootstrap.md) for rationale (L1 vs L2, idempotency, and what is intentionally *not* auto-created).

*(See [docs/ARCHITECTURE.md](docs/ARCHITECTURE.md) for advanced thermal pacing, context compression, and deep linter settings. Copy the full template from `.env.example` — it documents UI auth, rate limits, graph allowlists, and log redaction.)*

### Edge profile (large vaults / 16 GB RAM)

Copy the **v1.8 Edge computing & performance** block from [`.env.example`](.env.example). Highlights:

| Knob | Why |
|------|-----|
| `MATRYCA_BOOTSTRAP_YIELD_EVERY` | Keeps macOS/Windows responsive during Phase 1 file scans |
| `MATRYCA_RAM_BUDGET_MB` | Logs when daemon RSS exceeds a soft cap |
| `MATRYCA_BM25_MODE=ondemand` | Trade query latency for lower steady-state RAM |
| `MATRYCA_LLM_CLUSTER_HISTORY=false` | Shorter Ermes history — better KV reuse in cluster mode |
| `MATRYCA_CPU_SANDBOX=true` | Pin Plumber to idle cores; pair with manual LLM core mask |
| `MATRYCA_GRAPH_READ_MMAP=true` | Kernel-paged reads during Phase 1 regex catalog path |

Install CPU affinity support: `uv sync --extra edge` or `pip install matryca-plumber[edge]` (`psutil`).

Deep dive: [docs/v1.8-OPTIMIZATION-PLAN.md](docs/v1.8-OPTIMIZATION-PLAN.md) · [docs/v1.8-SOFTWARE-EDGE-PLAN.md](docs/v1.8-SOFTWARE-EDGE-PLAN.md) · [docs/openspec/llm-performance.md](docs/openspec/llm-performance.md)

**Load testing:** `uv run python scripts/gen_synthetic_graph.py /path/to/graph --count 1000` · **Slow CI:** `make perf`

---

## 🧑‍💻 Developer Setup

Want to contribute or run from source?

```bash
git clone [https://github.com/MarcoPorcellato/matryca-plumber.git](https://github.com/MarcoPorcellato/matryca-plumber.git)
cd matryca-plumber
make install

# Build the React frontend
cd frontend && npm install && npm run build && cd ..

# Run tests (550+ passing, Mypy strict)
make check

# Optional: slow memory / harvest soak tests
make perf
```

---

## 📚 Documentation Map

| Document | Description |
|----------|-------------|
| [`SYSTEM_PROMPT.md`](SYSTEM_PROMPT.md) | Agent discipline, `made-by::` authorship, OCC rules. |
| [`docs/ARCHITECTURE.md`](docs/ARCHITECTURE.md) | Data planes, Plumber lifecycle, RMW locking, v1.9 hygiene + v1.8 edge performance. |
| [`docs/v1.8-OPTIMIZATION-PLAN.md`](docs/v1.8-OPTIMIZATION-PLAN.md) | v1.8 scope, env vars, load testing. |
| [`docs/v1.8-SOFTWARE-EDGE-PLAN.md`](docs/v1.8-SOFTWARE-EDGE-PLAN.md) | CPU sandbox, frozen KV prefix, adaptive LLM, mmap reads. |
| [`docs/openspec/README.md`](docs/openspec/README.md) | Index of behavioral specs (lint, ingest, identity, v1.9 hygiene/DX). |
| [`docs/openspec/llm-performance.md`](docs/openspec/llm-performance.md) | LLM prompt layout, memory, and I/O contracts. |
| [`docs/BRANDING.md`](docs/BRANDING.md) | Product name (**Matryca Plumber**), Matryca.ai attribution, writing rules. |
| [`docs/openspec/runtime-bootstrap.md`](docs/openspec/runtime-bootstrap.md) | Startup provisioning: logs, L1, cache, wiki YAML. |
| [`docs/openspec/l1-l2-routing.md`](docs/openspec/l1-l2-routing.md) | L1 memory vs L2 graph routing for agents. |
| [`docs/openspec/identity-config.md`](docs/openspec/identity-config.md) | Telos / AI Constraints and `store_fact`. |
| [`docs/openspec/ingest.md`](docs/openspec/ingest.md) | `ingest_document` atomic ingestion pipeline. |
| [`docs/openspec/link-verification.md`](docs/openspec/link-verification.md) | v1.9 URL/asset hygiene and sidecar registry. |
| [`docs/openspec/agent-dx.md`](docs/openspec/agent-dx.md) | v1.9 CLI JSON, context macro, Journey Log. |
| [`docs/PROJECT_DIARY.md`](docs/PROJECT_DIARY.md) | Maintainer log, phase history, crushed bottlenecks. |
| [`CONTRIBUTING.md`](CONTRIBUTING.md) | Setup, `uv` commands, `make check` standards. |
| [`SECURITY.md`](SECURITY.md) | Vulnerability reporting and `.env` hardening controls. |

## License
Apache-2.0 — see [LICENSE](LICENSE).

![Matryca Plumber Cover](images/20260519-Logseq-Matryca-LLM-Wiki-copertina-github.jpg)
