Matryca Logseq LLM Wiki (v1.4.0 — Headless Edition)

Agentic Knowledge Management for Logseq OG. An MCP server that turns your favorite AI into a spatial Knowledge Architect. It treats your vault as a tree of blocks, not a flat document store. Local-first, database-free, and Markdown-purist.

Matryca is a 100% Headless, sandboxed MCP server and CLI built to turn your local Logseq graph into a high token-density agentic workspace — with no network APIs and no background desktop app required.

The shift from a stateful, network-bounded architecture (Logseq Electron + JSON-RPC) to a local-first, zero-dependency model is the milestone of v1.4.0 — The Headless Revolution: one required variable (LOGSEQ_GRAPH_PATH), atomic AST writes via logseq-matryca-parser==0.3.3, and X-Ray persistence in .matryca_xray_state.json.

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✨ Core Features

• 🌌 AST Spatial Intelligence: understands Logseq’s native parent-child block structure via a deterministic parser.
• 🤖 100% Headless & Local-First: does not require the Logseq desktop app to be open. Mutations use atomic file I/O directly on .md sources.
• 🩻 X-Ray Token Economy (Printing Press Mode): compresses Markdown trees and maps UUIDs to persistent aliases like [0], [1] — up to ~35× less context noise.
• 🔒 Sandboxed Privacy: mathematically blocks path-traversal attempts outside the graph root (path_sandbox.py).
• ⚡ Agent-Native CLI: fast, minimal matryca command optimized for terminal scripts and local LLMs (including matryca service for LaunchAgent / systemd).
• 🧱 Ironclad Data Plane: transactional swaps, code-block fence scanning, optional Git snapshots before mutations.
• 📊 Zero-DB Lexical Engine: in-memory Okapi BM25 and structural BFS traversals — no vector store.

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⚙️ Configuration (Zero-Friction)

Forget API tokens and port configuration. The only required variable is the absolute path to your graph:

Claude Desktop

Add this block to claude_desktop_config.json:

{
  "mcpServers": {
    "matryca-logseq": {
      "command": "uvx",
      "args": ["--from", "matryca-logseq", "matryca-logseq-llm-wiki"],
      "env": {
        "LOGSEQ_GRAPH_PATH": "/absolute/path/to/your/Logseq/graph"
      }
    }
  }
}

Requires uv on your PATH. No clone and no cwd — uvx pulls matryca-logseq from PyPI and runs the matryca-logseq-llm-wiki console script.

Restart the MCP host after edits. Optional: MATRYCA_GIT_SNAPSHOT_ON_WRITE=true for automatic commits before writes on git-backed graphs.

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🧪 Stability Markers

• 162 strict passing tests (unit, integration, subprocess).
• 100% strict MyPy type checking and Ruff compliance on src/ and tests/.
• The same bar on main in .github/workflows/ci.yml — run make check locally.

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Architecture stack

flowchart TB
  subgraph host["Host machine"]
    IDE["MCP client\n(Claude Desktop, Cursor, …)"]
  end
  subgraph proc["matryca-logseq-llm-wiki process"]
    MCP["FastMCP stdio"]
    SRV["MatrycaMCPServer\n+ Pydantic validators"]
    GD["graph_dispatch.py\n(headless CRUD)"]
    QG["quality_gate\n(credential / key scans)"]
    MCP --> SRV
    SRV --> GD
    SRV --> QG
  end
  subgraph data["Data plane (headless)"]
    FS[("LOGSEQ_GRAPH_PATH\npages/ · journals/ · templates/")]
    PAR["logseq-matryca-parser==0.3.3\n(spatial read + agent_writer)"]
    SBX["path_sandbox\n(is_relative_to graph root)"]
    LOCK["page_rmw_lock\n(per-page RMW)"]
    GFS["global_fence_scanner\n(dead-zone line index)"]
    ATW["atomic_write_bytes\n(tmp + fsync + replace)"]
    GC["generational_cache\n(mtime_ns signatures)"]
    XRAY[".matryca_xray_state.json\n(SessionAliasRegistry)"]
  end
  subgraph delivery["Delivery gates (repo)"]
    CI["GitHub Actions\nRuff · Mypy · Pytest"]
    DB["Dependabot\npip + Actions"]
    REL["tag v* → uv build\ngh release create"]
  end
  IDE <-->|JSON-RPC MCP| MCP
  GD <-->|AST splice + read| FS
  GD --> PAR
  GD --> LOCK
  SRV --> SBX
  SRV --> GFS
  SRV --> ATW
  SRV --> GC
  SRV --> XRAY
  CI -.->|enforces| proc
  DB -.->|updates| delivery
  REL -.->|artifacts| delivery

L1 versus L2 (two-layer context)

flowchart TB
  subgraph L1["L1 — session rules (small, capped)"]
    M1["MATRYCA_L1_PATH\nor matryca-l1/*.md\nor matryca-wiki.yml memory_path"]
  end
  subgraph L2["L2 — the graph"]
    M2["pages/ · journals/ · templates/"]
  end
  A[Agent] --> R{High-stakes\nbefore vault?}
  R -->|yes| T[read_l1_memory]
  R -->|no| Q[query_logseq_pages_local\nBM25 + generational cache]
  T --> M1
  Q --> M2
  M1 --> M2

Runtime agent loop (search → gate)

flowchart LR
  S[Search\nBM25 / hops] --> C[Scan\nread_logseq_page · lint]
  C --> U[Refactor\nheadless AST mutators]
  U --> G[Garden\nMOC · tags · split]
  G --> Q[Quality gate\nsecrets · fan-out · routing_hint]
  subgraph iron["Ironclad sub-loop"]
    F[fence scanner] --> A2[atomic swap]
    A2 --> I[incremental cache]
  end
  U -.-> iron
  G -.-> iron

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Feature matrix: architectural phases

Each phase adds capabilities; later phases harden earlier tools without necessarily renaming the MCP surface. Phase is the product narrative; modules are what you grep in src/.

Phase	Core capabilities	MCP tools (exposed names)
1 — Baseline bridge	FastMCP server, OutlineNode validation, DFS write_logseq_outline, spatial read_logseq_page, block-ref integrity scan, dashboard aggregation	read_logseq_page, write_logseq_outline, lint_logseq_block_refs, render_logseq_dashboard
2 — L1 / L2 routing	Capped read_l1_memory from configurable paths; routing hints on read/write responses for traceability (routing_hint.py)	read_l1_memory (hints on other tools’ payloads)
3 — PKM refinements	BM25 and substring local query; structural BFS hops and hub/orphan reports; surgical key:: property edits; templates; wiki-prefix lint; namespace index; optional git snapshot on outline and heavy mutators	query_logseq_pages_local, traverse_logseq_structural_hops, report_structural_hubs_orphans, patch_logseq_block_property_lines, list_logseq_templates, read_logseq_template, lint_matryca_wiki_pages, list_logseq_namespace_index, snapshot_logseq_graph_git
4 — Logseq superpowers	Advanced Query injection with preset or raw EDN; journal task mining; entity resolution via alias index; page alias append	search_graph / method=resolve_entity, mutate_graph / inject_query, append_journal
5 — Graph gardener	SRS-style flashcards from :: pairs; vault-wide tag unify; same-page reparent refactor	generate_logseq_flashcards, lint_unify_logseq_tags, refactor_logseq_blocks
6 — Synthesis engine	Unlinked mention discovery; MOC generation; long-bullet split; manual git snapshot	resolve_unlinked_mentions, generate_moc_page, refactor_large_blocks, snapshot_logseq_graph_git
7 — Mldoc guards	mldoc_properties (property grammar, CSV / wikilink / quote semantics); mldoc_guards (drawers, fences, macros) wired into property edit, tag unify, alias append, large-block split	Same tool names as phases 3–6; strengthened internals
8 — Ironclad data plane	compute_page_protected_line_indices (global fence lexer); atomic_write_bytes on mutators; generational_cache (st_mtime_ns keyed alias + BM25 corpus reuse, Salsa-style invalidation)	Same tool names; dead-zone and cache behavior upgraded
9 — Trust and policy plane	quality_gate: blocks credential-like outline properties and raw query EDN; lint_matryca_wiki_pages for configurable wiki discipline; structured dry-run / apply responses	Enforcement inside write_logseq_outline, inject_logseq_advanced_query; governance tools listed in phase 3
10 — Delivery and community	GitHub Actions (ci.yml): uv sync --locked, Ruff lint + format check, Mypy on src and tests, Pytest; Dependabot (pip + Actions); release.yml on v* tags (uv build, gh release create); SECURITY.md; Contributor Covenant (CODE_OF_CONDUCT.md); issue and PR templates	Repository operations — no additional MCP tools
11 — Fortress (v1.3.0)	path_sandbox.py traversal gate on all FS paths; mcp_tool_guard LLM-safe errors; lifespan lock and telemetry teardown	Same MCP tool names; adversarial path hardening
12 — Headless Revolution (v1.4.0)	Removed httpx / LogseqClient; graph_dispatch.py + agent_writer.append_child_to_node for atomic AST writes; .matryca_xray_state.json via SessionAliasRegistry; LogseqGraph.get_broken_references() for in-memory ref lint	Same MCP tool names; 100% disk-native persistence

Roadmaps and design history: docs/roadmaps/ (LLM Wiki, Phase 3, Logseq superpowers, Phase 5–6, mldoc compliance, Ironclad Shield).

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Zero-install execution (uvx)

You do not need to clone this repository. uv can run the published PyPI package in an ephemeral environment:

uvx --from matryca-logseq matryca-logseq-llm-wiki

For a bleeding-edge build from main, use the Git URL instead:

uvx --from git+https://github.com/MarcoPorcellato/matryca-logseq-llm-wiki.git matryca-logseq-llm-wiki

Set LOGSEQ_GRAPH_PATH to the absolute root of your Logseq graph (the folder containing pages/) in your MCP host’s server definition. For responsible vulnerability disclosure, see SECURITY.md.

Background service (matryca service) — persistent install only

matryca service install writes a per-user LaunchAgent (macOS) or systemd user unit (Linux) that runs matryca-logseq-llm-wiki on login. The unit records whatever path shutil.which("matryca-logseq-llm-wiki") resolves to at install time.

Do not run matryca service install via ephemeral uvx. uvx executes from a temporary uv cache that may be garbage-collected; after reboot, the daemon would fail with FileNotFound.

Install Matryca as a stable tool first, then install the service (with LOGSEQ_GRAPH_PATH and any optional vars exported in your shell):

uv tool install matryca-logseq
matryca service install

Use matryca service uninstall to remove the plist or unit. Set MATRYCA_DEBUG=true only when debugging MCP log bridging (disables privacy masking in client-visible logs).

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Safe testing on a copy of your graph

Because Matryca reads and writes the same folder pointed to by LOGSEQ_GRAPH_PATH, always point agents at a dedicated test graph before experimenting:

1. Clone the graph. Copy your real Logseq folder to a dedicated location (for example Logseq_Matryca_Test). Use a full copy, not a symlink.
2. Set the path. In .env or your MCP host env block, set LOGSEQ_GRAPH_PATH to that copy’s absolute path.
3. Optional rollback. With MATRYCA_GIT_SNAPSHOT_ON_WRITE=true, selected writes also create a local git commit on the test graph so you can revert experiments.

🛠️ Using Logseq Sync? Click here if Logseq refuses to open the test folder.
If you use Logseq Sync, the app tracks graphs by hidden UUIDs, not folder paths. A direct copy-paste will cause a UUID clash. Do a Clean Transplant instead:

1. Create a brand new, empty folder (e.g., Logseq_Matryca_Test).
2. Open Logseq, click "Add new graph", and select this empty folder to initialize a clean state.
3. Close Logseq completely.
4. Copy ONLY the pages/, journals/, and assets/ folders from your real graph into the test folder. (Do NOT copy the logseq/ folder or hidden git files).
5. Reopen Logseq and click Re-index.

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Quickstart (clone and develop)

Prerequisites

• Python 3.12+
• uv
• A Logseq OG graph on disk (the directory containing pages/)

Install

git clone https://github.com/MarcoPorcellato/matryca-logseq-llm-wiki.git
cd matryca-logseq-llm-wiki
make install

Environment

Copy .env.example to .env and set at minimum:

Variable	Role
LOGSEQ_GRAPH_PATH	Required. Absolute graph root (directory containing pages/)
MATRYCA_L1_PATH	Optional: file or directory of small Markdown “L1” session rules
MATRYCA_WIKI_CONFIG	Optional: path to matryca-wiki.yml (else $LOGSEQ_GRAPH_PATH/matryca-wiki.yml)
MATRYCA_GIT_SNAPSHOT_ON_WRITE	true or false — opt-in automatic git add -A + git commit before selected writes when the graph is a git checkout
MATRYCA_DEBUG	true — disable privacy masking in MCP client-visible log bridge (default: censored)

Optional graph orchestration: copy matryca-wiki.example.yml to your graph as matryca-wiki.yml for namespaces, template subdirectory, wiki lint prefix, and dashboard title.

Verify

make check

Runs Ruff (format + lint), strict Mypy on src/ and tests/, and pytest (162 strict passing tests). The same bar is enforced on main in .github/workflows/ci.yml.

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Documentation map

Document	Audience
SYSTEM_PROMPT.md	Agent operators — outline discipline, Search → Scan → Update, dry-run-first mutators
docs/ARCHITECTURE.md	Engineers — headless CRUD plane, Ironclad data plane, phase history
CONTRIBUTING.md	Contributors — uv, make check, MCP testing notes
CODE_OF_CONDUCT.md	Community standards (Contributor Covenant 2.1)
SECURITY.md	Private reporting via GitHub Security Advisories

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License

Apache-2.0 — see LICENSE.