Architecture

The Nucleus DSL

The LLM outputs commands in the Nucleus DSL—an S-expression language designed for document analysis:

; Search for patterns
(grep "ERROR")

; Filter results
(filter RESULTS (lambda x (match x "timeout" 0)))

; Aggregate
(sum RESULTS)    ; Auto-extracts numbers from lines
(count RESULTS)  ; Count matching items

; Final answer
<<<FINAL>>>13000000<<<END>>>

The Lattice Engine

The Lattice engine (src/logic/) processes Nucleus commands:

1. Parser (lc-parser.ts) - Parses S-expressions into an AST
2. Type Inference (type-inference.ts) - Validates types before execution
3. Constraint Resolver (constraint-resolver.ts) - Handles symbolic constraints like [Σ⚡μ]
4. Solver (lc-solver.ts) - Executes commands against the document

Lattice uses miniKanren (a relational programming engine) for pattern classification and filtering operations.

In-Memory Handle Storage

For large result sets, RLM uses a handle-based architecture with in-memory SQLite (src/persistence/) that achieves 97%+ token savings:

Traditional:  LLM sees full array    [15,000 tokens for 1000 results]
Handle-based: LLM sees stub          [50 tokens: "$grep_error: Array(1000) [preview...]"]

How it works:

1. Results are stored in SQLite with FTS5 full-text indexing
2. LLM receives descriptive handle references derived from the command (e.g., $grep_error, $bm25_timeout, $filter_status)
3. Operations execute server-side, returning new handles
4. Full data is only materialized when needed

Handle names are auto-generated from the Nucleus command: (grep "ERROR") produces $grep_error, (list_symbols "function") produces $list_symbols_function. Repeated commands get a numeric suffix ($grep_error_2, $grep_error_3).

Memory Pad

The Lattice engine doubles as a context memory for LLM agents. Instead of roundtripping large text blobs in every message, agents stash context server-side and carry only compact handle stubs:

Agent reads file, summarizes → lattice_memo "auth architecture"
                              → $memo_auth_architecture: "auth architecture" (2.1KB, 50 lines)

20 messages later, needs it  → lattice_expand $memo_auth_architecture
                              → Full 50-line summary

Token math (30-message session, 3 source files stashed):

• Traditional roundtripping: 836K tokens
• Memo-based (stubs + 6 expands): 57K tokens — 93% savings

Memos persist across document loads (lattice_load clears query handles but keeps memos), support LRU eviction (100 memo cap, 10MB budget), and can be explicitly deleted when stale. No document needs to be loaded to use memos.

The Role of the LLM

The LLM does reasoning, not code generation:

1. Understands intent - Interprets "total of north sales" as needing grep + filter + sum
2. Chooses operations - Decides which Nucleus commands achieve the goal
3. Verifies results - Checks if the current results answer the query
4. Iterates - Refines search if results are too broad or narrow

The LLM never writes JavaScript. It outputs Nucleus commands that Lattice executes safely.

Installation

Install from npm:

npm install -g matryoshka-rlm

Or run without installing:

npx matryoshka-rlm "How many ERROR entries are there?" ./server.log

Included Tools

The package provides several CLI tools:

| Command | Description | |---------|-------------| | rlm | Main CLI for document analysis with LLM reasoning | | rlm-mcp | MCP server with full RLM + LLM orchestration (analyze_document tool) | | lattice-mcp | MCP server exposing direct Nucleus commands (no LLM required) | | lattice-repl | Interactive REPL for Nucleus commands | | lattice-http | HTTP server for Nucleus queries | | lattice-pipe | Pipe adapter for programmatic access | | lattice-setup | Setup script for Claude Code integration |

From Source

git clone https://github.com/yogthos/Matryoshka.git
cd Matryoshka
npm install
npm run build

Configuration

Copy config.example.json to config.json and configure your LLM provider:

{
  "llm": {
    "provider": "ollama"
  },
  "providers": {
    "ollama": {
      "baseUrl": "http://localhost:11434",
      "model": "qwen3-coder:30b",
      "options": { "temperature": 0.2, "num_ctx": 8192 }
    },
    "deepseek": {
      "baseUrl": "https://api.deepseek.com",
      "apiKey": "${DEEPSEEK_API_KEY}",
      "model": "deepseek-chat",
      "options": { "temperature": 0.2 }
    }
  },
  "rlm": {
    "maxTurns": 10
  }
}

Usage

CLI

# Basic usage
rlm "How many ERROR entries are there?" ./server.log

# With options
rlm "Count all ERROR entries" ./server.log --max-turns 15 --verbose

# See all options
rlm --help

MCP Integration

RLM includes lattice-mcp, an MCP (Model Context Protocol) server for direct access to the Nucleus engine. This allows coding agents to analyze documents with 80%+ token savings compared to reading files directly.

The key advantage is handle-based results: query results are stored server-side in SQLite, and the agent receives compact stubs like $grep_error: Array(1000) [preview...] instead of full data. Handle names are derived from the command for easy identification. Operations chain server-side without roundtripping data.

Available Tools

| Tool | Description | |------|-------------| | lattice_load | Load a document for analysis | | lattice_query | Execute Nucleus commands on the loaded document | | lattice_expand | Expand a handle to see full data (with optional limit/offset) | | lattice_memo | Store arbitrary context as a memo handle (no document required) | | lattice_memo_delete | Delete a stale memo to free memory | | lattice_close | Close the session and free memory | | lattice_status | Get session status, document info, and memo usage | | lattice_bindings | Show current variable bindings and memo labels | | lattice_reset | Reset all bindings and memos but keep document loaded | | lattice_llm_respond | Respond to a pending (llm_query ...) suspension | | lattice_llm_batch_respond | Respond to a pending (llm_batch ...) suspension with all N responses | | lattice_help | Get Nucleus command reference |

Example MCP config

{
  "mcp": {
    "lattice": {
      "type": "stdio",
      "command": "lattice-mcp"
    }
  }
}

Efficient Usage Pattern

1. lattice_load("/path/to/large-file.txt")   # Load document (use for >500 lines)
2. lattice_query('(grep "ERROR")')           # Search → $grep_error: Array(500) [preview]
3. lattice_query('(filter RESULTS ...)')     # Narrow → $filter_timeout: Array(50) [preview]
4. lattice_query('(count RESULTS)')          # Count without seeing data → 50
5. lattice_expand("$filter_timeout", limit=10) # Expand only what you need to see
6. lattice_close()                           # Free memory when done

Token efficiency tips:

• Query results return descriptive handle stubs, not full data
• Use lattice_expand with limit to see only what you need
• Chain grep → filter → count/sum to refine progressively
• Use RESULTS in queries (always points to last result)
• Use descriptive handle names (e.g., $grep_error) with lattice_expand to inspect specific results

Chunking and Sub-LLM Recursion

Two primitive families power the paper's Ω(|P|²) semantic-horizon pattern:

Chunking — pre-slice a document that's too big to map over directly:

(chunk_by_size 2000)                ; 2000-character slices
(chunk_by_lines 100)                ; 100-line slices
(chunk_by_regex "\\n\\n")           ; Split on blank lines; capture groups ignored

Sub-LLM calls — (llm_query ...) invokes a sub-LLM with an interpolated prompt. Works at the top level and nested inside map / filter / reduce lambdas:

(llm_query "Summarize this")