layered-memory-mcp 1.0.0

Layered Memory MCP Server — Extend AI agent memory beyond token limits with a 4-tier knowledge architecture

Layered Memory MCP Server

Extend AI agent memory beyond token limits with a 4-tier knowledge architecture.

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The Problem

AI agents have limited memory — typically 2-4KB of persistent context injected every turn. Once it's full, the agent forgets everything else. You can't store project configurations, user preferences, API conventions, or domain knowledge without constantly fighting the space limit.

The Solution

Layered Memory organizes knowledge into 4 tiers, trading immediacy for capacity:

┌─────────────────────────────────────────────────────┐
│  L0 — Index Layer (2-4KB, injected every turn)      │
│  Pure pointers: "what knowledge exists and where"    │
├─────────────────────────────────────────────────────┤
│  L1 — Knowledge Files (unlimited, loaded on-demand)  │
│  Structured markdown: configs, conventions, facts    │
├─────────────────────────────────────────────────────┤
│  L2 — Skills Layer (loaded when needed)              │
│  Procedures, workflows, tool-specific knowledge      │
├─────────────────────────────────────────────────────┤
│  L3 — Raw Sessions (searched rarely)                 │
│  Full conversation history, searchable by keyword    │
└─────────────────────────────────────────────────────┘

L0 is your table of contents. L1 is your bookshelf. L2 is your cookbook. L3 is your diary.

Features

• Smart Knowledge Injection — Inject facts with auto-dedup and section merging (upsert/append/merge), auto L0 sync
• Keyword Search — Search with keyword, fuzzy, or BM25/TF-IDF scoring across all L1 files
• Agent-Agnostic L0 Access — get_l0_index tool lets any MCP agent retrieve the memory index
• Multi-Agent Namespace — Isolate knowledge per agent via LAYERED_MEMORY_NAMESPACE while sharing common knowledge
• Session Scanning — Extract knowledge candidates from recent agent sessions
• Health Validation — Check L0-L1 consistency, file structure, and knowledge quality
• Write Safety — Automatic .bak backup before every file modification
• Space Analysis — Monitor memory usage and get optimization suggestions
• Agent-Neutral — Works with any MCP-compatible agent (Hermes, Claude, Cursor, etc.)
• Zero Dependencies — Core engine uses Python stdlib only; only fastmcp for MCP transport
• Privacy First — All data stored locally, no external API calls

Quick Start

Install

pip install layered-memory-mcp

Hermes Agent

Add to ~/.hermes/config.yaml:

mcp_servers:
  layered-memory:
    command: layered-memory-mcp
    timeout: 30

OpenClaw

Install the MCP server, then register it:

pip install layered-memory-mcp

# Register as an MCP server
openclaw mcp set layered-memory --command layered-memory-mcp

Layered Memory complements OpenClaw's built-in vector-based memory:

• OpenClaw memory: semantic search over session transcripts (heavy, needs embeddings)
• Layered Memory: structured keyword search over curated knowledge files (light, instant)
• Use both: OpenClaw for "what did I say about X?" and Layered Memory for "what's the database connection string?"

Claude Desktop

Add to your Claude Desktop MCP config:

{
  "mcpServers": {
    "layered-memory": {
      "command": "layered-memory-mcp"
    }
  }
}

Cursor / Other MCP Clients

# stdio mode (default)
layered-memory-mcp

# HTTP mode
layered-memory-mcp --transport http --port 8080

# Verbose logging
layered-memory-mcp --verbose

Environment Variables

Variable	Description	Default
LAYERED_MEMORY_HOME	Root directory for memory data	~/.layered-memory/
LAYERED_MEMORY_SESSIONS_DIR	Agent sessions directory (auto-detected)	~/.hermes/sessions/
LAYERED_MEMORY_AUTO_SYNC_L0	Auto-sync L0 index after writes	true
LAYERED_MEMORY_DEDUP_THRESHOLD	Similarity threshold for dedup (0.0-1.0)	0.7
LAYERED_MEMORY_L0_FORMAT	L0 index format: hermes or generic	hermes
LAYERED_MEMORY_NAMESPACE	Agent namespace for multi-agent isolation	shared

Usage

1. Write Knowledge (Recommended)

The inject_knowledge tool is the primary write path for all agents. It handles deduplication, section targeting, and automatic L0 index sync in a single call.

Agent learns: "Production DB is PostgreSQL 15 on prod-db:5432"
→ inject_knowledge(
    domain="infrastructure",
    section="Database",
    content="PostgreSQL 15 on prod-db:5432, connection pool: 20 max",
    mode="upsert"
  )
← Creates/updates infrastructure.md, auto-syncs L0 index

Write modes:

Mode	Behavior
upsert (default)	Replace if similar content exists, append if new
append	Always append, skip dedup check
merge	Combine unique parts from new + existing

2. Read Knowledge

Agent: "What's the database connection string?"
→ recall_knowledge(keyword="database")
← Returns relevant sections from infrastructure.md

3. Validate Health

→ validate_knowledge()
← Checks L0↔L1 consistency, orphaned files, stale entries, file health

4. Session Compression (Cron Job)

Set up a daily cron to extract new knowledge from conversations:

1. scan_recent_sessions → get session summaries
2. AI analyzes summaries → identifies stable facts
3. New facts → written via inject_knowledge (auto L0 sync)
4. L0 index → always up to date

5. Legacy CRUD (Also Available)

For direct file manipulation:

Tool	Description
create_knowledge_file	Create a new .md file (auto L0 sync)
update_knowledge_file	Overwrite an existing file (auto L0 sync)
delete_knowledge_file	Delete a file (auto L0 sync)

MCP Tools

Read Tools

Tool	Description
recall_knowledge	Search L1 knowledge files by keyword with relevance scoring
get_knowledge_file	Read a specific knowledge file by name
list_memory_stats	Get space statistics, file sizes, and optimization suggestions
scan_recent_sessions	Scan recent sessions for knowledge extraction candidates
search_sessions_by_keyword	Search session content by keyword
get_l0_index	Retrieve the full L0 index (agent-agnostic)

Write Tools (5)

Tool	Description
inject_knowledge	Primary write path — smart injection with dedup, section targeting, auto L0 sync
create_knowledge_file	Create a new .md file (auto L0 sync)
update_knowledge_file	Overwrite an existing file (auto L0 sync)
delete_knowledge_file	Delete a file (auto L0 sync)

Management Tools

Tool	Description
sync_l0_index	Manually rebuild L0 index from L1 files (supports dry_run)
validate_knowledge	Health check: L0↔L1 consistency, file quality, duplicates
manage_l0_entry	Add / remove / replace individual L0 entries

MCP Resources

Resource	Description
memory://status	Overall system status and configuration
knowledge://files	List all knowledge files with metadata

MCP Prompts

Prompt	Description
knowledge_compression_prompt	Template for AI-driven knowledge extraction from sessions
cognitive_decision_prompt	Decision framework for disciplined memory usage

Architecture Deep Dive

Why 4 Tiers?

Tier	Cost	Capacity	Use Case
L0 (Index)	Tokens per turn	~2KB	Quick lookup table
L1 (Knowledge)	1 file read	Unlimited	Structured facts
L2 (Skills)	1 skill load	Unlimited	Procedures
L3 (Sessions)	Full search	Unlimited	Historical recall

Write-Once, Fully-Visible Pipeline (v0.5.0)

The key innovation in v0.5.0 is that every write path automatically syncs the L0 index:

Agent calls inject_knowledge(domain="infra", section="Proxy", content="...")
  │
  ├─ 1. Dedup check (SequenceMatcher, threshold=0.7)
  ├─ 2. Resolve action: upsert / append / merge / skip
  ├─ 3. Section targeting (finds or creates ## heading)
  ├─ 4. File write (with fcntl.flock for concurrency safety)
  └─ 5. Auto L0 index sync
        │
        ↓
  L0 index updated → Agent sees it next turn

This eliminates the "write-but-invisible" problem where agents write L1 files but the L0 index (injected into every turn) doesn't update, causing future sessions to ignore the new knowledge.

Relevance Scoring

When you call recall_knowledge, files are scored by:

1. Filename match (+10 points) — keyword appears in filename
2. Heading match (+3 points) — keyword appears in a ## heading
3. Content frequency (+0.5 per occurrence, capped at 5) — how often keyword appears

Results are sorted by score, and only matching ## sections are returned (not entire files).

Namespace Isolation (v0.6.0)

Set LAYERED_MEMORY_NAMESPACE to isolate knowledge per agent:

knowledge/
├── shared/           ← Common knowledge, visible to all agents
│   ├── infrastructure.md
│   └── coding-standards.md
├── claude/           ← Claude Desktop's private knowledge
│   └── claude-specific.md
├── cursor/           ← Cursor IDE's private knowledge
│   └── cursor-config.md
└── hermes/           ← Hermes Agent's private knowledge
    └── hermes-setup.md

Each agent sees its own namespace first, then falls back to shared/. File name collisions resolve in favor of the namespace. All read/search/inject tools automatically merge both directories.

# Claude Desktop config
LAYERED_MEMORY_NAMESPACE=claude layered-memory-mcp

# Backward compatible: default "shared" = no isolation
layered-memory-mcp

L0 Index Formats

Two index formats are supported:

Format	Example	Best For
hermes	[L0索引] infra: servers, DB → knowledge/infra.md	Hermes Agent memory injection
generic	[infra.md] Server Configuration → proxy, db, deploy	Standalone / other agents

Configure via LAYERED_MEMORY_L0_FORMAT env var or the l0_format constructor argument.

Session Compression

The scan_recent_sessions tool is designed for cron-job automation:

1. It scans session files from the past N days
2. Extracts user messages, assistant topics, and tool calls
3. Returns a structured JSON for an AI to analyze
4. The AI identifies stable knowledge and writes it to L1 files via inject_knowledge

This creates a self-improving memory system — the agent gets smarter over time as more knowledge is distilled from conversations.

Agent Compatibility

Layered Memory is an MCP server — it works with any MCP-compatible agent.

Agent	Config Method	Notes
Hermes Agent	config.yaml → mcp_servers	Native MCP client, L0 auto-injection via memory
OpenClaw	openclaw mcp set	Complements built-in vector memory
Claude Desktop	claude_desktop_config.json	Full MCP support, L0 via tool calls
Cursor	Settings → MCP	Full MCP support
Codex CLI	Codex MCP config	Full MCP support
Any MCP client	stdio or HTTP transport	Standard MCP protocol

When to use Layered Memory vs. built-in memory

Most agents have limited persistent memory (2-4KB per turn). Layered Memory solves this by:

1. Separating index from content — L0 stays small (fits in agent memory), L1 holds unlimited knowledge
2. On-demand loading — the agent only reads what it needs, when it needs it
3. Self-improving — session compression automatically extracts new knowledge over time

Integration patterns

Agent (2KB memory limit)
  └── L0 index (injected every turn, ~500 bytes)
        ├── [L0] infrastructure: servers, DB → knowledge/infrastructure.md
        ├── [L0] api: REST conventions → knowledge/api-conventions.md
        └── [L0] dev: code style, testing → knowledge/development.md
              │
              ↓ (on demand via recall_knowledge)
        L1 knowledge files (unlimited, loaded by keyword)

Cognitive Decision Framework

The 4-tier architecture only works if the agent follows a disciplined decision process. This framework should be injected into the agent's system prompt (or loaded via the cognitive_decision_prompt MCP prompt) to ensure consistent behavior.

Decision Tree

Agent encounters a problem or receives a request
  │
  ├─ Step 1: Scan L0 index for relevant domains
  │
  ├─ Step 2: Match found?
  │   ├─ YES → Load the corresponding L1 knowledge file / L2 skill
  │   │   │
  │   │   ├─ Knowledge solves it → Use it. Do NOT bypass with guessing.
  │   │   ├─ Knowledge partially covers it → Use it, then enhance the entry.
  │   │   └─ Knowledge insufficient → Treat as new problem (Step 3).
  │   │
  │   └─ NO → Treat as new problem (Step 3).
  │
  ├─ Step 3: Handle as new problem/requirement
  │   Use standard tools and reasoning to solve.
  │
  └─ Step 4: Post-solution evaluation
      Is this worth preserving?
      ├─ YES → Write to L1 (via inject_knowledge) or L2 (skill) for future reuse.
      └─ NO  → Done.

Why This Matters

Without this decision framework, agents tend to:

• Ignore existing knowledge — they see the L0 index but forget to load L1 files, then waste time guessing
• Repeat mistakes — solved problems aren't captured, so the agent re-learns from scratch next session
• Bypass established conventions — each session starts from zero instead of building on accumulated knowledge

The framework turns the memory system from a passive storage into an active cognitive loop: consult → act → learn → improve.

Integration

Add this to your agent's system prompt:

You use a 4-tier layered memory system. Before tackling any problem:
1. Check L0 index for matching domains
2. If matched, load and follow L1/L2 before acting
3. If unmatched, solve normally
4. After solving, use inject_knowledge to preserve new knowledge

Or use the built-in MCP prompt cognitive_decision_prompt to get the full decision framework at runtime.

Development

# Clone
git clone https://github.com/LAIguapi/layered-memory-mcp.git
cd layered-memory-mcp

# Install in dev mode
pip install -e ".[dev]"

# Run tests
pytest

# Run locally
python -m layered_memory_mcp.server

Changelog

v0.6.0 — Agent-Agnostic L0, BM25, Namespaces

• get_l0_index tool — Any MCP agent can now retrieve the L0 index, not just Hermes
• BM25/TF-IDF search mode — Better relevance scoring for long-form knowledge files (use search_mode: "bm25")
• Multi-agent namespace isolation — Set LAYERED_MEMORY_NAMESPACE to isolate per-agent knowledge with shared fallback
• .bak backup — Automatic backup before every file modification via inject_knowledge or update_knowledge_file
• L0 staleness check — recall_knowledge detects stale L0 index and warns with l0_staleness_warning
• Multi-language docs — Japanese and Korean READMEs synced to v0.6.0

v0.5.0 — Smart Injection & Auto-Sync

• inject_knowledge tool — Primary write path with dedup, section targeting, auto L0 sync
• sync_l0_index tool — Manual L0 index rebuild with dry_run preview
• validate_knowledge tool — L0↔L1 consistency check, health diagnostics
• manage_l0_entry tool — Fine-grained L0 entry add/remove/replace
• Auto L0 sync — All write tools (create/update/delete/inject) automatically sync L0 index
• Dedup engine — SequenceMatcher-based similarity detection with configurable threshold
• File locking — fcntl.flock for concurrent write safety
• Knowledge watcher — File changes trigger debounced L0 sync (HTTP mode)
• cognitive_decision_prompt — Built-in decision framework prompt

v0.4.0 — Initial Release

• 4-tier knowledge architecture (L0/L1/L2/L3)
• Keyword search with relevance scoring
• Session scanning and compression
• MCP protocol support (stdio + HTTP)
• Zero external dependencies (core engine)

License

MIT License — see LICENSE for details.