lemma-mcp 0.9.1 → 0.10.0

package/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2026 Lemma Project Contributors
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2026 Lemma Project Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

@@ -1,155 +1,183 @@
-<p align="center">
-  <img src="assets/logo.png" width="200" alt="Lemma Logo">
-</p>
-
-# Lemma — Persistent Memory for LLMs via MCP
-
-[English](README.md) | [Türkçe](docs/README.tr.md)
-
-Lemma is an MCP server that gives LLMs persistent, cross-session memory. Memories are injected automatically into every session — no explicit tool call needed. Knowledge evolves through use: frequently accessed memories strengthen, unused ones fade, and patterns are promoted into reusable skills.
-
-## Quick Start
-
-Add Lemma to your MCP client configuration:
-
-**Claude Desktop (Windows):** `%APPDATA%\Claude\claude_desktop_config.json`
-**Claude Desktop (macOS):** `~/Library/Application Support/Claude/claude_desktop_config.json`
-**opencode:** `%APPDATA%\opencode\opencode.json`
-
-```json
-{
-  "mcpServers": {
-    "lemma": {
-      "command": "npx",
-      "args": ["-y", "lemma-mcp@latest"]
-    }
-  }
-}
-```
-
-> Using `@latest` ensures npx always fetches the newest version.
-
-**Requirements:** Node.js 20.0.0 or higher
-
-## How It Works
-
-Memories are injected into tool descriptions via `tools/list`. The LLM starts every session already knowing its most important memories — works on every MCP client.
-
-**3-layer injection:**
-- Full content for top memories (token-budgeted)
-- Summary index for remaining memories
-- Active guides with learnings
-
-**Memory types:** `fact`, `pattern`, `lesson`, `warning`, `context`
-
-**Knowledge pipeline:** Memory (what you know, `memory_add`) ↔ Guide (how you work, `guide_practice`/`guide_distill`)
-
-## Tools (21)
-
-### Memory (11)
-
-| Tool | Purpose |
-|------|---------|
-| `memory_read` | Read/search fragments. Summary mode or full detail by ID |
-| `memory_add` | Save findings. Auto-redacts secrets |
-| `memory_update` | Update fragment by ID |
-| `memory_feedback` | Positive/negative feedback, adjusts confidence |
-| `memory_forget` | Delete fragment |
-| `memory_merge` | Merge fragments, inherit relations & guide links |
-| `memory_relate` | Create typed links (`contradicts`, `supersedes`, `supports`, `related_to`) |
-| `memory_stats` | Fragment counts, confidence, project breakdown |
-| `memory_audit` | Integrity check for orphans, duplicates, anomalies |
-
-### Guides (8)
-
-| Tool | Purpose |
-|------|---------|
-| `guide_get` | Get guides sorted by usage, filter by category or task |
-| `guide_practice` | Record guide usage. Mandatory during work |
-| `guide_create` | Create guide with manual |
-| `guide_distill` | Transform memory → guide learning (bidirectional link) |
-| `guide_update` | Update guide properties |
-| `guide_forget` | Remove guide |
-| `guide_merge` | Merge guides, inherit source memories |
-
-### Sessions (2)
-
-| Tool | Purpose |
-|------|---------|
-| `session_start` | Start traced session, pre-loads relevant context |
-| `session_end` | End session with review and suggestions |
-| `session_stats` | Virtual session statistics |
-
-## Configuration
-
-Optional config at `~/.lemma/config.json`:
-
-```json
-{
-  "token_budget": {
-    "full_content": 5000,
-    "summary_index": 1000,
-    "guides_detail": 1000
-  },
-  "injection": {
-    "max_full_content_fragments": 15,
-    "max_summary_fragments": 30,
-    "max_guides": 20
-  },
-  "virtual_session": {
-    "timeout_minutes": 30
-  }
-}
-```
-
-## File Locations
-
-| OS | Path |
-|---|---|
-| **Windows** | `C:\Users\{username}\.lemma\` |
-| **macOS/Linux** | `~/.lemma/` |
-
-Files: `memory.jsonl`, `guides.jsonl`, `config.json`, `sessions/`, `logs/`, `.bak` backups
-
-## Semantic Search
-
-Lemma uses **vector-first semantic search** powered by `@huggingface/transformers` (optionalDependency). When active, all search, dedup, and topic overlap detection runs on cosine similarity instead of keyword matching.
-
-**Model:** `Xenova/paraphrase-multilingual-MiniLM-L12-v2`
-- **Size:** ~470 MB (cached at `~/.lemma/models/` after first download)
-- **Dimensions:** 384-dim vectors
-- **Languages:** 50+ languages including Turkish, English, German, French, Spanish, Chinese, Japanese
-- **Why this model:** Optimized for paraphrase detection and cross-lingual similarity. In TR-EN benchmarks, it outperforms `all-MiniLM-L12-v2` by 2-3x on semantic similarity tasks.
-
-**Architecture:**
-- `searchAndSortFragments()` — Pure vector search when model ready, Fuse.js fallback when not
-- `findSimilarFragment()` — Cosine dedup (threshold 0.85) replaces keyword dedup
-- `findTopicOverlaps()` — Cosine range (0.5–0.85) detects related but non-duplicate memories
-- Guide name matching — Always uses Fuse.js (keyword-based, embeddings add no value)
-
-**Config** (`~/.lemma/config.json`):
-```json
-{
-  "embeddings": {
-    "enabled": true,
-    "model": "Xenova/paraphrase-multilingual-MiniLM-L12-v2"
-  }
-}
-```
-
-Set `"enabled": false` to disable embeddings and use keyword search only. No restart needed — model loads lazily on first search. Startup auto-backfills any fragments missing vectors.
-
-## Security
-
-All data is stored locally in `~/.lemma/`. Nothing is sent to external servers. Secrets are automatically redacted from memory fragments (17 regex patterns for API keys, tokens, connection strings).
-
-## Documentation
-
-- [Development Guide](docs/development/DEVELOPMENT.md) — Architecture, project structure, testing
-- [Roadmap](docs/development/ROADMAP.md) — v0.9, v0.10, v1.0 plans
-- [Research](docs/research/README.md) — Academic papers that influenced Lemma's design
-- [Changelog](CHANGELOG.md) — Version history
-
-## License
-
-MIT
+<p align="center">
+  <img src="assets/logo.png" width="200" alt="Lemma Logo">
+</p>
+
+# Lemma — Persistent Memory for LLMs via MCP
+
+[English](README.md) | [Türkçe](docs/README.tr.md)
+
+Lemma is an MCP server that gives LLMs persistent, cross-session memory. Memories are injected automatically into every session — no explicit tool call needed. Knowledge evolves through use: frequently accessed memories strengthen, unused ones fade, and patterns are promoted into reusable skills. An autonomous intelligence layer runs in the background — detecting conflicts, suggesting actions, and auto-linking related knowledge.
+
+## Quick Start
+
+Add Lemma to your MCP client configuration:
+
+**Claude Desktop (Windows):** `%APPDATA%\Claude\claude_desktop_config.json`
+**Claude Desktop (macOS):** `~/Library/Application Support/Claude/claude_desktop_config.json`
+**Claude Code (Linux):** `~/.claude.json` or `~/.claude/settings.json`
+**opencode:** `~/.config/opencode/opencode.json` (Linux/macOS) or `%APPDATA%\opencode\opencode.json` (Windows)
+
+```json
+{
+  "mcpServers": {
+    "lemma": {
+      "command": "npx",
+      "args": ["-y", "lemma-mcp@latest"]
+    }
+  }
+}
+```
+
+> Using `@latest` ensures npx always fetches the newest version.
+
+**Requirements:** Node.js 20.0.0 or higher
+
+### CLI Usage
+
+```bash
+lemma -lib    # Library Mode: snapshot of your entire knowledge base
+```
+
+Outputs a full analysis of all memories, guides, relations, stale fragments, distill candidates, and suggested actions. Useful for periodic maintenance and review.
+
+## How It Works
+
+Memories are injected into tool descriptions via `tools/list`. The LLM starts every session already knowing its most important memories — works on every MCP client.
+
+**3-layer injection:**
+- Full content for top memories (token-budgeted)
+- Summary index for remaining memories
+- Active guides with learnings
+
+**Memory types:** `fact`, `pattern`, `lesson`, `warning`, `context`
+
+**Knowledge pipeline:** Memory (what you know, `memory_add`) → Pattern (`type: "pattern"`) → Guide (how you work, `guide_distill` → `guide_practice`)
+
+**AGENTS.md injection:** Lemma automatically injects a system prompt into your project's `AGENTS.md`, teaching the LLM how to use the memory system effectively. This ensures consistent behavior across all MCP clients.
+
+## Autonomous Intelligence
+
+Lemma runs intelligence in the background — no manual triggering needed:
+
+- **Conflict Detection:** Automatically checks new memories against existing knowledge for contradictions. Reports conflicts with suggestions to resolve.
+- **Proactive Suggestions:** After adding memories or practicing guides, suggests actions like distilling patterns, merging duplicates, or refining low-performing guides.
+- **Auto-linking:** Frequently co-read memories and topic-overlapping fragments are automatically connected with relations.
+
+Manual deep analysis is also available via dedicated tools.
+
+## Tools (24)
+
+### Memory (11)
+
+| Tool | Purpose |
+|------|---------|
+| `memory_read` | Read/search fragments. Summary mode or full detail by ID |
+| `memory_add` | Save findings. Auto-redacts secrets, detects duplicates and conflicts |
+| `memory_update` | Update fragment by ID |
+| `memory_feedback` | Positive/negative feedback, adjusts confidence |
+| `memory_forget` | Delete fragment |
+| `memory_merge` | Merge fragments, inherit relations & guide links |
+| `memory_relate` | Create typed links (`contradicts`, `supersedes`, `supports`, `related_to`) |
+| `memory_stats` | Fragment counts, confidence, project breakdown |
+| `memory_audit` | Integrity check for orphans, duplicates, anomalies |
+| `memory_library` | Full knowledge base snapshot with analysis signals and suggestions |
+
+### Guides (8)
+
+| Tool | Purpose |
+|------|---------|
+| `guide_get` | Get guides sorted by usage, filter by category or task |
+| `guide_practice` | Record guide usage. Auto-creates guide if missing |
+| `guide_create` | Create guide with detailed manual |
+| `guide_distill` | Transform memory → guide learning (bidirectional link) |
+| `guide_update` | Update guide properties, anti-patterns, pitfalls |
+| `guide_forget` | Remove guide |
+| `guide_merge` | Merge guides, inherit source memories |
+
+### Sessions (3)
+
+| Tool | Purpose |
+|------|---------|
+| `session_start` | Start traced session, pre-loads relevant context |
+| `session_end` | End session with review, auto-linking, and suggestions |
+| `session_stats` | Virtual session statistics |
+
+### Intelligence (4)
+
+| Tool | Purpose |
+|------|---------|
+| `conflict_scan` | Scan all memories for contradictions |
+| `proactive_analysis` | Full knowledge base analysis: stale, orphan, distill, deprecated |
+| `project_analytics` | Cross-session project health, growth rate, skill coverage |
+| `semantic_search` | TF-IDF similarity search across memories |
+
+## Configuration
+
+Optional config at `~/.lemma/config.json`:
+
+```json
+{
+  "token_budget": {
+    "full_content": 5000,
+    "summary_index": 1000,
+    "guides_detail": 1000
+  },
+  "injection": {
+    "max_full_content_fragments": 15,
+    "max_summary_fragments": 30,
+    "max_guides": 20
+  },
+  "virtual_session": {
+    "timeout_minutes": 30
+  }
+}
+```
+
+## File Locations
+
+| OS | Path |
+|---|---|
+| **Windows** | `C:\Users\{username}\.lemma\` |
+| **macOS/Linux** | `~/.lemma/` |
+
+Files: `lemma.db` (SQLite), `config.json`, `sessions/`, `logs/`
+
+## Search
+
+Lemma uses **SQLite FTS5** full-text search for memory lookup, dedup, and topic overlap detection.
+
+**Architecture:**
+- `searchAndSortFragments()` — FTS5 full-text search, fallback to in-memory ranking
+- `findSimilarFragment()` — FTS5 BM25-based dedup with keyword overlap fallback
+- `findTopicOverlaps()` — FTS5 search + word overlap scoring for related fragment detection
+
+## Data Storage
+
+All data is stored in a single SQLite database (`~/.lemma/lemma.db`):
+
+| Table | Purpose |
+|-------|---------|
+| `memories` | Memory fragments (FTS5 + metadata) |
+| `guides` | Procedural knowledge with learnings |
+| `sessions` | Session tracking and outcomes |
+| `relations` | Typed links between memories |
+| `guide_learnings` | Per-guide accumulated learnings |
+| `guide_memory_links` | Bidirectional guide ↔ memory links |
+
+Legacy JSONL files are automatically migrated on first run.
+
+## Security
+
+All data is stored locally in `~/.lemma/`. Nothing is sent to external servers. Secrets are automatically redacted from memory fragments (17 regex patterns for API keys, tokens, connection strings).
+
+## Documentation
+
+- [Development Guide](docs/development/DEVELOPMENT.md) — Architecture, project structure, testing
+- [Handlers Refactor](docs/development/HANDLERS-REFACTOR.md) — Targeted SQL migration plan
+- [Roadmap](docs/development/ROADMAP.md) — v0.9, v0.10, v1.0 plans
+- [Research](docs/research/README.md) — Academic papers that influenced Lemma's design
+- [Changelog](CHANGELOG.md) — Version history
+
+## License
+
+MIT

package/dist/db/database.d.ts

@@ -0,0 +1,12 @@
+import Database from "better-sqlite3";
+export declare class LemmaDB {
+    readonly db: Database.Database;
+    private stmtCache;
+    constructor(dbPath?: string);
+    prepareCached(sql: string): Database.Statement;
+    close(): void;
+}
+export declare function setDataDir(dir: string): void;
+export declare function getDb(dbPath?: string): LemmaDB;
+export declare function closeDb(): void;
+//# sourceMappingURL=database.d.ts.map

package/dist/db/database.d.ts.map

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package/dist/db/database.js

@@ -0,0 +1,77 @@
+import path from "path";
+import os from "os";
+import fs from "fs";
+import Database from "better-sqlite3";
+import * as sqliteVec from "sqlite-vec";
+import { logger } from "../logger.js";
+import { runMigrations } from "./migration.js";
+const DEFAULT_DB_PATH = path.join(os.homedir(), ".lemma", "lemma.db");
+export class LemmaDB {
+    db;
+    stmtCache = new Map();
+    constructor(dbPath = DEFAULT_DB_PATH) {
+        const dir = path.dirname(dbPath);
+        if (!fs.existsSync(dir)) {
+            fs.mkdirSync(dir, { recursive: true });
+        }
+        this.db = new Database(dbPath);
+        sqliteVec.load(this.db);
+        this.db.pragma("journal_mode = WAL");
+        this.db.pragma("synchronous = NORMAL");
+        this.db.pragma("foreign_keys = ON");
+        this.db.pragma("busy_timeout = 5000");
+        this.db.pragma("cache_size = -64000");
+        this.db.pragma("temp_store = MEMORY");
+        logger.info("Database opened", { path: dbPath });
+    }
+    prepareCached(sql) {
+        let stmt = this.stmtCache.get(sql);
+        if (!stmt) {
+            stmt = this.db.prepare(sql);
+            this.stmtCache.set(sql, stmt);
+        }
+        return stmt;
+    }
+    close() {
+        this.stmtCache.clear();
+        this.db.close();
+        logger.info("Database closed");
+    }
+}
+let _instance = null;
+let _currentPath = null;
+let _dataDir = null;
+export function setDataDir(dir) {
+    _dataDir = dir;
+    if (_instance) {
+        try {
+            _instance.close();
+        }
+        catch { }
+        _instance = null;
+        _currentPath = null;
+    }
+}
+export function getDb(dbPath) {
+    const resolvedPath = dbPath ?? (_dataDir ? path.join(_dataDir, "lemma.db") : DEFAULT_DB_PATH);
+    if (!_instance || _currentPath !== resolvedPath) {
+        if (_instance) {
+            try {
+                _instance.close();
+            }
+            catch { }
+        }
+        _instance = new LemmaDB(resolvedPath);
+        _currentPath = resolvedPath;
+        runMigrations(_instance);
+    }
+    return _instance;
+}
+export function closeDb() {
+    if (_instance) {
+        _instance.close();
+        _instance = null;
+        _currentPath = null;
+    }
+}
+//# sourceMappingURL=database.js.map

package/dist/db/database.js.map

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package/dist/db/index.d.ts

@@ -0,0 +1,6 @@
+export { getDb, closeDb, setDataDir, LemmaDB } from "./database.js";
+export { SCHEMA_V1, MIGRATIONS } from "./schema.js";
+export { runMigrations, migrateFromJsonl } from "./migration.js";
+export { addMemory, getMemoryById, updateMemory, deleteMemory, searchMemories, addRelation, getRelations, boostConfidence, decayMemories, getMemoryStats, mergeMemories } from "./memory-store.js";
+export declare function initDatabase(dbPath?: string): void;
+//# sourceMappingURL=index.d.ts.map

package/dist/db/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/db/index.js

@@ -0,0 +1,17 @@
+export { getDb, closeDb, setDataDir, LemmaDB } from "./database.js";
+export { SCHEMA_V1, MIGRATIONS } from "./schema.js";
+export { runMigrations, migrateFromJsonl } from "./migration.js";
+export { addMemory, getMemoryById, updateMemory, deleteMemory, searchMemories, addRelation, getRelations, boostConfidence, decayMemories, getMemoryStats, mergeMemories } from "./memory-store.js";
+import { getDb } from "./database.js";
+import { runMigrations, migrateFromJsonl } from "./migration.js";
+import { logger } from "../logger.js";
+export function initDatabase(dbPath) {
+    const db = getDb(dbPath);
+    runMigrations(db);
+    const migration = migrateFromJsonl(db);
+    if (migration.memories > 0 || migration.guides > 0 || migration.sessions > 0) {
+        logger.info("JSONL migration completed", migration);
+    }
+    logger.info("Database initialized");
+}
+//# sourceMappingURL=index.js.map

package/dist/db/index.js.map

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package/dist/db/library-store.d.ts

@@ -0,0 +1,117 @@
+import type { LemmaDB } from "./database.js";
+export interface FragmentSummary {
+    id: string;
+    title: string;
+    type: string;
+    project: string | null;
+    confidence: number;
+    age_days: number;
+    access_count: number;
+    positive_feedback: number;
+    negative_feedback: number;
+    distill_candidate: boolean;
+    relation_count: number;
+    fragment_preview: string;
+}
+export interface GuideSummary {
+    name: string;
+    category: string;
+    usage_count: number;
+    success_count: number;
+    failure_count: number;
+    success_rate: number | null;
+    learning_count: number;
+    deprecated: boolean;
+    source_memory_count: number;
+}
+export interface RelationSummary {
+    total: number;
+    by_type: Record<string, number>;
+    isolated_fragment_ids: string[];
+    hub_fragments: Array<{
+        id: string;
+        title: string;
+        count: number;
+    }>;
+}
+export interface AnalysisSignals {
+    confidence_distribution: Record<string, number>;
+    age_distribution: Record<string, number>;
+    stale_fragments: Array<{
+        id: string;
+        title: string;
+        age_days: number;
+        confidence: number;
+    }>;
+    similarity_candidates: Array<{
+        id_a: string;
+        id_b: string;
+        title_a: string;
+        title_b: string;
+        overlap: number;
+    }>;
+    distill_candidates: Array<{
+        id: string;
+        title: string;
+        type: string;
+    }>;
+    low_performing_guides: Array<{
+        name: string;
+        success_rate: number;
+        usage: number;
+    }>;
+    type_distribution: Record<string, number>;
+    project_distribution: Record<string, number>;
+    never_accessed_count: number;
+    deprecated_guides: string[];
+    superseded_fragments: Array<{
+        id: string;
+        title: string;
+    }>;
+    dangling_guide_links: Array<{
+        guide: string;
+        memory_id: string;
+    }>;
+}
+export interface SessionActivity {
+    recent_count: number;
+    outcomes: Record<string, number>;
+    most_accessed: Array<{
+        id: string;
+        title: string;
+        count: number;
+    }>;
+    never_accessed_count: number;
+}
+export interface LibrarySnapshot {
+    generated_at: string;
+    total_memories: number;
+    total_guides: number;
+    total_sessions: number;
+    health_status: string;
+    fragments: FragmentSummary[];
+    guides: GuideSummary[];
+    relations: RelationSummary;
+    signals: AnalysisSignals;
+    session_activity: SessionActivity;
+    suggestions: string[];
+}
+export declare function collectFragmentSummaries(db: LemmaDB, projectFilter?: string | null): FragmentSummary[];
+export declare function collectGuideSummaries(db: LemmaDB): GuideSummary[];
+export declare function collectRelationSummary(db: LemmaDB, fragmentIds: string[]): RelationSummary;
+export declare function findSimilarPairs(fragments: FragmentSummary[], threshold?: number): Array<{
+    id_a: string;
+    id_b: string;
+    title_a: string;
+    title_b: string;
+    overlap: number;
+}>;
+export declare function collectAnalysisSignals(db: LemmaDB, fragments: FragmentSummary[]): AnalysisSignals;
+export declare function collectSessionActivity(db: LemmaDB): SessionActivity;
+export declare function generateSuggestions(snapshot: LibrarySnapshot): string[];
+export declare function collectLibrarySnapshot(db: LemmaDB, options?: {
+    project?: string | null;
+    focus?: string;
+}): LibrarySnapshot;
+export declare function formatLibrarySnapshot(snapshot: LibrarySnapshot, focus: string): string;
+//# sourceMappingURL=library-store.d.ts.map

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