@danielsimonjr/memory-mcp 11.1.1 → 12.2.3

package/README.md

@@ -1,6 +1,6 @@
 # Memory MCP Server
 
-[![Version](https://img.shields.io/badge/version-10.1.0-blue.svg)](https://github.com/danielsimonjr/memory-mcp)
+[![Version](https://img.shields.io/badge/version-12.2.0-blue.svg)](https://github.com/danielsimonjr/memory-mcp)
 [![NPM](https://img.shields.io/npm/v/@danielsimonjr/memory-mcp.svg)](https://www.npmjs.com/package/@danielsimonjr/memory-mcp)
 [![License](https://img.shields.io/badge/license-MIT-green.svg)](LICENSE)
 [![MCP](https://img.shields.io/badge/MCP-1.0-purple.svg)](https://modelcontextprotocol.io)
@@ -9,7 +9,7 @@
 
 An **enhanced fork** of the official [Model Context Protocol](https://modelcontextprotocol.io) memory server with advanced features for **hierarchical nesting**, **intelligent compression**, **semantic search**, **graph algorithms**, **archiving**, **advanced search**, and **multi-format import/export**.
 
-> **Enterprise-grade knowledge graph** with 59 tools, hierarchical organization, semantic search with embeddings, graph traversal algorithms, duplicate detection, smart archiving, and sophisticated search capabilities for long-term memory management.
+> **Enterprise-grade knowledge graph** with **160 tools** including hierarchical organization, semantic search with embeddings, graph traversal algorithms, duplicate detection, smart archiving, project scoping, temporal knowledge graph, semantic forget, agent diary, **entity bitemporal validity (η.4.4)**, **optimistic concurrency control (η.5.5.c)**, **role-based access control (η.6.1)**, **W3C Linked Data exports** (Turtle / JSON-LD / RDF/XML — η.5.4), **PII redaction on export** (η.6.3), **procedural memory (3B.4)**, **active retrieval (3B.5)**, **causal reasoning (3B.6)**, and **world model (3B.7)** for long-term memory management.
 
 ## Table of Contents
 
@@ -50,6 +50,27 @@ An **enhanced fork** of the official [Model Context Protocol](https://modelconte
 | **Saved Searches** | 5 | Store and execute frequent queries |
 | **Import/Export** | 2 | 7 export formats with brotli compression, 3 import formats |
 | **Graph Analytics** | 2 | Statistics, validation, integrity checks |
+| **Ref Index** | 4 | Cross-session symbolic reference registration and resolution |
+| **Artifacts** | 3 | Named versioned content blobs attached to entities |
+| **Temporal Search** | 1 | Time-window filtered search across the knowledge graph |
+| **Distillation** | 1 | Configure automated observation distillation pipelines |
+| **Freshness** | 5 | Staleness tracking, expiry detection, and freshness reporting |
+| **LLM Query** | 1 | Natural-language question answering over the graph |
+| **Governance** | 4 | Transactional audit trail, history, and rollback |
+| **Role Profiles** | 2 | Per-agent role assignment and profile listing |
+| **Entropy** | 2 | Entropy-based noise filtering and information density scoring |
+| **Consolidation** | 3 | Background memory consolidation scheduling and control |
+| **Formatter** | 1 | Salience-budget-aware context formatting |
+| **Collaborative** | 1 | Multi-agent context synthesis |
+| **Failure Handling** | 2 | Session failure distillation and graceful session end |
+| **Cognitive Load** | 2 | Working-memory load analysis and adaptive reduction |
+| **Project Scoping** | 1 | List and filter entities by project |
+| **Memory Versioning** | 2 | Entity version chains and per-entity version history |
+| **Semantic Forget** | 1 | Two-tier deletion: exact match → semantic similarity fallback |
+| **Profiles** | 2 | User/agent profile get and update |
+| **Temporal KG** | 3 | Temporal relation invalidation, time-travel queries, relation timeline |
+| **Ingestion** | 1 | Format-agnostic conversation/document ingestion pipeline |
+| **Agent Diary** | 2 | Per-agent persistent journal write and read |
 
 ### Comparison with Official Memory Server
 
@@ -72,7 +93,7 @@ An **enhanced fork** of the official [Model Context Protocol](https://modelconte
 | **Backup & Restore** | ❌ | ✅ Compressed snapshots |
 | **Intelligent Search** | ❌ | ✅ Hybrid + Query Analysis + Reflection |
 | **Observation Normalization** | ❌ | ✅ Coreference resolution + temporal anchoring |
-| **Total Tools** | 11 | **59** |
+| **Total Tools** | 11 | **106** |
 | **Code Structure** | Monolithic | **Modular** (77 files) |
 
 ## Quick Start
@@ -221,7 +242,9 @@ Discrete facts about entities. Each observation should be atomic and independent
 
 ## API Reference
 
-### Complete Tool List (59 Tools)
+### Complete Tool List (160 Tools)
+
+> Tool count: 160 tools across 51 categories. The 23 newest tools (Phase 15 / memoryjs v1.14+) are documented at the end under **Phase 15** sections. For full per-tool schemas see [docs/architecture/API.md](docs/architecture/API.md).
 
 #### Entity Operations (4 tools)
 | Tool | Description |
@@ -338,6 +361,190 @@ Discrete facts about entities. Each observation should be atomic and independent
 | `export_graph` | Export in 7 formats (JSON, CSV, GraphML, GEXF, DOT, Markdown, Mermaid) with compression |
 | `import_graph` | Import from JSON/CSV/GraphML with merge strategies |
 
+#### Ref Index (4 tools)
+| Tool | Description |
+|------|-------------|
+| `register_ref` | Register a symbolic reference pointing to an entity |
+| `resolve_ref` | Resolve a symbolic reference to its target entity |
+| `deregister_ref` | Remove a registered symbolic reference |
+| `list_refs` | List all registered symbolic references |
+
+#### Artifacts (3 tools)
+| Tool | Description |
+|------|-------------|
+| `create_artifact` | Create a named versioned content blob attached to an entity |
+| `get_artifact` | Retrieve an artifact by name and optional version |
+| `list_artifacts` | List all artifacts, optionally filtered by entity |
+
+#### Temporal Search (1 tool)
+| Tool | Description |
+|------|-------------|
+| `search_by_time` | Search entities and observations within a time window |
+
+#### Distillation (1 tool)
+| Tool | Description |
+|------|-------------|
+| `configure_distillation` | Configure automated observation distillation pipelines |
+
+#### Freshness (5 tools)
+| Tool | Description |
+|------|-------------|
+| `check_freshness` | Check freshness status of a specific entity |
+| `get_stale_entities` | List entities that have exceeded their staleness threshold |
+| `get_expired_entities` | List entities past their explicit expiry date |
+| `refresh_entity` | Reset the freshness timestamp on an entity |
+| `freshness_report` | Generate a full freshness report across the graph |
+
+#### LLM Query (1 tool)
+| Tool | Description |
+|------|-------------|
+| `query_natural_language` | Answer natural-language questions over the knowledge graph |
+
+#### Governance (4 tools)
+| Tool | Description |
+|------|-------------|
+| `governance_transaction` | Execute a governed, audited graph transaction |
+| `audit_query` | Query the audit log with filters |
+| `audit_history` | Retrieve full audit history for an entity |
+| `rollback_operation` | Roll back a previously recorded operation |
+
+#### Role Profiles (2 tools)
+| Tool | Description |
+|------|-------------|
+| `set_agent_role` | Assign a role profile to the current agent context |
+| `list_role_profiles` | List all available agent role profiles |
+
+#### Entropy (2 tools)
+| Tool | Description |
+|------|-------------|
+| `enable_entropy_filter` | Enable entropy-based noise filtering for search results |
+| `compute_entropy` | Compute information-density entropy score for an entity |
+
+#### Consolidation (3 tools)
+| Tool | Description |
+|------|-------------|
+| `start_consolidation` | Start the background memory consolidation service |
+| `stop_consolidation` | Stop the background memory consolidation service |
+| `run_consolidation_now` | Trigger an immediate consolidation pass |
+
+#### Formatter (1 tool)
+| Tool | Description |
+|------|-------------|
+| `format_with_salience_budget` | Format context output respecting a token salience budget |
+
+#### Collaborative (1 tool)
+| Tool | Description |
+|------|-------------|
+| `synthesize_collaborative_context` | Synthesize a unified context view from multiple agent memory spaces |
+
+#### Failure Handling (2 tools)
+| Tool | Description |
+|------|-------------|
+| `distill_failure` | Distill and store key observations from a failed session |
+| `end_session` | Gracefully end a session and persist in-flight state |
+
+#### Cognitive Load (2 tools)
+| Tool | Description |
+|------|-------------|
+| `analyze_cognitive_load` | Analyze working-memory load in the current context |
+| `adaptive_reduce_memories` | Adaptively reduce memory set to fit cognitive load target |
+
+#### Project Scoping (1 tool)
+| Tool | Description |
+|------|-------------|
+| `list_projects` | List all project IDs present in the graph and filter entities by project |
+
+#### Memory Versioning (2 tools)
+| Tool | Description |
+|------|-------------|
+| `get_entity_versions` | Retrieve all versions of a versioned entity by name |
+| `get_version_chain` | Get the full version chain from root to latest for an entity |
+
+#### Semantic Forget (1 tool)
+| Tool | Description |
+|------|-------------|
+| `forget_memory` | Delete an entity by exact name, falling back to semantic similarity if no exact match found |
+
+#### Profiles (2 tools)
+| Tool | Description |
+|------|-------------|
+| `get_profile` | Retrieve a user or agent profile entity |
+| `update_profile` | Update observations and metadata on a profile entity |
+
+#### Temporal KG (3 tools)
+| Tool | Description |
+|------|-------------|
+| `invalidate_relation` | Mark a relation as ended by setting its temporal validity end date |
+| `query_as_of` | Retrieve all relations for an entity that were valid at a given point in time |
+| `timeline` | Return a chronological list of relation events for an entity |
+
+#### Ingestion (1 tool)
+| Tool | Description |
+|------|-------------|
+| `ingest` | Ingest a conversation, document, or free-form text into the knowledge graph |
+
+#### Agent Diary (2 tools)
+| Tool | Description |
+|------|-------------|
+| `diary_write` | Append an entry to the agent's persistent diary |
+| `diary_read` | Read diary entries for an agent, optionally filtered by date range |
+
+#### Entity Bitemporal Validity (5 tools) — Phase 15 / memoryjs η.4.4
+| Tool | Description |
+|------|-------------|
+| `invalidate_entity` | Stamp `validUntil` on an entity (idempotent; entity remains queryable for past timestamps via `entity_as_of`) |
+| `entity_as_of` | Time-travel query: returns entity state at a given ISO 8601 timestamp, or `null` if invalidated then |
+| `entity_timeline` | All temporal versions of an entity in chronological order; integrates the v1.8 supersession chain |
+| `invalidate_observation` | Per-observation invalidation via parallel `observationMeta[]` entry on the entity |
+| `observations_as_of` | Filter observations valid at a given timestamp; observations without meta are treated as unbounded |
+
+#### Optimistic Concurrency Control (1 tool) — Phase 15 / memoryjs η.5.5.c
+| Tool | Description |
+|------|-------------|
+| `update_entity` | Update an entity with optional `expectedVersion`; throws `VersionConflictError` on stale version. OCC-guarded writes auto-increment `version`. Omit `expectedVersion` for legacy last-write-wins. |
+
+#### RBAC (4 tools) — Phase 15 / memoryjs η.6.1
+| Tool | Description |
+|------|-------------|
+| `rbac_assign_role` | Grant `reader` / `writer` / `admin` / `owner` (or custom) role to an agent; optional `resourceType`, `scope` prefix, `validFrom` / `validUntil` window |
+| `rbac_revoke_role` | Remove a specific role assignment matched by `agentId + role + resourceType` |
+| `rbac_check_permission` | Check whether an agent can perform `read` / `write` / `delete` / `manage` on a resource type; falls back to `defaultRole=reader` for unassigned agents |
+| `rbac_list_assignments` | List all role assignments for an agent; optional `activeOnly` filter |
+
+#### Procedural Memory (5 tools) — Phase 15 / memoryjs 3B.4
+| Tool | Description |
+|------|-------------|
+| `add_procedure` | Persist an executable how-to sequence: 1-indexed steps with optional fallback chains and free-form trigger phrases |
+| `get_procedure` | Load a procedure by id |
+| `match_procedure` | Token-overlap match a context description against stored procedures; returns ranked Jaccard-like scores |
+| `refine_procedure` | Apply caller feedback after execution; updates `successRate` via EWMA (α=0.2) |
+| `get_procedure_step` | Load step by 1-indexed `order`, or get the next step relative to `currentOrder` |
+
+#### Active Retrieval (1 tool) — Phase 15 / memoryjs 3B.5
+| Tool | Description |
+|------|-------------|
+| `adaptive_retrieve` | Iterative query-rewriting retrieval (search → score coverage → rewrite); stops early when `coverage ≥ minCoverage`. Pure symbolic — no LLM provider required. |
+
+#### Causal Reasoning (4 tools) — Phase 15 / memoryjs 3B.6
+| Tool | Description |
+|------|-------------|
+| `find_causes` | Causal chains ending at the named effect; sorted by product-of-edge causalStrength |
+| `find_effects` | Symmetric counterpart starting at the named cause |
+| `counterfactual_query` | "If we remove edge (removeFrom → removeTo), is `predict` still reachable from `seed`?" Returns surviving chains. Pure: does not mutate the graph. |
+| `detect_causal_cycles` | Detect cycles in the causal subgraph rooted at `seed` |
+
+#### World Model (3 tools) — Phase 15 / memoryjs 3B.7
+| Tool | Description |
+|------|-------------|
+| `get_world_state` | Capture a fresh snapshot of the live graph (capped at 1000 entities; over-cap prefers high-importance) |
+| `validate_fact_against_world` | Validate a candidate observation against a target entity via `MemoryValidator.validateConsistency`. Returns `{result: null, reason: 'embedding_provider_unavailable'}` when the local embedding provider is selected without `@xenova/transformers` installed. |
+| `predict_outcome` | Predict downstream effects of an action by walking the causal subgraph (delegates to `find_effects`) |
+
+#### Phase 15 enhancements to existing tools
+- **`export_graph`** — Now accepts `format: 'turtle' | 'rdf-xml' | 'json-ld'` for W3C Linked Data exports (memoryjs η.5.4) and `redactPii: true` to scrub PII (email / SSN / credit-card / phone / IPv4) from observations using the η.6.3 `PiiRedactor`.
+- **`create_entities`** — Now accepts v1.6 freshness fields (`ttl`, `confidence`), v1.8 project scope (`projectId`), and η.4.4 bitemporal fields (`validFrom`, `validUntil`, `observationMeta`) per entity.
+- **`set_memory_visibility`** — Auto-promotes plain entities to `AgentEntity` (stamps `agentId` / `memoryType` / `confidence`) instead of silently returning `null`. Supports η.5.5.b extensions (`allowedRoles`, `visibleFrom`, `visibleUntil`).
+
 ## Configuration
 
 ### Environment Variables
@@ -433,7 +640,7 @@ npm run docs:deps     # Generate dependency graph
 ```
 ┌─────────────────────────────────────────────────────┐
 │  Layer 1: MCP Protocol Layer                        │
-│  server/MCPServer.ts + toolDefinitions (59 tools)   │
+│  server/MCPServer.ts + toolDefinitions (160 tools)  │
 │  + toolHandlers + responseCompressor                │
 └──────────────────────┬──────────────────────────────┘
                        │
@@ -478,7 +685,7 @@ memory-mcp/
 │   │   └── index.ts
 │   ├── server/                     # MCP protocol (4 files)
 │   │   ├── MCPServer.ts                # Server setup
-│   │   ├── toolDefinitions.ts          # 59 tool schemas
+│   │   ├── toolDefinitions.ts          # 160 tool schemas
 │   │   ├── toolHandlers.ts             # Handler registry
 │   │   └── responseCompressor.ts       # Brotli compression
 │   ├── search/                     # Search implementations (29 files)
@@ -543,7 +750,7 @@ memory-mcp/
 Comprehensive documentation in `docs/`:
 
 **Architecture**
-- [API.md](docs/architecture/API.md) - Complete API documentation for all 59 tools
+- [API.md](docs/architecture/API.md) - Complete API documentation for all 160 tools
 - [ARCHITECTURE.md](docs/architecture/ARCHITECTURE.md) - Technical architecture and system design
 - [COMPONENTS.md](docs/architecture/COMPONENTS.md) - Component breakdown and responsibilities
 - [OVERVIEW.md](docs/architecture/OVERVIEW.md) - High-level project overview
@@ -578,12 +785,14 @@ We welcome contributions!
 
 All notable changes are documented in **[CHANGELOG.md](CHANGELOG.md)**.
 
-**Current version**: v10.1.0 - [View full changelog](CHANGELOG.md)
+**Current version**: v12.2.0 - [View full changelog](CHANGELOG.md)
 
 Recent highlights:
-- **v10.1.0**: Documentation updates, 5 missing Phase 12 test files, architecture docs refresh
-- **v10.0.0**: Phase 12 Performance Optimization - BM25 search, parallel execution, query plan caching, embedding cache, incremental indexing
-- **v9.8.3**: SQLite storage support fix, JSON-RPC communication fix
+- **v12.2.0** (160 tools): 23 new tools — entity bitemporal validity (η.4.4), OCC update (η.5.5.c), RBAC (η.6.1), procedural memory (3B.4), active retrieval (3B.5), causal reasoning (3B.6), world model (3B.7), plus W3C Linked Data exports (η.5.4) and PII redaction (η.6.3) wired into existing `export_graph`. Plus four pre-publish fixes from end-to-end MCP smoke testing (memoryjs v1.14+).
+- **v12.1.0** (106 tools): 12 new tools — Project Scoping, Memory Versioning, Semantic Forget, Profiles, Temporal KG, Ingestion, Agent Diary (memoryjs v1.8.0/v1.9.0)
+- **v12.0.0** (94 tools): 32 new tools — Ref Index, Artifacts, Temporal Search, Distillation, Freshness, LLM Query, Governance, Role Profiles, Entropy, Consolidation, Formatter, Collaborative, Failure Handling, Cognitive Load
+- **v11.1.1**: npm tarball cleanup, excluded data files from published package
+- **v11.1.0**: MCP error framing, dynamic server version, handler smoke tests, response compressor tests
 
 ## License
 

package/dist/index.d.ts

@@ -7,9 +7,9 @@
  *
  * @module index
  */
-import { defaultMemoryPath, ensureMemoryFilePath, ManagerContext, type Entity, type Relation, type KnowledgeGraph, type GraphStats, type ValidationReport, type ValidationIssue, type ValidationWarning, type SavedSearch, type TagAlias, type SearchResult, type BooleanQueryNode, type ImportResult, type CompressionResult } from '@danielsimonjr/memoryjs';
+import { defaultMemoryPath, ensureMemoryFilePath, ManagerContext, type Entity, type Relation, type KnowledgeGraph, type GraphStats, type ValidationReport, type ValidationIssue, type ValidationWarning, type SavedSearch, type TagAlias, type SearchResult, type BooleanQueryNode, type ImportResult, type CompressionResult, type ArtifactEntity, type ArtifactType, type ArtifactFilter, type FreshnessReport, type AuditEntry, type AuditOperation, type RefEntry, type RefIndexStats, type AgentRole, type RoleProfile, type CognitiveLoadMetrics, type AdaptiveReductionResult, type SynthesisResult, type FailureDistillationResult, type DistilledLesson } from '@danielsimonjr/memoryjs';
 export { defaultMemoryPath, ensureMemoryFilePath };
-export type { Entity, Relation, KnowledgeGraph, GraphStats, ValidationReport, ValidationIssue, ValidationWarning, SavedSearch, TagAlias, SearchResult, BooleanQueryNode, ImportResult, CompressionResult, };
+export type { Entity, Relation, KnowledgeGraph, GraphStats, ValidationReport, ValidationIssue, ValidationWarning, SavedSearch, TagAlias, SearchResult, BooleanQueryNode, ImportResult, CompressionResult, ArtifactEntity, ArtifactType, ArtifactFilter, FreshnessReport, AuditEntry, AuditOperation, RefEntry, RefIndexStats, AgentRole, RoleProfile, CognitiveLoadMetrics, AdaptiveReductionResult, SynthesisResult, FailureDistillationResult, DistilledLesson, };
 export { ManagerContext };
 export { ManagerContext as KnowledgeGraphManager };
 //# sourceMappingURL=index.d.ts.map

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package/dist/server/toolDefinitions.d.ts

@@ -2,7 +2,7 @@
  * MCP Tool Definitions
  *
  * Extracted from MCPServer.ts to reduce file size and improve maintainability.
- * Contains all 59 tool schemas for the Knowledge Graph MCP Server.
+ * Contains all 106 tool schemas for the Knowledge Graph MCP Server.
  *
  * @module server/toolDefinitions
  */

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