Gnapsis

Code intelligence graph - MCP server for semantic codebase understanding with PostgreSQL + Apache AGE.

What is Gnapsis?

Gnapsis is an MCP (Model Context Protocol) server that helps AI assistants understand codebases through a semantic knowledge graph. Instead of just searching text, it tracks entities (domains, features, modules, structs, functions), their relationships, and anchors them to specific code locations.

Think of it as a structured memory layer for AI coding assistants.

Features

• Semantic Knowledge Graph: Organize entities in a hierarchy (Domain → Feature → Namespace → Component → Unit)
• Document References: Anchor entities to code with line-level precision
• Semantic Search: Find entities by meaning, not just keywords
• Subgraph Queries: Extract relevant context within token budgets
• Staleness Detection: Know when references become outdated via git
• TOON Output: Token-efficient output format (40-60% fewer tokens than JSON)
• Multi-Project Support: Each project gets its own graph in a shared database

Quick Start

1. Prerequisites

PostgreSQL with Apache AGE and pgvector:

# Using Docker Compose (recommended)
# Builds a custom image with AGE 1.6.0 (PG17) + pgvector 0.8.0
docker compose up -d

This starts a PostgreSQL instance with Apache AGE and pgvector extensions pre-configured, including the initial graph creation.

Rust 1.75+ for building from source.

2. Installation

git clone https://github.com/e7nd7r/gnapsis.git
cd gnapsis

# Install the binary
cargo install --path .

3. Configuration

Gnapsis uses a layered configuration approach (highest priority last):

1. Global config (~/.config/gnapsis/config.toml) - database and embedding settings
2. Project config (.gnapsis.toml in your project root) - project name and sources
3. Environment variables (GNAPSIS_*) - overrides for any setting

Global config (~/.config/gnapsis/config.toml):

[postgres]
uri = "postgresql://postgres:postgres@localhost:5432/gnapsis_dev"

[embedding]
provider = "fastembed"
model = "BAAI/bge-small-en-v1.5"
dimensions = 384

Project config (.gnapsis.toml in your project root):

[project]
name = "my-project"
# Graph name is always gnapsis_<name> (e.g., gnapsis_my_project)

Multi-source projects - span multiple directories (e.g., code + docs):

[project]
name = "my-project"

[[project.sources]]
id = "default"
path = "/path/to/code-repo"

[[project.sources]]
id = "docs"
path = "/path/to/documentation-vault"

See .gnapsis.toml.example for a complete reference.

4. MCP Setup

Add to your project's .mcp.json:

{
  "mcpServers": {
    "gnapsis": {
      "command": "gnapsis",
      "args": ["mcp"]
    }
  }
}

5. Initialize the Project

Once connected via MCP, initialize the database:

Use init_project to set up the database schema

This creates the schema, scopes, and default categories.

Workflow

Understanding the Hierarchy

Gnapsis organizes knowledge in scopes (levels of abstraction):

Domain          (e.g., "Authentication", "Payments")
  └── Feature   (e.g., "JWT Validation", "OAuth Flow")
      └── Namespace   (e.g., "auth::providers", "services")
          └── Component   (e.g., UserService struct, AuthTrait)
              └── Unit   (e.g., validate() method, MAX_RETRIES constant)

Each entity has a category that classifies it within its scope:

• Domain: core, infrastructure
• Feature: functional, technical, non-functional
• Namespace: module, library
• Component: struct, trait, enum, class
• Unit: function, method, constant, field

Creating Entities

Entities need: name, description, category, and at least one reference to code.

Example - creating a domain:

Use create_entity with:
- name: "Authentication"
- description: "Domain for user authentication and authorization"
- category_ids: [<core-domain-category-id>]
- commands: [{ type: "add", ref_type: "text", document_path: "README.md", description: "Auth section", start_line: 10, end_line: 20 }]

Example - creating a component under a namespace:

Use create_entity with:
- name: "UserService"
- description: "Service for user management operations"
- category_ids: [<struct-category-id>]
- parent_ids: [<services-namespace-id>]
- commands: [{ type: "add", ref_type: "code", document_path: "src/services/user.rs", lsp_symbol: "UserService", description: "UserService struct" }]

Querying the Graph

Get project overview - See all domains, features, namespaces, and categories:

Use project_overview

Semantic search - Find entities by meaning:

Use search with query: "user authentication validation"

Subgraph query - Get related entities within a token budget:

Use query with semantic_query: "how does authentication work"

Find entities - Filter by scope, category, or parent:

Use find_entities with scope: "Component", category: "struct"

Analyzing Documents

Check what's tracked in a file and detect stale references:

Use analyze_document with document_path: "src/services/user.rs"

Validating the Graph

Check for integrity issues (orphans, cycles, missing references):

Use validate_graph

Output Formats

Tools that return large results support TOON (Token-Oriented Object Notation) for 40-60% token savings:

Use query with semantic_query: "...", output_format: "toon"

Supported on: query, search, analyze_document, project_overview

Tools Reference

Tool	Description
init_project	Initialize database schema
project_overview	Get taxonomy, entities, and stats
create_category	Create new category at a scope
create_entity	Create entity with references
update_entity	Update entity (re-embeds on description change)
delete_entity	Delete entity (must have no children)
get_entity	Get entity with full context
find_entities	Find entities by scope/category/parent
search	Semantic search across entities and references
query	Semantic subgraph extraction
get_document_entities	Get entities referenced in a document
analyze_document	Document analysis with staleness detection
alter_references	Bulk update/delete references
validate_graph	Check graph integrity
lsp_refresh	Refresh references using LSP data
get_changed_files	Get files changed between commits

Development

Gnapsis uses just for development tasks:

just db-up          # Start the database
just build          # Build the project
just test           # Run unit tests
just test-integration  # Run integration tests (requires db-up)
just lint           # Run clippy
just fmt            # Format code
just db-shell       # Connect to psql
just cypher "MATCH (n) RETURN n"  # Run a Cypher query

Run just with no arguments to see all available commands.

License

MIT - See LICENSE for details.