Project Structure

AutoMem Server (`verygoodplugins/automem`)

The AutoMem server repository follows a hybrid Python/Node.js structure with three primary deployment targets: the core Flask API service, the MCP bridge server, and operational scripts.

Directory Layout

graph TB
    Root["automem/\nRepository Root"]

    subgraph "Python Source"
        AppPy["app.py\nMain Flask application"]
        ConsolPy["consolidation.py\nBackground workers"]

        Root --> AppPy
        Root --> ConsolPy
    end

    subgraph "Node.js Integration"
        MCPDir["mcp-sse-server/\nMCP bridge service"]
        MCPNode["node_modules/\n(ignored)"]

        Root --> MCPDir
        MCPDir --> MCPNode
    end

    subgraph "Scripts & Tools"
        ScriptsDir["scripts/\nOperational scripts"]
        BackupScript["backup_automem.py"]
        RecoverScript["recover_from_qdrant.py"]
        MonitorScript["health_monitor.py"]

        Root --> ScriptsDir
        ScriptsDir --> BackupScript
        ScriptsDir --> RecoverScript
        ScriptsDir --> MonitorScript
    end

    subgraph "Configuration"
        Env[".env\n(ignored, contains secrets)"]
        Requirements["requirements.txt\nrequirements-dev.txt"]
        Dockerfile["Dockerfile"]
        RailwayToml["railway.toml"]

        Root --> Requirements
        Root --> Dockerfile
        Root --> RailwayToml
    end

Core Service Modules

`app.py` — Flask API Service

The monolithic Flask application serving all REST API endpoints.

Component	Lines	Responsibility
Flask Routes	~100-600	`/memory`, `/recall`, `/associate`, `/consolidate`, `/health`
Authentication	209-211	`API_TOKEN` and `ADMIN_TOKEN` validation
MemoryClassifier	996-1084	Pattern-based + LLM memory classification
Enrichment Pipeline	1200-1800	Entity extraction, temporal links, semantic neighbors
Embedding Worker	1900-2100	Batch embedding generation (OpenAI API)
Graph Operations	Various	FalkorDB query wrappers
Vector Operations	Various	Qdrant search/store wrappers
Scoring Functions	476-521	Hybrid recall scoring logic

Key classes:

MemoryClassifier (app.py:996-1084): Classifies memories into types (Decision, Pattern, etc.)
Background worker threads start at application initialization

Configuration constants defined at app.py:74-211.

`consolidation.py` — Dream-Inspired Maintenance

Self-contained consolidation engine with no Flask dependencies. Designed for both scheduled background execution and manual CLI invocation.

Class	Purpose	Key Methods
`MemoryConsolidator`	Execute consolidation tasks	`consolidate()`, `calculate_relevance_score()`, `discover_creative_associations()`, `cluster_similar_memories()`, `apply_controlled_forgetting()`
`ConsolidationScheduler`	Manage task intervals	`run_scheduled_tasks()`, `should_run()`, `get_next_runs()`
`GraphLike` (Protocol)	Database abstraction	`query()` method only
`VectorStoreProtocol` (Protocol)	Vector store abstraction	`delete()` method only

Caching optimization: Relationship count queries use @lru_cache with hourly invalidation (consolidation.py:152-176).

`mcp-sse-server/` — Node.js SSE Bridge

Translates Model Context Protocol (MCP) tool calls into AutoMem REST API requests. Enables ChatGPT, ElevenLabs, and other SSE-compatible AI platforms to access AutoMem.

Port: 8080 (configurable via PORT environment variable)
Connects to Flask API at AUTOMEM_URL (default: http://localhost:8001)
Key files: index.js (SSE endpoint handlers, JSON-RPC to REST translation), package.json

Operational Scripts

Production-ready Python scripts for data protection and disaster recovery.

Script	Purpose	Dependencies
`backup_automem.py`	Export FalkorDB + Qdrant to S3/local	`boto3`, `falkordb`, `qdrant-client`
`recover_from_qdrant.py`	Rebuild FalkorDB graph from Qdrant payloads	`falkordb`, `qdrant-client`
`restore_from_backup.py`	Restore from compressed JSON backups	`falkordb`, `qdrant-client`
`health_monitor.py`	Detect count drift between databases	`requests`, optional webhook client

All scripts connect directly to FalkorDB and Qdrant, bypassing the Flask API. They read the same environment variables as app.py. The backup_automem.py script runs every 6 hours via a GitHub Actions workflow.

Configuration Management

Environment Variable Load Order (app.py:43-45)

Load .env from repository root
Load ~/.config/automem/.env (user-specific overrides)
Railway injects secrets as environment variables

Key Configuration Categories

Category	Example Variables	Defined In
Database Connections	`FALKORDB_HOST`, `QDRANT_URL`	app.py:75-78
Authentication	`AUTOMEM_API_TOKEN`, `ADMIN_API_TOKEN`	app.py:209-210
Consolidation Intervals	`CONSOLIDATION_DECAY_INTERVAL_SECONDS`	app.py:82-92
Enrichment Tuning	`ENRICHMENT_MAX_ATTEMPTS`, `ENRICHMENT_SIMILARITY_THRESHOLD`	app.py:104-112
Embedding Batching	`EMBEDDING_BATCH_SIZE`, `EMBEDDING_BATCH_TIMEOUT_SECONDS`	app.py:115-116
Search Weights	`SEARCH_WEIGHT_VECTOR`, `SEARCH_WEIGHT_KEYWORD`	app.py:201-207

Containerization Files

File	Purpose	Key Settings
`Dockerfile`	Container image definition	Python 3.11, installs spaCy model
`docker-compose.yml`	Local development stack	Orchestrates Flask + FalkorDB + Qdrant
`railway.json`	Railway deployment config	Service definitions, port mappings

Docker Compose services:

memory-service: Flask API (port 8001)
falkordb: Graph database (port 6379)
qdrant: Vector database (port 6333)

Testing Infrastructure

`tests/` — Pytest Test Suites

Test coverage focuses on consolidation engine logic, which has the most complex state management.

Mock objects (tests/test_consolidation_engine.py:12-78):

FakeGraph: Implements GraphLike protocol with in-memory state
FakeVectorStore: Implements VectorStoreProtocol for deletion tracking
FakeResult: Mimics FalkorDB query result structure

Test philosophy: Consolidation tests use deterministic mocks and frozen time to ensure reproducible relevance score calculations.

File Naming Conventions

Pattern	Purpose	Examples
`*.py`	Python modules	`app.py`, `consolidation.py`
`test_*.py`	Pytest test files	`test_consolidation_engine.py`
`*_automem.py`	Operational scripts	`backup_automem.py`, `restore_from_backup.py`
`*.md`	Markdown documentation	`README.md`, `OPTIMIZATIONS.md`
`*.sh`	Shell scripts	`test-optimizations.sh`
`.env`	Environment configuration	`.env`, `~/.config/automem/.env`
`*.yml`	YAML configuration	`docker-compose.yml`

Gitignored patterns: __pycache__/, venv/, .venv/, backups/, node_modules/, .env

Deployment Artifact Boundaries

Different deployment scenarios use different subsets of the repository:

Railway (Production): Single container running app.py, consolidation runs in background thread
Docker Compose (Local): Multi-container with separate database services
Bare Metal (Development): Python process + external databases
MCP Bridge: Optional Node.js service for AI platform integration
Scripts: Standalone utilities connecting directly to databases

MCP Client (`verygoodplugins/mcp-automem`)

The mcp-automem package uses a TypeScript project structure with distinct directories for source code, templates, build artifacts, and configuration files.

Directory Layout

graph TB
    ROOT["."]

    ROOT --> SRC["src/"]
    ROOT --> TEMPLATES["templates/"]
    ROOT --> PLUGINS["plugins/"]
    ROOT --> DIST["dist/"]
    ROOT --> GITHUB[".github/"]
    ROOT --> HUSKY[".husky/"]

    SRC --> INDEX["index.ts\n(MCP server entry point)"]
    SRC --> CLIENT["automem-client.ts\n(HTTP client)"]
    SRC --> TYPES["types.ts\n(TypeScript interfaces)"]
    SRC --> CLI["cli/"]

    CLI --> SETUP["setup.ts"]
    CLI --> CLAUDECODE["claude-code.ts"]
    CLI --> QUEUE["queue.ts"]
    CLI --> CONFIG["config.ts"]
    CLI --> CURSOR["cursor.ts"]
    CLI --> CODEX["codex.ts"]
    CLI --> OPENCLAW["openclaw.ts"]

    TEMPLATES --> TCCLI["claude-code/\nhooks, scripts, settings"]
    TEMPLATES --> TCUR["cursor/\n.mdc rule files"]
    TEMPLATES --> TCODEX["codex/\nAGENTS.md"]
    TEMPLATES --> TOCLAW["openclaw/\nSKILL.md"]
    TEMPLATES --> TWARP["warp/\nwarp-rules.md"]

    PLUGINS --> PCCLI[".claude-plugin/\nmarketplace files"]
    PLUGINS --> PSERVER["server/\nserver.json metadata"]

    GITHUB --> WORKFLOWS["workflows/\nCI/CD YAML files"]

    DIST --> DISTJS["*.js\n(Compiled code)"]
    DIST --> DISTDTS["*.d.ts\n(Type definitions)"]
    DIST --> DISTMAP["*.js.map\n(Source maps)"]

Source Directory (`src/`)

Entry Point: `index.ts`

The src/index.ts file serves dual purposes based on command-line arguments:

Server Mode (no arguments): Launches an MCP server using StdioServerTransport from @modelcontextprotocol/sdk
CLI Mode (with arguments): Routes commands to appropriate CLI handlers in src/cli/

HTTP Client: `automem-client.ts`

The src/automem-client.ts file implements the AutoMemClient class, providing a typed HTTP interface to the AutoMem backend service.

Method	HTTP Endpoint	Purpose
`storeMemory()`	`POST /memory`	Store new memory with content, tags, metadata
`recallMemory()`	`GET /recall`	Hybrid search (vector + keyword + tags)
`recallMemoryByTag()`	`GET /memory/by-tag`	Tag-only filtering
`associateMemories()`	`POST /associate`	Create typed relationships
`updateMemory()`	`PATCH /memory/:id`	Update existing memory fields
`deleteMemory()`	`DELETE /memory/:id`	Remove memory and embedding
`checkHealth()`	`GET /health`	Database connectivity status

Configuration resolution (priority order):

Constructor parameters (if provided)
Environment variables (AUTOMEM_ENDPOINT, AUTOMEM_API_KEY)
.env file (loaded via dotenv)

Type Definitions: `types.ts`

The src/types.ts file defines TypeScript interfaces for all data structures:

Configuration types: AutoMemConfig, MCPServerConfig, ClaudeCodeConfig
Memory operation arguments: StoreMemoryArgs, RecallMemoryArgs, AssociateMemoriesArgs
API response types: RecallResult, MemoryMetadata, RelationshipType
CLI types: SetupAnswers, QueueEntry

CLI Commands (`src/cli/`)

Each CLI command is implemented as a separate module with a main run*() function. CLI handlers follow a consistent pattern: --dry-run flag for safe preview, --verbose flag for detailed logging, template rendering from templates/ directory, filesystem operations with error handling, and user-friendly output with next-step instructions.

Templates Directory (`templates/`)

The templates/ directory contains platform-specific integration files that are copied to user systems during installation. These files are included in the published npm package.

templates/
├── claude-code/
│   ├── hooks/               # Shell scripts triggered by Claude events
│   │   ├── PostToolUse.sh  # After tool execution
│   │   └── Stop.sh         # Session end (queue processor)
│   ├── scripts/             # Support utilities
│   │   ├── session-memory.sh
│   │   ├── memory-filters.json
│   │   └── queue-processor.sh
│   ├── settings.json        # Base hook configuration
│   └── profiles/
│       ├── settings.lean.json
│       └── settings.extras.json
├── cursor/
│   ├── automem.mdc          # Cursor rule template
│   └── mcp-config.json      # MCP server config snippet
├── codex/
│   ├── AGENTS.md            # Codex agent rules
│   └── config.toml.snippet  # Server config for ~/.codex/
├── openclaw/
│   └── SKILL.md             # OpenClaw skill definition
└── warp/
    └── warp-rules.md        # Warp terminal rules

Template file types:

Type	Extension	Purpose	Target Platform
Hook Scripts	`.sh`	Event-driven automation	Claude Code
Rule Files	`.md`, `.mdc`	AI assistant instructions	Cursor, Codex, Warp, OpenClaw
Config Snippets	`.json`, `.toml`	MCP server configuration	All platforms
Settings	`.json`	Hook permissions & matchers	Claude Code
Filter Configs	`.json`	Memory significance rules	Claude Code

Build Artifacts (`dist/`)

The dist/ directory is generated by TypeScript compilation (tsc) and contains:

JavaScript files (.js) — Compiled from TypeScript source
Type declarations (.d.ts) — For TypeScript consumers
Source maps (.js.map) — For debugging compiled code

TypeScript configuration (tsconfig.json):

outDir: "./dist" — Output location
declaration: true — Generate .d.ts files
sourceMap: true — Generate source maps
module: "ES2020" — ES module format
target: "ES2020" — JavaScript target version

Build scripts:

Script	Command	Purpose
`build`	`tsc && npm run postbuild`	Compile + make executable
`postbuild`	`chmod +x dist/index.js`	Add execute permission
`dev`	`tsx watch src/index.ts`	Hot-reload development
`typecheck`	`tsc --noEmit`	Validate types without building

Plugins Directory (`plugins/`)

The plugins/ directory contains a packaged version of the MCP server for Claude Desktop’s plugin system. This directory duplicates content from templates/ to support the .mcpb extension format, which requires a self-contained plugin directory with all resources included.

Configuration Files

Root-Level Configuration

The repository root contains multiple configuration files:

File	Purpose
`package.json`	npm scripts, dependencies, package metadata
`tsconfig.json`	TypeScript compiler options
`eslint.config.js`	ESLint flat config (ESLint 9+)
`.commitlintrc.cjs`	Conventional commit message validation
`.prettierrc`	Code formatting rules
`release-please-config.json`	Automated release configuration
`.release-please-manifest.json`	Current version tracking
`env.example`	Template for required environment variables

Version Synchronization

Five files must maintain version consistency (managed by release-please):

package.json — "version": "0.12.0"
plugins/mcp-automem/server.json — "version": "0.12.0"
manifest.json — "version": "0.12.0"
plugin.json — "version": "0.12.0"
marketplace.json — "version": "0.12.0"

The release-please.yml workflow automatically updates all five files when creating releases based on conventional commits.

GitHub Workflows (`.github/`)

Workflow	Trigger	Purpose
`ci.yml`	PR, push to main	Lint, build, test, coverage
`security.yml`	PR, push, schedule	CodeQL, npm audit
`release-please.yml`	Push to main	Version bump, changelog, publish
`semantic-pr-title.yml`	PR open/edit	Validate PR title format

Git Hooks (`.husky/`)

The .husky/commit-msg hook runs commitlint to validate commit messages against Conventional Commits format before allowing the commit.

Accepted types: fix, feat, chore, docs, refactor, test, ci, build, perf, revert

Published Package Contents

The files array in package.json specifies what gets included in the npm package:

What’s included: dist/, templates/, plugins/, env.example, README.md, CHANGELOG.md

What’s excluded: Source code (src/), tests, development configs, CI/CD files, .tsbuildinfo

File Locations by Use Case

Task	Files to Modify
Add a new MCP tool	`src/index.ts` (schema + handler), `src/automem-client.ts` (client method), `src/types.ts`
Add a new CLI command	Create `src/cli/new-command.ts`, import and route in `src/index.ts`
Modify platform integration	Edit `templates/<platform>/`, update `src/cli/<platform>.ts`, sync to `plugins/`
Change build output	Modify `tsconfig.json`, update `package.json` `main` and `types` fields
Add release automation	Edit `.github/workflows/release-please.yml`, update `.release-please-manifest.json`

Project Structure

AutoMem Server (verygoodplugins/automem)

Directory Layout

Core Service Modules

app.py — Flask API Service

consolidation.py — Dream-Inspired Maintenance

mcp-sse-server/ — Node.js SSE Bridge

Operational Scripts

Configuration Management

Environment Variable Load Order (app.py:43-45)

Key Configuration Categories

Containerization Files

Testing Infrastructure

tests/ — Pytest Test Suites

File Naming Conventions

Deployment Artifact Boundaries

MCP Client (verygoodplugins/mcp-automem)

Directory Layout

Source Directory (src/)

Entry Point: index.ts

HTTP Client: automem-client.ts

Type Definitions: types.ts

CLI Commands (src/cli/)

Templates Directory (templates/)

Build Artifacts (dist/)

Plugins Directory (plugins/)

Configuration Files

Root-Level Configuration

Version Synchronization

GitHub Workflows (.github/)

Git Hooks (.husky/)

Published Package Contents

File Locations by Use Case

AutoMem Server (`verygoodplugins/automem`)

`app.py` — Flask API Service

`consolidation.py` — Dream-Inspired Maintenance

`mcp-sse-server/` — Node.js SSE Bridge

`tests/` — Pytest Test Suites

MCP Client (`verygoodplugins/mcp-automem`)

Source Directory (`src/`)

Entry Point: `index.ts`

HTTP Client: `automem-client.ts`

Type Definitions: `types.ts`

CLI Commands (`src/cli/`)

Templates Directory (`templates/`)

Build Artifacts (`dist/`)

Plugins Directory (`plugins/`)

GitHub Workflows (`.github/`)

Git Hooks (`.husky/`)