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MCP Memory Server Architecture & Workflow Design

1. Core Architecture

The mcp-memory system runs as a single, continuously running background daemon natively on Windows. It manages the state of the Antigravity knowledge graph and serves as a universal backend for both Windows and WSL environments.

Why this design?

  • Cross-OS I/O Optimization: Prevents the WSL agent from performing slow, heavy filesystem writes against the mounted Windows C:\ drive.
  • Concurrency & Locking: A single daemon holds the lock on the mcp_memory JSON files, preventing data corruption and eliminating complex delta-reconciliation between parallel WSL and Windows processes.
  • Dual Transport System: Utilizes both stdio and HTTP transports concurrently. The local Windows agy instance connects natively via standard stdio, while the Axum HTTP server provides synchronous, non-blocking access for WSL clients and external scripts.

2. Server Transport & Endpoints (Axum)

The daemon uses the axum and rust-mcp-axum crates, binding to 0.0.0.0:3000 to serve the network.

Standard MCP Endpoints

  • GET /ws: The WebSocket endpoint for efficient, low-latency, full-duplex JSON-RPC communication (preferred for proxies and the UI dashboard).
  • GET /sse: The Server-Sent Events (SSE) endpoint. Antigravity clients connect here to keep a one-way pipe open for receiving pushed responses.
  • POST /messages: The JSON-RPC endpoint. Clients use this to send tool calls and resource reads up to the server when connected via SSE.

Custom Integration Endpoints

  • GET /: The Brain Monitor live HTML dashboard (returns real-time metrics UI).
  • GET /api/stats: Returns a JSON snapshot of current entity, relation, task, and tech debt counts.
  • GET /gate/verify: A lightweight, deterministic endpoint used by external scripts to verify if an action (like a git push) is authorized based on the current state.

3. Client Connections

The Antigravity configurations (mcp_config.json) utilize the dual-transport system:

  • Windows agy: Spawns and connects to the local daemon natively via stdio subprocess execution.
  • WSL (Linux) agy: Connects to the running Windows HTTP daemon via the host network proxy, e.g., http://127.0.0.1:3000/sse.

4. Git Integration (Global Wrapper)

Instead of relying on localized per-repository Git hooks (like .git/hooks/pre-push), the system leverages a global bash/PowerShell alias wrapper for the git command. This intercepts git commands universally across the OS.

Workflow Example (Push Safety Gate)

  1. The user types git push.
  2. The global wrapper intercepts the command.
  3. It makes a synchronous HTTP request to the local daemon: curl -s http://localhost:3000/gate/verify.
  4. If the endpoint returns 200 OK (indicating the PrePushAuditor subagent has verified that unit tests pass and history is squashed), the push proceeds.
  5. If not 200 OK, the wrapper blocks the push and alerts the user to fix tests or run gsquash.

Benefits of the Wrapper Approach

  • Universal Enforcement: The push safety gate is protected across all repositories automatically, without copying hook scripts.
  • No File Locks: Uses safe, lightweight, parallelizable HTTP requests rather than executing the Rust binary directly.
  • Action Logging: The wrapper can be seamlessly extended to log actions (like checkout or commit) directly into the knowledge graph in real-time.

5. Storage Architecture & Persistence (Redb LSM-Tree)

The daemon has completely eliminated raw JSON file sprawl and fragmented delta-file reconciliation. It now utilizes a pure-Rust, embedded Key-Value engine (redb) that implements a robust Log-Structured Merge-Tree (LSM-tree) architecture.

Key Principles:

  • Embedded Database Engine: All structured components (Tasks, Snippets, Tech Debt, Checklists, etc.) are stored as binary-encoded values inside a unified redb database file (store.redb).
  • ACID Compliance & File Locks: The Windows daemon holds an exclusive read-write lock on the database file, guaranteeing zero data corruption, race conditions, or lock contention during concurrent access.
  • Asynchronous Checkpointing: The core Knowledge Graph (Entities, Relations, Observations) still utilizes a Write-Ahead Logging (WAL) pattern (wal.jsonl) and a master snapshot (master.json) to allow safe, lock-free memory mutations which are reconciled in the background.

6. Domain Models & Component Stores

The system leverages a modular, thread-safe generic Store<T> abstraction that automatically transparently serializes and deserializes native Rust structs directly into the underlying redb tables. Currently implemented persistent stores include:

  • Audit Ledger & Tasks: Tracks agent actions and active background tasks.
  • Context & Handoffs: Sticky notes, Session Summaries, Handoff Memos, and Context Workspaces.
  • Engineering Tracking: ADRs (Architecture Decision Records), Snippets, Error Fixes, Tech Debt, and PR Checklists.
  • Environment State: Pinned Files, Env Fingerprints, Milestones, and Environments.
  • Safety Gates: Authorized execution gates (Push Safety).

7. Full-Text Search Engine (Tantivy)

To support blazing-fast, intelligent semantic retrieval across the sprawling knowledge graph, the daemon embeds Tantivy, a full-text search engine (inspired by Apache Lucene).

  • The MemoryIndex: Whenever the graph or auxiliary stores mutate, a background thread dynamically rebuilds the Tantivy index (tantivy_index/ dir).
  • Global Omni-Search: This architecture powers the omni_search tool, allowing subagents to instantly fuzzy-search and rank documents across Entities, Tasks, Snippets, Error Fixes, and ADRs simultaneously in milliseconds, without loading massive JSON arrays into RAM.

8. The Gate System (Push Safety Verification)

The binary supports a flexible safety gate authorization system, accessible both via the HTTP API and CLI subcommands.

  • API / CLI set: Records an authorization status (authorized, blocked, or pending) for a specific target and namespace. Can be invoked via POST /gate/set (JSON) or mcp-memory-stub gate set.
  • API / CLI verify: Evaluates a pending action against the gate store. It returns standard HTTP status codes (200 OK, 403 Forbidden, 404 Not Found) via GET /gate/verify?action=... or POSIX exit codes (0, 1, 2) via mcp-memory-stub gate verify. Both support a consume parameter/flag to immediately revoke the authorization after a successful check.

9. Operational Configuration & Paths

The physical storage location of the knowledge graph and all persistent stores is strictly controlled by the MCP_MEMORY_STORE_DIR environment variable.

  • Default Path: If not set, the daemon defaults to ~/.gemini/mcp_memory.
  • Port Binding: The Axum HTTP server strictly binds to .0.0.0:3000.

10. Exposed MCP Capabilities (Tools)

The server implements the Model Context Protocol (MCP) by exposing a vast suite of tools via the JSON-RPC interface, categorized broadly into:

  • Graph Management: create_entities, create_relations, merge_entities, ead_graph, etc.
  • Task & Context Tracking: add_task, add_sticky_note, add_session_summary, etc.
  • Engineering & DevOps: log_code_change, log_error_fix, log_tech_debt, add_pr_checklist_item.
  • Environment & Workspaces: egister_environment, save_context_workspace, pin_file.

11. Concurrency & Thread Safety

With the introduction of the Dual Transport System, the daemon must safely handle simultaneous read/write requests from both Stdio (Windows agy) and HTTP (WSL agy) clients.

  • Shared State: The entire server operates on a cloned Arc.
  • Locking Mechanism: The unified Knowledge Graph and modular Store components are protected by RwLock primitives.
  • Safe Mutation: Store modifications utilize closure-based modify(|store| { ... }) methods to ensure locks are safely acquired, mutations applied, and file writes executed sequentially without deadlocking the asynchronous Tokio runtimes.

12. Lifecycle & Startup Management (Server/Stub Architecture)

The mcp-memory daemon employs a strict Server/Client paradigm to maintain separation of concerns. There are no dual roles or morphing executables.

The Windows Background Daemon (mcp-memory-server.exe)

The server executable is responsible exclusively for running the Axum HTTP and WebSockets daemon and managing the Knowledge Graph. It does not contain any proxy logic. If port 3000 is already in use by an existing server instance, it gracefully exits instead of attempting to run.

The Client Proxy (mcp-memory-stub.exe)

All Antigravity sessions (Windows and WSL) use the lightweight mcp-memory-stub as their proxy. The stub connects to the server via WebSockets and acts as the bridge for standard stdio JSON-RPC traffic.

  • Startup via Interop/Spawn: Upon launch, the stub attempts to connect to the Windows host on port 3000. If the server is offline, the stub automatically executes a spawn command (e.g., executing mcp-memory-server.exe --daemon natively, or via WSL interop) to silently wake up the Windows Leader before commencing the proxy loop.
  • MPSC Queue Resilience: The stub utilizes an asynchronous multi-producer, single-consumer (MPSC) channel queue. If the Windows Leader daemon restarts or momentarily drops, the proxy buffers incoming JSON-RPC tool calls and infinitely retries them until the connection is restored. This guarantees zero message loss and zero thread leaks without crashing the active agy session.
  • Zero I/O Penalty (WSL): This ensures the Linux binary never directly touches the Windows NTFS files, reserving all heavy disk operations for the native Windows host.

13. Cargo Workspace & Binary Artifacts

To optimize for different environments, the codebase is structured as a Cargo Workspace containing two distinct crates:

1. mcp-memory-server (The "Full-Fat" Daemon)

  • Path: server/
  • Size/Complexity: Heavy (contains Axum, MCP SDK, JSON parsing, Tokio runtime).
  • Role: This is the primary background daemon. It binds to .0.0.0:3000, holds file locks, and manages the graph.
  • Windows Behavior: It is designed to run in the background as a standalone service.

2. mcp-memory-stub (The Ultra-Lightweight Proxy)

  • Path: stub/
  • Size/Complexity: Extremely light (only relies on eqwest and okio).
  • Role: A dedicated, OS-agnostic proxy binary used strictly for routing stdio JSON-RPC traffic over HTTP to a remote Leader. Windows gy clients point directly to this binary to bypass loading the heavy Server daemon into memory.
  • WSL Behavior: Compiled as a Linux native binary (x86_64-unknown-linux-musl). When executed by WSL agy, it acts as a transparent proxy to http://127.0.0.1:3000. It can also execute wake_cmd (e.g., WSL interop) to silently wake the Windows host if the Leader is offline.

14. Neovim Integration Architecture & "God Mode"

To enable seamless pair-programming inside Neovim, the daemon integrates with Neovim using two complementary systems: a Webhook Telemetry pipeline and dedicated MCP binaries.

Telemetry Pipeline (Last Focused Wins)

A lightweight Lua script (gemini-integration.lua) is loaded into Neovim, which fires an asynchronous curl POST to http://127.0.0.1:3000/nvim/telemetry whenever the user focuses a buffer or moves the cursor. The server then writes this data (including session_id, ile, line, and col) to both the Windows and WSL ctive_nvim.txt files and broadcasts it over WebSockets.

Native MCP Binaries (win-nvim & linux-nvim)

The project compiles two standalone, highly-performant binaries that implement the MCP JSON-RPC protocol over Stdio and bridge it directly to Neovim's Msgpack-RPC Named Pipes/Sockets. These binaries avoid hardcoding infinite tools by utilizing a "God Mode" escape hatch.

Exposed Neovim Tools:

vim_get_active_buffer & vim_get_cursor**: Read file state.

vim_goto_line & vim_set_diagnostics**: Manipulate IDE state.

vim_get_visual_selection**: Read exact highlight coordinates (handles mode dynamically).

vim_list_buffers**: Discover unsaved work and context.

vim_get_diagnostics**: Read live LSP errors dynamically instead of requiring a compiler.

vim_execute_lua ("God Mode")**: The ultimate fallback tool. Evaluates raw Lua scripts inside the active Neovim instance and returns JSON. This prevents the need to continuously recompile the Rust server whenever a new Neovim capability is required.

15. Build & Deployment Strategy

Because the background server operates as an always-on Windows daemon, standard recompilation and file-copying strategies will fail due to active Windows OS file locks.

Randomized Lock Bypassing

The \uild.ps1\ deployment pipeline intercepts locked .exe\ files by appending a unique, timestamped/randomized suffix (e.g., \mcp-memory-server.exe.12345.old) when forcing a \Move-Item. This guarantees that rapid sequential deployments (where a previous .old\ file might still be locked by a zombie process) never silently fail or collide.

Dynamic Versioning

To trace binary provenances during rapid deployment cycles, all binaries embed dynamic versioning directly at compile time (via \uild.rs\ and \uild_template.rs). The injected \APP_VERSION\ environment variable combines the static Cargo \ ersion\ with the live \git\ short hash and UTC timestamp, allowing the CLI --version\ commands and the HTTP /api/version\ endpoints to guarantee exactly which iteration of the code is actively executing.

16. Testing Architecture (Native Rust E2E)

Historically, the project relied on a complex Python testing suite (\pytest\ + \mcp_client.py) to validate the server over HTTP/SSE. This has been fully deprecated in favor of Native Rust End-to-End Testing.

  • Unit Tests: Handlers and business logic are tested directly inside \server/src/handlers.rs\ using native \ okio::test\ constructs.
  • E2E Tests: Integration and full-system tests run via \stub/tests/e2e.rs\ and \win-nvim/tests/integration_test.rs, ensuring type safety, faster execution, and eliminating Python environment dependencies.
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