MCP Server (m1nd-mcp)

m1nd-mcp is the transport and session layer. It exposes m1nd-core and m1nd-ingest as 43 MCP tools over JSON-RPC stdio, manages the shared graph lifecycle, handles multi-agent sessions, and provides perspective branching and lock-based change tracking.

Source: mcp/m1nd/m1nd-mcp/src/

Module Map

Transport Layer

Dual Transport Mode

m1nd-mcp accepts two JSON-RPC transport formats on stdin, auto-detected per message:

Framed mode (HTTP-style headers):

Content-Length: 142\r\n
\r\n
{"jsonrpc":"2.0","method":"tools/call","params":{"name":"m1nd.activate","arguments":{"query":"chat","agent_id":"orchestrator"}},"id":1}

Line mode (raw JSON):

{"jsonrpc":"2.0","method":"tools/call","params":{"name":"m1nd.activate","arguments":{"query":"chat","agent_id":"orchestrator"}},"id":1}

Detection is based on the first non-whitespace byte: if it is { or [, the message is treated as line-mode JSON. Otherwise, it is parsed as framed with Content-Length headers. Responses are written in the same mode as the incoming request.

#![allow(unused)]
fn main() {
fn read_request_payload<R: BufRead>(
    reader: &mut R,
) -> std::io::Result<Option<(String, TransportMode)>> {
    loop {
        let buffer = reader.fill_buf()?;
        if buffer.is_empty() { return Ok(None); }
        let first_non_ws = buffer.iter().copied()
            .find(|byte| !byte.is_ascii_whitespace());
        let starts_framed = matches!(first_non_ws, Some(byte) if byte != b'{' && byte != b'[');
        // ...
    }
}
}

This dual-mode support allows m1nd to work with both Claude Code (which uses framed headers) and other MCP clients that send raw line JSON.

Request/Response Format

Requests follow the JSON-RPC 2.0 specification with MCP conventions:

{
    "jsonrpc": "2.0",
    "method": "tools/call",
    "params": {
        "name": "m1nd.activate",
        "arguments": {
            "query": "chat handler",
            "agent_id": "orchestrator",
            "top_k": 20,
            "dimensions": ["structural", "semantic", "temporal", "causal"],
            "xlr": true
        }
    },
    "id": 1
}

Responses:

{
    "jsonrpc": "2.0",
    "result": {
        "content": [{
            "type": "text",
            "text": "..."
        }]
    },
    "id": 1
}

The tools/list method returns all 43 tool schemas with full inputSchema per MCP spec, enabling auto-discovery by any MCP client.

Server Lifecycle

sequenceDiagram
    participant Main as main.rs
    participant Server as McpServer
    participant Session as SessionState
    participant Tokio as tokio runtime

    Main->>Main: load_config()
    Main->>Server: McpServer::new(config)
    Server->>Session: SessionState::initialize(graph, config, domain)
    Session->>Session: Build all engines (orchestrator, temporal, counterfactual, topology, resonance, plasticity)
    Main->>Server: server.start()
    Main->>Tokio: spawn_blocking(server.serve())

    loop Until EOF or SIGINT
        Tokio->>Server: read JSON-RPC request
        Server->>Server: dispatch to tool handler
        Server->>Session: execute tool logic
        Session->>Session: auto-persist check
        Server->>Tokio: write JSON-RPC response
    end

    Tokio->>Server: server.shutdown()
    Server->>Session: final persist

Configuration

Configuration is resolved in priority order: CLI argument (JSON file path) > environment variables > defaults.

#![allow(unused)]
fn main() {
pub struct McpConfig {
    pub graph_source: PathBuf,          // default: "./graph_snapshot.json"
    pub plasticity_state: PathBuf,      // default: "./plasticity_state.json"
    pub auto_persist_interval: u32,     // default: 50 (queries between persists)
    pub learning_rate: f32,             // default: 0.08
    pub decay_rate: f32,                // default: 0.005
    pub xlr_enabled: bool,             // default: true
    pub max_concurrent_reads: usize,    // default: 32
    pub write_queue_size: usize,        // default: 64
    pub domain: Option<String>,         // default: None ("code")
}
}

Environment variables: M1ND_GRAPH_SOURCE, M1ND_PLASTICITY_STATE, M1ND_XLR_ENABLED.

Startup Sequence

1. load_config(): Resolve config from CLI args, env vars, or defaults.
2. McpServer::new(config): Load graph snapshot from disk (or create empty graph). Load plasticity state. Initialize SessionState with all engines.
3. server.start(): Prepare the server for serving (no-op currently, reserved for future setup).
4. tokio::task::spawn_blocking(server.serve()): The serve loop does synchronous stdio I/O in a blocking task.
5. tokio::select! waits for either SIGINT (ctrl_c()) or serve loop completion.

Shutdown

On SIGINT or stdin EOF:

1. server.shutdown(): Final persist of graph and plasticity state.
2. Process exits.

The atomic write pattern (temp file + rename) ensures that even if shutdown is interrupted, the previous snapshot remains intact.

Tool Registration and Dispatch

Schema Registry

tool_schemas() returns a JSON array of all 43 tool definitions with full inputSchema objects. Each tool specifies:

• name: Dot-namespaced (e.g., m1nd.activate)
• description: Human-readable purpose
• inputSchema: JSON Schema with properties, required, type, defaults

Example schema entry:

{
    "name": "m1nd.activate",
    "description": "Spreading activation query across the connectome",
    "inputSchema": {
        "type": "object",
        "properties": {
            "query": { "type": "string" },
            "agent_id": { "type": "string" },
            "top_k": { "type": "integer", "default": 20 },
            "dimensions": {
                "type": "array",
                "items": { "type": "string", "enum": ["structural", "semantic", "temporal", "causal"] },
                "default": ["structural", "semantic", "temporal", "causal"]
            },
            "xlr": { "type": "boolean", "default": true }
        },
        "required": ["query", "agent_id"]
    }
}

Tool Categories

The 43 tools are organized into functional groups:

Core Query Tools (13):

Graph Mutation Tools:

Perspective Tools (12):

Lock Tools (5):

Trail Tools (4):

Topology Tools:

Dispatch

All tools require an agent_id parameter. The serve loop matches the tool name from the JSON-RPC request and dispatches to the corresponding handler in tools.rs. The handler extracts parameters from the arguments JSON object, acquires the appropriate lock on SessionState, executes the operation, and returns the result as a JSON-RPC response.

Session Management

SessionState

SessionState is the central state object. It owns the graph, all engines, and all session metadata:

#![allow(unused)]
fn main() {
pub struct SessionState {
    pub graph: SharedGraph,                    // Arc<RwLock<Graph>>
    pub domain: DomainConfig,
    pub orchestrator: QueryOrchestrator,       // activation + XLR + semantic
    pub temporal: TemporalEngine,
    pub counterfactual: CounterfactualEngine,
    pub topology: TopologyAnalyzer,
    pub resonance: ResonanceEngine,
    pub plasticity: PlasticityEngine,

    pub queries_processed: u64,
    pub auto_persist_interval: u32,            // default: 50
    pub start_time: Instant,
    pub last_persist_time: Option<Instant>,
    pub graph_path: PathBuf,
    pub plasticity_path: PathBuf,
    pub sessions: HashMap<String, AgentSession>,

    // Perspective/lock state
    pub graph_generation: u64,
    pub plasticity_generation: u64,
    pub cache_generation: u64,
    pub perspectives: HashMap<(String, String), PerspectiveState>,
    pub locks: HashMap<String, LockState>,
    pub perspective_counter: HashMap<String, u64>,
    pub lock_counter: HashMap<String, u64>,
    pub pending_watcher_events: Vec<WatcherEvent>,
    pub perspective_limits: PerspectiveLimits,
    pub peek_security: PeekSecurityConfig,
    pub ingest_roots: Vec<String>,
}
}

SharedGraph

SharedGraph = Arc<parking_lot::RwLock<Graph>> provides concurrent access:

• Reads (activation, impact, predict, etc.): Acquire read lock. Multiple concurrent reads allowed.
• Writes (ingest, learn): Acquire write lock. Exclusive access. Blocks all readers.

parking_lot::RwLock is used instead of std::sync::RwLock for two reasons:

1. Writer starvation prevention: parking_lot uses a fair queue, so plasticity writes do not starve behind continuous read queries.
2. Performance: parking_lot’s implementation is faster for the read-heavy, write-rare access pattern of m1nd.

Engine Rebuild

After ingestion replaces the graph, all engines must be rebuilt because they hold indexes derived from the old graph:

#![allow(unused)]
fn main() {
pub fn rebuild_engines(&mut self) -> M1ndResult<()> {
    {
        let graph = self.graph.read();
        self.orchestrator = QueryOrchestrator::build(&graph)?;
        self.temporal = TemporalEngine::build(&graph)?;
        self.plasticity = PlasticityEngine::new(
            &graph, PlasticityConfig::default(),
        );
    }
    self.invalidate_all_perspectives();
    self.mark_all_lock_baselines_stale();
    self.graph_generation += 1;
    self.cache_generation = self.cache_generation.max(self.graph_generation);
    Ok(())
}
}

The rebuild also invalidates all perspective and lock state, bumping generation counters so that stale caches are detected.

Auto-Persist

Every auto_persist_interval queries (default 50), the session persists state to disk:

1. Graph first: save_graph() writes the CSR graph to JSON via atomic temp-file-then-rename.
2. Plasticity second: export_state() extracts per-edge SynapticState, then save_plasticity_state() writes to JSON.
3. If graph save fails, plasticity save is skipped (prevents inconsistent state).
4. If plasticity save fails after graph succeeds, a warning is logged but the server continues.

#![allow(unused)]
fn main() {
pub fn persist(&mut self) -> M1ndResult<()> {
    let graph = self.graph.read();
    m1nd_core::snapshot::save_graph(&graph, &self.graph_path)?;
    match self.plasticity.export_state(&graph) {
        Ok(states) => {
            if let Err(e) = save_plasticity_state(&states, &self.plasticity_path) {
                eprintln!("[m1nd] WARNING: plasticity persist failed: {}", e);
            }
        }
        Err(e) => eprintln!("[m1nd] WARNING: plasticity export failed: {}", e),
    }
    self.last_persist_time = Some(Instant::now());
    Ok(())
}
}

Multi-Agent Support

Agent Sessions

Each unique agent_id gets an AgentSession:

#![allow(unused)]
fn main() {
pub struct AgentSession {
    pub agent_id: String,
    pub first_seen: Instant,
    pub last_seen: Instant,
    pub query_count: u64,
}
}

Sessions are created on first query and updated on each subsequent query. The last_seen timestamp enables timeout-based cleanup.

Agent Isolation

All agents share one graph (writes are immediately visible), but isolation is provided through:

• Perspectives: Per-agent branching views with independent route caches. A perspective opened by Agent A is invisible to Agent B.
• Locks: Per-agent change tracking baselines. Each agent can create independent locks to track changes from their perspective.
• Query Memory: The plasticity engine’s ring buffer is global (shared learning), but perspective-level route caches are per-agent.

Generation Counters

Three generation counters detect stale state:

When a perspective’s cached results were computed at a different generation than the current cache_generation, the perspective is marked stale and results are recomputed on next access.

Perspective System

Perspectives are per-agent named branches that cache activation results and enable comparative analysis.

Lifecycle

stateDiagram-v2
    [*] --> Open: perspective_start
    Open --> Active: first query (activate/impact/etc)
    Active --> Active: additional queries
    Active --> Branched: perspective_branch
    Active --> Stale: graph mutation (ingest/learn)
    Stale --> Active: re-query (auto-refresh)
    Active --> [*]: perspective_close
    Open --> [*]: perspective_close

Perspective IDs

Generated as persp_{agent_prefix}_{counter:03}. Each agent has an independent monotonic counter. Example: Agent “jimi” creates perspectives persp_jimi_001, persp_jimi_002, etc.

Resource Limits

PerspectiveLimits caps resource usage:

• Maximum open perspectives per agent
• Maximum total perspectives across all agents
• Maximum locks per agent

Peek Security

perspective_peek allows reading source file content from within a perspective context. Security restrictions:

• Files must be within an ingest_roots allow-list (populated during ingest).
• Path traversal (..) is blocked.
• Symlinks outside the allow-list are rejected.

Lock System

Locks capture a baseline snapshot of graph state for change tracking.

Lock Lifecycle

stateDiagram-v2
    [*] --> Created: lock_create
    Created --> Active: baseline captured
    Active --> Diffed: lock_diff (non-destructive)
    Diffed --> Active: continue tracking
    Active --> Rebased: lock_rebase (new baseline)
    Rebased --> Active: continue tracking
    Active --> Stale: graph mutation
    Stale --> Rebased: lock_rebase
    Active --> [*]: lock_release

Operations

• lock_create: Captures current graph state (generation counter + weight snapshot for tracked edges).
• lock_diff: Compares current state against baseline. Reports weight changes, new/removed edges. Non-destructive.
• lock_rebase: Updates baseline to current state. Clears staleness flag.
• lock_release: Frees the lock.
• lock_watch: Returns pending watcher events (changes that occurred since last check).

When a graph mutation occurs (ingest, learn), all locks are marked baseline_stale = true. lock_diff reports this staleness and suggests lock_rebase.

Engine Operations (Perspective Synthesis)

engine_ops.rs provides read-only wrappers around engine operations for use within perspective synthesis. These wrappers operate under a SynthesisBudget:

• Max calls: 8 engine calls per synthesis operation.
• Wall-clock timeout: 500ms total.

This prevents perspective synthesis from monopolizing the server. Each wrapper (activate_readonly, impact_readonly, etc.) checks budget before executing and returns a budget-exhausted error if limits are exceeded.

Concurrency Model

flowchart TD
    STDIN["stdin (JSON-RPC)"]
    TOKIO["tokio::task::spawn_blocking"]
    SERVE["McpServer.serve()<br/>(synchronous loop)"]
    RW["SharedGraph<br/>Arc&lt;parking_lot::RwLock&lt;Graph&gt;&gt;"]
    READ["Read Lock<br/>(activate, impact, predict, ...)"]
    WRITE["Write Lock<br/>(ingest, graph swap)"]
    PERSIST["Auto-Persist<br/>(write lock on graph)"]

    STDIN --> TOKIO
    TOKIO --> SERVE
    SERVE --> READ
    SERVE --> WRITE
    SERVE --> PERSIST
    READ --> RW
    WRITE --> RW
    PERSIST --> RW

The serve loop is single-threaded (synchronous stdio I/O), but graph access is concurrent-safe through SharedGraph. Within a single request:

• Read operations acquire a read lock (shared, non-blocking with other reads).
• Write operations acquire a write lock (exclusive, blocks all other access).
• Plasticity weight updates use atomic CAS (no lock needed for individual weight writes).

The tokio runtime is used solely for the select! between SIGINT and serve loop completion. All actual tool processing happens synchronously within spawn_blocking.