@cleocode/brain 2026.5.3 → 2026.5.4

package/dist/src/adapters/index.js

@@ -0,0 +1,194 @@
+/**
+ * Barrel for all substrate adapters.
+ *
+ * Re-exports individual adapter functions and provides the unified
+ * `getAllSubstrates()` function that merges results from all five databases
+ * into a single BrainGraph.
+ */
+export { getBrainSubstrate } from './brain.js';
+export { getConduitSubstrate } from './conduit.js';
+export { getNexusSubstrate } from './nexus.js';
+export { getSignaldockSubstrate } from './signaldock.js';
+export { getTasksSubstrate } from './tasks.js';
+import { allTyped, getNexusDb } from '../db-connections.js';
+import { getBrainSubstrate } from './brain.js';
+import { getConduitSubstrate } from './conduit.js';
+import { getNexusSubstrate } from './nexus.js';
+import { getSignaldockSubstrate } from './signaldock.js';
+import { getTasksSubstrate } from './tasks.js';
+/** Substrate names ordered for iteration. */
+const ALL_SUBSTRATES = ['brain', 'nexus', 'tasks', 'conduit', 'signaldock'];
+/** Maps substrate name to its adapter function. */
+const ADAPTER_MAP = {
+    brain: getBrainSubstrate,
+    nexus: getNexusSubstrate,
+    tasks: getTasksSubstrate,
+    conduit: getConduitSubstrate,
+    signaldock: getSignaldockSubstrate,
+};
+/**
+ * Loads minimal stub nodes for any edge target IDs not already loaded.
+ *
+ * This second-pass loader ensures that cross-substrate edges
+ * (particularly brain→nexus bridges) don't reference unloaded target nodes.
+ *
+ * Stub nodes carry only minimal metadata: {id, substrate, kind, label}.
+ * Full details defer to side-panel click or future full-load request.
+ *
+ * @param loadedNodeIds - Set of already-loaded node IDs (substrate-prefixed).
+ * @param edges - All edges collected from substrates (may reference unloaded targets).
+ * @returns Array of stub BrainNode objects for missing targets.
+ */
+function loadStubNodesForEdgeTargets(loadedNodeIds, edges) {
+    // Collect all target IDs referenced by edges but not yet loaded
+    const missingTargetIds = new Set();
+    for (const edge of edges) {
+        if (!loadedNodeIds.has(edge.target)) {
+            missingTargetIds.add(edge.target);
+        }
+    }
+    if (missingTargetIds.size === 0)
+        return [];
+    // Partition missing target IDs by substrate
+    const stubsBySubstrate = new Map();
+    for (const nodeId of missingTargetIds) {
+        const sep = nodeId.indexOf(':');
+        if (sep === -1)
+            continue;
+        const substrateStr = nodeId.slice(0, sep);
+        const substrate = substrateStr;
+        if (!['brain', 'nexus', 'tasks', 'conduit', 'signaldock'].includes(substrate)) {
+            continue;
+        }
+        if (!stubsBySubstrate.has(substrate)) {
+            stubsBySubstrate.set(substrate, []);
+        }
+        stubsBySubstrate.get(substrate).push(nodeId);
+    }
+    const stubs = [];
+    // Load stubs for nexus targets (most common cross-substrate case)
+    const nexusStubs = stubsBySubstrate.get('nexus');
+    if (nexusStubs && nexusStubs.length > 0) {
+        const db = getNexusDb();
+        if (db) {
+            try {
+                const rawNexusIds = nexusStubs.map((id) => id.replace(/^nexus:/, ''));
+                const placeholders = rawNexusIds.map(() => '?').join(',');
+                // Query minimal node data: id, kind, name
+                const stubRows = allTyped(db.prepare(`SELECT id, kind, name
+             FROM nexus_nodes
+             WHERE id IN (${placeholders})`), ...rawNexusIds);
+                for (const row of stubRows) {
+                    const kind = row.kind === 'file' || row.kind === 'folder' || row.kind === 'module'
+                        ? 'file'
+                        : 'symbol';
+                    stubs.push({
+                        id: `nexus:${row.id}`,
+                        kind,
+                        substrate: 'nexus',
+                        label: row.name,
+                        weight: undefined,
+                        createdAt: null,
+                        meta: { nexus_kind: row.kind, isStub: true },
+                    });
+                }
+            }
+            catch {
+                // Silently continue on error; stubs are supplemental
+            }
+        }
+    }
+    // For other substrates (tasks, brain, conduit, signaldock), create minimal stubs
+    // without DB queries — they are rare as cross-substrate edge targets.
+    for (const [substrate, nodeIds] of stubsBySubstrate) {
+        if (substrate === 'nexus')
+            continue; // already handled above
+        for (const nodeId of nodeIds) {
+            const rawId = nodeId.replace(new RegExp(`^${substrate}:`), '');
+            stubs.push({
+                id: nodeId,
+                kind: 'observation', // generic fallback kind
+                substrate,
+                label: rawId,
+                weight: undefined,
+                createdAt: null,
+                meta: { isStub: true },
+            });
+        }
+    }
+    return stubs;
+}
+/**
+ * Queries all five substrates and merges the results into a unified BrainGraph.
+ *
+ * When `options.substrates` is provided, only those substrates are queried.
+ * Node IDs are substrate-prefixed, so deduplication is safe to perform
+ * by ID equality alone.
+ *
+ * After all substrates are loaded, performs a second-pass stub-node load:
+ * any edge target ID not yet in the loaded node set is fetched as a minimal
+ * stub (id, substrate, kind, label). This recovers cross-substrate edges
+ * that would otherwise be silently dropped.
+ *
+ * Stub nodes carry `meta.isStub: true` for optional UI differentiation.
+ *
+ * @param options - Query options forwarded to each substrate adapter.
+ * @returns Merged BrainGraph across all requested substrates, with stub nodes for unresolved edge targets.
+ */
+export function getAllSubstrates(options = {}) {
+    const substrates = options.substrates ?? ALL_SUBSTRATES;
+    const limit = options.limit ?? 500;
+    const allNodes = [];
+    const allEdges = [];
+    const nodeCounts = Object.fromEntries(ALL_SUBSTRATES.map((s) => [s, 0]));
+    const edgeCounts = Object.fromEntries([...ALL_SUBSTRATES, 'cross'].map((s) => [s, 0]));
+    for (const substrate of substrates) {
+        const adapter = ADAPTER_MAP[substrate];
+        if (!adapter)
+            continue;
+        const { nodes, edges } = adapter({ ...options, limit });
+        allNodes.push(...nodes);
+        allEdges.push(...edges);
+        nodeCounts[substrate] = nodes.length;
+        for (const edge of edges) {
+            edgeCounts[edge.substrate] = (edgeCounts[edge.substrate] ?? 0) + 1;
+        }
+    }
+    // Deduplicate nodes by ID (substrate-prefix guarantees uniqueness across
+    // substrates; duplicates can only occur within a substrate on malformed data)
+    const seenIds = new Set();
+    const uniqueNodes = [];
+    for (const node of allNodes) {
+        if (!seenIds.has(node.id)) {
+            seenIds.add(node.id);
+            uniqueNodes.push(node);
+        }
+    }
+    // Second pass: load stub nodes for any edge target IDs not yet loaded.
+    // This recovers cross-substrate edges that would otherwise be silently dropped
+    // (e.g. brain→nexus bridges to low-in-degree symbols).
+    //
+    // When a substrates filter is explicitly provided, only add stubs for substrates
+    // within the requested set — never inject nodes from excluded substrates, as that
+    // would violate the caller's filter contract.
+    const requestedSubstrateSet = options.substrates ? new Set(options.substrates) : null;
+    const stubNodes = loadStubNodesForEdgeTargets(seenIds, allEdges);
+    for (const stubNode of stubNodes) {
+        if (!seenIds.has(stubNode.id)) {
+            // Skip stubs from substrates not in the requested set
+            if (requestedSubstrateSet && !requestedSubstrateSet.has(stubNode.substrate)) {
+                continue;
+            }
+            seenIds.add(stubNode.id);
+            uniqueNodes.push(stubNode);
+        }
+    }
+    const truncated = uniqueNodes.length >= limit;
+    return {
+        nodes: truncated ? uniqueNodes.slice(0, limit) : uniqueNodes,
+        edges: allEdges,
+        counts: { nodes: nodeCounts, edges: edgeCounts },
+        truncated,
+    };
+}
+//# sourceMappingURL=index.js.map

package/dist/src/adapters/index.js.map

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package/dist/src/adapters/nexus.d.ts

@@ -0,0 +1,24 @@
+/**
+ * NEXUS substrate adapter for the Living Brain API.
+ *
+ * Queries nexus.db (global) and returns BrainNodes/BrainEdges for code symbols and files.
+ * Prioritises high-in-degree nodes (most-called functions, most-imported files)
+ * since the full nexus graph can exceed 10k nodes.
+ *
+ * Node IDs are prefixed with "nexus:" to prevent collisions.
+ */
+import type { BrainEdge, BrainNode, BrainQueryOptions } from '../types.js';
+/**
+ * Returns all BrainNodes and BrainEdges sourced from nexus.db.
+ *
+ * Fetches the highest in-degree nodes (capped at perSubstrateLimit) and
+ * all relations between those nodes.
+ *
+ * @param options - Query options (limit, minWeight).
+ * @returns Nodes and edges from the NEXUS substrate.
+ */
+export declare function getNexusSubstrate(options?: BrainQueryOptions): {
+    nodes: BrainNode[];
+    edges: BrainEdge[];
+};
+//# sourceMappingURL=nexus.d.ts.map

package/dist/src/adapters/nexus.d.ts.map

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package/dist/src/adapters/nexus.js

@@ -0,0 +1,83 @@
+/**
+ * NEXUS substrate adapter for the Living Brain API.
+ *
+ * Queries nexus.db (global) and returns BrainNodes/BrainEdges for code symbols and files.
+ * Prioritises high-in-degree nodes (most-called functions, most-imported files)
+ * since the full nexus graph can exceed 10k nodes.
+ *
+ * Node IDs are prefixed with "nexus:" to prevent collisions.
+ */
+import { allTyped, getNexusDb } from '../db-connections.js';
+/** Maps nexus node kinds to BrainNodeKind. */
+function mapKind(nexusKind) {
+    if (nexusKind === 'file' || nexusKind === 'folder' || nexusKind === 'module')
+        return 'file';
+    return 'symbol';
+}
+/**
+ * Returns all BrainNodes and BrainEdges sourced from nexus.db.
+ *
+ * Fetches the highest in-degree nodes (capped at perSubstrateLimit) and
+ * all relations between those nodes.
+ *
+ * @param options - Query options (limit, minWeight).
+ * @returns Nodes and edges from the NEXUS substrate.
+ */
+export function getNexusSubstrate(options = {}) {
+    const db = getNexusDb();
+    if (!db)
+        return { nodes: [], edges: [] };
+    const perSubstrateLimit = Math.ceil((options.limit ?? 500) / 5);
+    const nodes = [];
+    const edges = [];
+    try {
+        // Count in-degree for each node to use as weight
+        const nodeRows = allTyped(db.prepare(`SELECT n.id, n.kind, n.name, n.indexed_at,
+                COUNT(r.target_id) AS in_degree
+         FROM nexus_nodes n
+         LEFT JOIN nexus_relations r ON r.target_id = n.id
+         WHERE n.kind IN (
+           'file', 'function', 'method', 'class', 'interface',
+           'type_alias', 'constant', 'module', 'enum'
+         )
+         GROUP BY n.id
+         ORDER BY in_degree DESC
+         LIMIT ?`), perSubstrateLimit);
+        for (const row of nodeRows) {
+            nodes.push({
+                id: `nexus:${row.id}`,
+                kind: mapKind(row.kind),
+                substrate: 'nexus',
+                label: row.name,
+                weight: row.in_degree > 0 ? Math.min(1, row.in_degree / 50) : undefined,
+                createdAt: row.indexed_at ?? null,
+                meta: { nexus_kind: row.kind, in_degree: row.in_degree },
+            });
+        }
+        // Edges between loaded nodes only
+        const nodeIds = new Set(nodes.map((n) => n.id));
+        const rawIds = new Set([...nodeIds].map((id) => id.replace(/^nexus:/, '')));
+        // Fetch all relations touching these nodes (both directions)
+        const placeholders = [...rawIds].map(() => '?').join(',');
+        if (rawIds.size === 0)
+            return { nodes, edges };
+        const relRows = allTyped(db.prepare(`SELECT source_id, target_id, type, confidence
+         FROM nexus_relations
+         WHERE source_id IN (${placeholders})
+           AND target_id IN (${placeholders})`), ...rawIds, ...rawIds);
+        for (const row of relRows) {
+            edges.push({
+                source: `nexus:${row.source_id}`,
+                target: `nexus:${row.target_id}`,
+                type: row.type,
+                weight: row.confidence ?? 0.5,
+                substrate: 'nexus',
+            });
+        }
+    }
+    catch {
+        // Return partial results on error
+    }
+    return { nodes, edges };
+}
+//# sourceMappingURL=nexus.js.map

package/dist/src/adapters/nexus.js.map

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package/dist/src/adapters/signaldock.d.ts

@@ -0,0 +1,25 @@
+/**
+ * SIGNALDOCK substrate adapter for the Living Brain API.
+ *
+ * Queries signaldock.db (global) and returns BrainNodes/BrainEdges for agents
+ * and agent-to-agent social connections.
+ *
+ * Node IDs are prefixed with "signaldock:" to prevent collisions.
+ * Agents are the cross-substrate identity bridge — they appear in TASKS
+ * (assignee), CONDUIT (from/to), and BRAIN (source agent).
+ */
+import type { BrainEdge, BrainNode, BrainQueryOptions } from '../types.js';
+/**
+ * Returns all BrainNodes and BrainEdges sourced from signaldock.db.
+ *
+ * Fetches all active agents plus their declared connections.
+ * Agent nodes serve as the cross-substrate identity anchors.
+ *
+ * @param options - Query options (limit).
+ * @returns Nodes and edges from the SIGNALDOCK substrate.
+ */
+export declare function getSignaldockSubstrate(options?: BrainQueryOptions): {
+    nodes: BrainNode[];
+    edges: BrainEdge[];
+};
+//# sourceMappingURL=signaldock.d.ts.map

package/dist/src/adapters/signaldock.d.ts.map

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package/dist/src/adapters/signaldock.js

@@ -0,0 +1,86 @@
+/**
+ * SIGNALDOCK substrate adapter for the Living Brain API.
+ *
+ * Queries signaldock.db (global) and returns BrainNodes/BrainEdges for agents
+ * and agent-to-agent social connections.
+ *
+ * Node IDs are prefixed with "signaldock:" to prevent collisions.
+ * Agents are the cross-substrate identity bridge — they appear in TASKS
+ * (assignee), CONDUIT (from/to), and BRAIN (source agent).
+ */
+import { allTyped, getSignaldockDb } from '../db-connections.js';
+/**
+ * Converts a UNIX epoch seconds value to an ISO-8601 string.
+ * Returns null when the value is not a finite positive number.
+ *
+ * @param epoch - UNIX timestamp in seconds, or null.
+ * @returns ISO-8601 string or null.
+ */
+function epochToIso(epoch) {
+    if (epoch === null || !Number.isFinite(epoch) || epoch <= 0)
+        return null;
+    return new Date(epoch * 1000).toISOString();
+}
+/**
+ * Returns all BrainNodes and BrainEdges sourced from signaldock.db.
+ *
+ * Fetches all active agents plus their declared connections.
+ * Agent nodes serve as the cross-substrate identity anchors.
+ *
+ * @param options - Query options (limit).
+ * @returns Nodes and edges from the SIGNALDOCK substrate.
+ */
+export function getSignaldockSubstrate(options = {}) {
+    const db = getSignaldockDb();
+    if (!db)
+        return { nodes: [], edges: [] };
+    const perSubstrateLimit = Math.ceil((options.limit ?? 500) / 5);
+    const nodes = [];
+    const edges = [];
+    try {
+        // Active agents
+        const agentRows = allTyped(db.prepare(`SELECT agent_id, name, status, created_at
+         FROM agents
+         WHERE status != 'deleted'
+         ORDER BY created_at DESC
+         LIMIT ?`), perSubstrateLimit);
+        const agentIds = new Set();
+        for (const row of agentRows) {
+            agentIds.add(row.agent_id);
+            nodes.push({
+                id: `signaldock:${row.agent_id}`,
+                kind: 'agent',
+                substrate: 'signaldock',
+                label: row.name,
+                weight: row.status === 'active' ? 1.0 : 0.5,
+                createdAt: epochToIso(row.created_at),
+                meta: {
+                    status: row.status,
+                    created_at: row.created_at,
+                },
+            });
+        }
+        // Agent connections (declared social graph)
+        if (agentIds.size > 0) {
+            const placeholders = [...agentIds].map(() => '?').join(',');
+            const connRows = allTyped(db.prepare(`SELECT from_agent_id, to_agent_id, connection_type, strength
+           FROM agent_connections
+           WHERE from_agent_id IN (${placeholders})
+             AND to_agent_id IN (${placeholders})`), ...agentIds, ...agentIds);
+            for (const row of connRows) {
+                edges.push({
+                    source: `signaldock:${row.from_agent_id}`,
+                    target: `signaldock:${row.to_agent_id}`,
+                    type: row.connection_type,
+                    weight: row.strength ?? 0.5,
+                    substrate: 'signaldock',
+                });
+            }
+        }
+    }
+    catch {
+        // Return partial results on error
+    }
+    return { nodes, edges };
+}
+//# sourceMappingURL=signaldock.js.map

package/dist/src/adapters/signaldock.js.map

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package/dist/src/adapters/tasks.d.ts

@@ -0,0 +1,23 @@
+/**
+ * TASKS substrate adapter for the Living Brain API.
+ *
+ * Queries tasks.db and returns BrainNodes/BrainEdges for tasks and sessions.
+ * Prioritises critical/high priority tasks and active sessions.
+ *
+ * Node IDs are prefixed with "tasks:" to prevent collisions.
+ */
+import type { BrainEdge, BrainNode, BrainQueryOptions } from '../types.js';
+/**
+ * Returns all BrainNodes and BrainEdges sourced from tasks.db.
+ *
+ * Fetches tasks ordered by priority, plus recent sessions.
+ * Synthesizes parent→child, dependency, and relation edges.
+ *
+ * @param options - Query options (limit, minWeight).
+ * @returns Nodes and edges from the TASKS substrate.
+ */
+export declare function getTasksSubstrate(options?: BrainQueryOptions): {
+    nodes: BrainNode[];
+    edges: BrainEdge[];
+};
+//# sourceMappingURL=tasks.d.ts.map

package/dist/src/adapters/tasks.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/adapters/tasks.js

@@ -0,0 +1,143 @@
+/**
+ * TASKS substrate adapter for the Living Brain API.
+ *
+ * Queries tasks.db and returns BrainNodes/BrainEdges for tasks and sessions.
+ * Prioritises critical/high priority tasks and active sessions.
+ *
+ * Node IDs are prefixed with "tasks:" to prevent collisions.
+ */
+import { allTyped, getTasksDb } from '../db-connections.js';
+import { resolveDefaultProjectContext } from '../project-context.js';
+/** Maps priority string to numeric weight for BrainNode.weight. */
+function priorityWeight(priority) {
+    const map = {
+        critical: 1.0,
+        high: 0.75,
+        medium: 0.5,
+        low: 0.25,
+    };
+    return map[priority] ?? 0.25;
+}
+/**
+ * Returns all BrainNodes and BrainEdges sourced from tasks.db.
+ *
+ * Fetches tasks ordered by priority, plus recent sessions.
+ * Synthesizes parent→child, dependency, and relation edges.
+ *
+ * @param options - Query options (limit, minWeight).
+ * @returns Nodes and edges from the TASKS substrate.
+ */
+export function getTasksSubstrate(options = {}) {
+    const ctx = options.projectCtx ?? resolveDefaultProjectContext();
+    const db = getTasksDb(ctx);
+    if (!db)
+        return { nodes: [], edges: [] };
+    const perSubstrateLimit = Math.ceil((options.limit ?? 500) / 5);
+    const minWeight = options.minWeight ?? 0;
+    const nodes = [];
+    const edges = [];
+    try {
+        // Tasks (prioritised by severity, then recency)
+        const taskRows = allTyped(db.prepare(`SELECT id, title, status, priority, type, parent_id, created_at
+         FROM tasks
+         WHERE status NOT IN ('archived', 'cancelled')
+         ORDER BY
+           CASE priority
+             WHEN 'critical' THEN 0 WHEN 'high' THEN 1 WHEN 'medium' THEN 2 ELSE 3
+           END,
+           created_at DESC
+         LIMIT ?`), Math.ceil(perSubstrateLimit * 0.8));
+        const taskIds = new Set();
+        for (const row of taskRows) {
+            const weight = priorityWeight(row.priority);
+            if (weight < minWeight)
+                continue;
+            taskIds.add(row.id);
+            nodes.push({
+                id: `tasks:${row.id}`,
+                kind: 'task',
+                substrate: 'tasks',
+                label: row.title,
+                weight,
+                createdAt: row.created_at,
+                meta: {
+                    status: row.status,
+                    priority: row.priority,
+                    type: row.type,
+                    parent_id: row.parent_id,
+                    created_at: row.created_at,
+                },
+            });
+        }
+        // Sessions (most recent)
+        const sessionRows = allTyped(db.prepare(`SELECT id, status, started_at, ended_at
+         FROM sessions
+         ORDER BY started_at DESC
+         LIMIT ?`), Math.ceil(perSubstrateLimit * 0.2));
+        const sessionIds = new Set();
+        for (const row of sessionRows) {
+            sessionIds.add(row.id);
+            nodes.push({
+                id: `tasks:${row.id}`,
+                kind: 'session',
+                substrate: 'tasks',
+                label: `Session ${row.id.slice(-8)}`,
+                weight: row.status === 'active' ? 0.9 : 0.4,
+                createdAt: row.started_at,
+                meta: {
+                    status: row.status,
+                    started_at: row.started_at,
+                    ended_at: row.ended_at,
+                },
+            });
+        }
+        // Parent → child task edges
+        for (const row of taskRows) {
+            if (row.parent_id && taskIds.has(row.parent_id)) {
+                edges.push({
+                    source: `tasks:${row.parent_id}`,
+                    target: `tasks:${row.id}`,
+                    type: 'parent_of',
+                    weight: 0.9,
+                    substrate: 'tasks',
+                });
+            }
+        }
+        // Task relations
+        if (taskIds.size > 0) {
+            const placeholders = [...taskIds].map(() => '?').join(',');
+            const relRows = allTyped(db.prepare(`SELECT task_id, related_task_id, relation_type
+           FROM task_relations
+           WHERE task_id IN (${placeholders})
+             AND related_task_id IN (${placeholders})`), ...taskIds, ...taskIds);
+            for (const row of relRows) {
+                edges.push({
+                    source: `tasks:${row.task_id}`,
+                    target: `tasks:${row.related_task_id}`,
+                    type: row.relation_type,
+                    weight: 0.7,
+                    substrate: 'tasks',
+                });
+            }
+            // Task dependencies
+            const depRows = allTyped(db.prepare(`SELECT task_id, depends_on_task_id
+           FROM task_dependencies
+           WHERE task_id IN (${placeholders})
+             AND depends_on_task_id IN (${placeholders})`), ...taskIds, ...taskIds);
+            for (const row of depRows) {
+                edges.push({
+                    source: `tasks:${row.task_id}`,
+                    target: `tasks:${row.depends_on_task_id}`,
+                    type: 'depends_on',
+                    weight: 0.85,
+                    substrate: 'tasks',
+                });
+            }
+        }
+    }
+    catch {
+        // Return partial results on error
+    }
+    return { nodes, edges };
+}
+//# sourceMappingURL=tasks.js.map

package/dist/src/adapters/tasks.js.map

@@ -0,0 +1 @@
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