gnosys 4.0.0

package/dist/lib/wikilinks.js

@@ -0,0 +1,146 @@
+/**
+ * Gnosys Wikilinks — Obsidian-compatible cross-references between memories.
+ *
+ * Scans memory content for [[wikilinks]] and builds a link graph.
+ * Supports both [[title]] and [[path|display text]] formats.
+ */
+// Regex to match [[target]] or [[target|display text]]
+const WIKILINK_RE = /\[\[([^\]|]+?)(?:\|([^\]]+?))?\]\]/g;
+/**
+ * Extract all wikilinks from a memory's content.
+ */
+export function extractLinks(memory) {
+    const links = [];
+    let match;
+    // Reset regex state
+    WIKILINK_RE.lastIndex = 0;
+    while ((match = WIKILINK_RE.exec(memory.content)) !== null) {
+        links.push({
+            target: match[1].trim(),
+            displayText: match[2]?.trim() || null,
+            sourcePath: memory.relativePath,
+            sourceTitle: memory.frontmatter.title,
+        });
+    }
+    return links;
+}
+/**
+ * Resolve a wikilink target to a memory.
+ * Tries matching by: exact relative path, title (case-insensitive), id.
+ */
+export function resolveLink(target, memories) {
+    // 1. Exact relative path match
+    const byPath = memories.find((m) => m.relativePath === target);
+    if (byPath)
+        return byPath;
+    // 2. Path with .md extension
+    const withMd = memories.find((m) => m.relativePath === target + ".md");
+    if (withMd)
+        return withMd;
+    // 3. Filename match (target might be just the filename without category dir)
+    const byFilename = memories.find((m) => {
+        const filename = m.relativePath.split("/").pop()?.replace(/\.md$/, "");
+        return filename === target;
+    });
+    if (byFilename)
+        return byFilename;
+    // 4. Title match (case-insensitive)
+    const lowerTarget = target.toLowerCase();
+    const byTitle = memories.find((m) => m.frontmatter.title.toLowerCase() === lowerTarget);
+    if (byTitle)
+        return byTitle;
+    // 5. ID match
+    const byId = memories.find((m) => m.frontmatter.id === target);
+    if (byId)
+        return byId;
+    return null;
+}
+/**
+ * Build a full link graph from all memories.
+ */
+export function buildLinkGraph(memories) {
+    const nodes = new Map();
+    const orphanedLinks = [];
+    let totalLinks = 0;
+    // Initialize nodes for all memories
+    for (const m of memories) {
+        nodes.set(m.relativePath, {
+            path: m.relativePath,
+            title: m.frontmatter.title,
+            outgoing: [],
+            incoming: [],
+        });
+    }
+    // Extract links and resolve them
+    for (const m of memories) {
+        const links = extractLinks(m);
+        totalLinks += links.length;
+        for (const link of links) {
+            const resolved = resolveLink(link.target, memories);
+            if (resolved) {
+                // Add outgoing link to source
+                const sourceNode = nodes.get(m.relativePath);
+                sourceNode.outgoing.push(link);
+                // Add backlink to target
+                const targetNode = nodes.get(resolved.relativePath);
+                targetNode.incoming.push(link);
+            }
+            else {
+                orphanedLinks.push(link);
+            }
+        }
+    }
+    return { nodes, totalLinks, orphanedLinks };
+}
+/**
+ * Get backlinks for a specific memory.
+ */
+export function getBacklinks(memories, targetPath) {
+    const graph = buildLinkGraph(memories);
+    const node = graph.nodes.get(targetPath);
+    return node?.incoming || [];
+}
+/**
+ * Get outgoing links for a specific memory.
+ */
+export function getOutgoingLinks(memories, sourcePath) {
+    const graph = buildLinkGraph(memories);
+    const node = graph.nodes.get(sourcePath);
+    return node?.outgoing || [];
+}
+/**
+ * Format the link graph as a simple text summary.
+ */
+export function formatGraphSummary(graph) {
+    const lines = [];
+    lines.push(`Link Graph: ${graph.totalLinks} total links, ${graph.orphanedLinks.length} orphaned\n`);
+    // Find most-connected nodes
+    const connected = Array.from(graph.nodes.values())
+        .filter((n) => n.outgoing.length > 0 || n.incoming.length > 0)
+        .sort((a, b) => (b.incoming.length + b.outgoing.length) - (a.incoming.length + a.outgoing.length));
+    if (connected.length === 0) {
+        lines.push("No cross-references found. Use [[Title]] in memory content to create links.");
+        return lines.join("\n");
+    }
+    for (const node of connected) {
+        lines.push(`**${node.title}** (${node.path})`);
+        lines.push(`  → ${node.outgoing.length} outgoing, ← ${node.incoming.length} backlinks`);
+        if (node.outgoing.length > 0) {
+            const targets = node.outgoing.map((l) => l.displayText || l.target).join(", ");
+            lines.push(`  Links to: ${targets}`);
+        }
+        if (node.incoming.length > 0) {
+            const sources = node.incoming.map((l) => l.sourceTitle).join(", ");
+            lines.push(`  Referenced by: ${sources}`);
+        }
+        lines.push("");
+    }
+    if (graph.orphanedLinks.length > 0) {
+        lines.push("Orphaned links (targets not found):");
+        for (const link of graph.orphanedLinks) {
+            lines.push(`  [[${link.target}]] in ${link.sourceTitle}`);
+        }
+    }
+    return lines.join("\n");
+}
+//# sourceMappingURL=wikilinks.js.map

package/dist/lib/wikilinks.js.map

@@ -0,0 +1 @@
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package/dist/sandbox/client.d.ts

@@ -0,0 +1,82 @@
+/**
+ * Gnosys Sandbox Client
+ *
+ * Connects to the running sandbox server over a Unix domain socket
+ * and provides typed async methods for all sandbox operations.
+ */
+export declare class SandboxClient {
+    private socketPath;
+    constructor(socketPath?: string);
+    /**
+     * Send a request to the sandbox server and wait for a response.
+     * Each request gets a unique ID and is sent as newline-delimited JSON.
+     */
+    private send;
+    /** Check if the sandbox is reachable */
+    ping(): Promise<{
+        status: string;
+        pid: number;
+    }>;
+    /** Add a new memory to the central database */
+    add(params: {
+        content: string;
+        title?: string;
+        category?: string;
+        project_id?: string;
+        scope?: "project" | "user" | "global";
+        tags?: string | string[];
+        relevance?: string;
+        author?: string;
+        authority?: string;
+        confidence?: number;
+    }): Promise<{
+        id: string;
+        title: string;
+    }>;
+    /** Search/recall memories by query */
+    recall(query: string, opts?: {
+        limit?: number;
+        project_id?: string;
+    }): Promise<Array<{
+        id: string;
+        title: string;
+        content: string;
+        category: string;
+        confidence: number;
+        score: number;
+    }>>;
+    /** Reinforce an existing memory (boost confidence) */
+    reinforce(idOrQuery: string): Promise<{
+        id: string;
+        reinforcement_count: number;
+        confidence: number;
+    }>;
+    /** Get a specific memory by ID */
+    get(id: string): Promise<Record<string, unknown>>;
+    /** List memories, optionally filtered by category or project */
+    list(opts?: {
+        category?: string;
+        project_id?: string;
+        limit?: number;
+    }): Promise<Array<{
+        id: string;
+        title: string;
+        category: string;
+        confidence: number;
+        project_id: string | null;
+        scope: string;
+    }>>;
+    /** Get database statistics */
+    stats(): Promise<{
+        active: number;
+        archived: number;
+        total: number;
+        categories: string[];
+        projects: number;
+    }>;
+    /** Gracefully shut down the sandbox server */
+    shutdown(): Promise<void>;
+    /** Check if the sandbox is running (non-throwing) */
+    isRunning(): Promise<boolean>;
+}
+//# sourceMappingURL=client.d.ts.map

package/dist/sandbox/client.d.ts.map

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package/dist/sandbox/client.js

@@ -0,0 +1,128 @@
+/**
+ * Gnosys Sandbox Client
+ *
+ * Connects to the running sandbox server over a Unix domain socket
+ * and provides typed async methods for all sandbox operations.
+ */
+import net from "net";
+import { getSocketPath } from "./server.js";
+export class SandboxClient {
+    socketPath;
+    constructor(socketPath) {
+        this.socketPath = socketPath || getSocketPath();
+    }
+    /**
+     * Send a request to the sandbox server and wait for a response.
+     * Each request gets a unique ID and is sent as newline-delimited JSON.
+     */
+    send(method, params = {}) {
+        return new Promise((resolve, reject) => {
+            const id = `req-${Date.now()}-${Math.random().toString(36).slice(2, 6)}`;
+            const req = { id, method, params };
+            const socket = net.createConnection(this.socketPath, () => {
+                socket.write(JSON.stringify(req) + "\n");
+            });
+            let buffer = "";
+            socket.on("data", (data) => {
+                buffer += data.toString();
+                const newlineIdx = buffer.indexOf("\n");
+                if (newlineIdx !== -1) {
+                    const line = buffer.slice(0, newlineIdx).trim();
+                    try {
+                        const res = JSON.parse(line);
+                        socket.end();
+                        resolve(res);
+                    }
+                    catch (err) {
+                        socket.end();
+                        reject(new Error(`Invalid response from sandbox: ${line}`));
+                    }
+                }
+            });
+            socket.on("error", (err) => {
+                reject(new Error(`Cannot connect to Gnosys sandbox at ${this.socketPath}. ` +
+                    `Is the sandbox running? Start it with: gnosys sandbox start\n` +
+                    `(${err.message})`));
+            });
+            socket.setTimeout(10_000, () => {
+                socket.destroy();
+                reject(new Error("Sandbox request timed out after 10 seconds"));
+            });
+        });
+    }
+    /** Check if the sandbox is reachable */
+    async ping() {
+        const res = await this.send("ping");
+        if (!res.ok)
+            throw new Error(res.error || "Ping failed");
+        return res.result;
+    }
+    /** Add a new memory to the central database */
+    async add(params) {
+        const res = await this.send("add", {
+            ...params,
+            tags: Array.isArray(params.tags) ? JSON.stringify(params.tags) : params.tags,
+        });
+        if (!res.ok)
+            throw new Error(res.error || "Add failed");
+        return res.result;
+    }
+    /** Search/recall memories by query */
+    async recall(query, opts) {
+        const res = await this.send("recall", { query, ...opts });
+        if (!res.ok)
+            throw new Error(res.error || "Recall failed");
+        return res.result;
+    }
+    /** Reinforce an existing memory (boost confidence) */
+    async reinforce(idOrQuery) {
+        // If it looks like a memory ID, pass as id; otherwise treat as query
+        const isId = idOrQuery.startsWith("mem-") || idOrQuery.match(/^[a-z]+-\d+/);
+        const params = isId ? { id: idOrQuery } : { query: idOrQuery };
+        const res = await this.send("reinforce", params);
+        if (!res.ok)
+            throw new Error(res.error || "Reinforce failed");
+        return res.result;
+    }
+    /** Get a specific memory by ID */
+    async get(id) {
+        const res = await this.send("get", { id });
+        if (!res.ok)
+            throw new Error(res.error || "Get failed");
+        return res.result;
+    }
+    /** List memories, optionally filtered by category or project */
+    async list(opts) {
+        const res = await this.send("list", opts || {});
+        if (!res.ok)
+            throw new Error(res.error || "List failed");
+        return res.result;
+    }
+    /** Get database statistics */
+    async stats() {
+        const res = await this.send("stats");
+        if (!res.ok)
+            throw new Error(res.error || "Stats failed");
+        return res.result;
+    }
+    /** Gracefully shut down the sandbox server */
+    async shutdown() {
+        try {
+            await this.send("shutdown");
+        }
+        catch {
+            // Server may close before we get the response — that's expected
+        }
+    }
+    /** Check if the sandbox is running (non-throwing) */
+    async isRunning() {
+        try {
+            await this.ping();
+            return true;
+        }
+        catch {
+            return false;
+        }
+    }
+}
+//# sourceMappingURL=client.js.map

package/dist/sandbox/client.js.map

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package/dist/sandbox/helper-template.d.ts

@@ -0,0 +1,14 @@
+/**
+ * Gnosys Helper Library Generator
+ *
+ * Generates a self-contained `gnosys-helper.ts` file that agents
+ * can import and use immediately — zero config, zero MCP overhead.
+ *
+ * The generated file connects to the sandbox server via Unix socket
+ * and auto-starts the sandbox if it's not running.
+ */
+/**
+ * Write the helper library file to the specified directory.
+ */
+export declare function generateHelper(targetDir: string): Promise<string>;
+//# sourceMappingURL=helper-template.d.ts.map

package/dist/sandbox/helper-template.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"helper-template.d.ts","sourceRoot":"","sources":["../../src/sandbox/helper-template.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAqQH;;GAEG;AACH,wBAAsB,cAAc,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAevE"}

package/dist/sandbox/helper-template.js

@@ -0,0 +1,285 @@
+/**
+ * Gnosys Helper Library Generator
+ *
+ * Generates a self-contained `gnosys-helper.ts` file that agents
+ * can import and use immediately — zero config, zero MCP overhead.
+ *
+ * The generated file connects to the sandbox server via Unix socket
+ * and auto-starts the sandbox if it's not running.
+ */
+import fs from "fs";
+import path from "path";
+import { findProjectIdentity } from "../lib/projectIdentity.js";
+/**
+ * Generate the helper library source code.
+ * This is a self-contained TypeScript file with no external deps
+ * (other than Node built-ins).
+ */
+function generateHelperSource(projectId) {
+    return `/**
+ * Gnosys Helper — Auto-generated agent helper library.
+ *
+ * Import this file in your agent/script to get instant access
+ * to the Gnosys memory system with zero overhead.
+ *
+ * Usage:
+ *   import { gnosys } from "./gnosys-helper";
+ *   await gnosys.add("We use conventional commits");
+ *   const ctx = await gnosys.recall("auth decisions");
+ *   await gnosys.reinforce("payment logic");
+ *
+ * The sandbox auto-starts if not running. No MCP required.
+ *
+ * Generated: ${new Date().toISOString()}
+ * Project: ${projectId || "(none — global scope)"}
+ */
+
+import net from "net";
+import { execSync, spawn } from "child_process";
+import path from "path";
+import os from "os";
+import fs from "fs";
+
+// ─── Configuration ────────────────────────────────────────────────────────
+
+const PROJECT_ID: string | null = ${projectId ? `"${projectId}"` : "null"};
+
+function getSocketPath(): string {
+  if (process.platform === "win32") return "\\\\\\\\.\\\\pipe\\\\gnosys-sandbox";
+  const dir = path.join(os.homedir(), ".gnosys", "sandbox");
+  return path.join(dir, "gnosys.sock");
+}
+
+// ─── Low-level transport ──────────────────────────────────────────────────
+
+interface SandboxResponse {
+  id: string;
+  ok: boolean;
+  result?: unknown;
+  error?: string;
+}
+
+function send(method: string, params: Record<string, unknown> = {}): Promise<SandboxResponse> {
+  return new Promise((resolve, reject) => {
+    const id = \`req-\${Date.now()}-\${Math.random().toString(36).slice(2, 6)}\`;
+    const socket = net.createConnection(getSocketPath(), () => {
+      socket.write(JSON.stringify({ id, method, params }) + "\\n");
+    });
+    let buffer = "";
+    socket.on("data", (data) => {
+      buffer += data.toString();
+      const idx = buffer.indexOf("\\n");
+      if (idx !== -1) {
+        try {
+          resolve(JSON.parse(buffer.slice(0, idx).trim()));
+        } catch { reject(new Error("Invalid sandbox response")); }
+        socket.end();
+      }
+    });
+    socket.on("error", (err) => reject(err));
+    socket.setTimeout(10_000, () => { socket.destroy(); reject(new Error("Timeout")); });
+  });
+}
+
+// ─── Auto-start ───────────────────────────────────────────────────────────
+
+let _ensured = false;
+
+async function ensureRunning(): Promise<void> {
+  if (_ensured) return;
+  try {
+    await send("ping");
+    _ensured = true;
+    return;
+  } catch {
+    // Not running — start it
+  }
+
+  try {
+    execSync("npx gnosys sandbox start", { stdio: "ignore", timeout: 10_000 });
+  } catch {
+    // Try direct node invocation as fallback
+    const sandboxDir = path.join(os.homedir(), ".gnosys", "sandbox");
+    fs.mkdirSync(sandboxDir, { recursive: true });
+    const gnosysBin = execSync("which gnosys 2>/dev/null || echo ''", { encoding: "utf8" }).trim();
+    if (gnosysBin) {
+      execSync(\`\${gnosysBin} sandbox start\`, { stdio: "ignore", timeout: 10_000 });
+    } else {
+      throw new Error("Cannot auto-start sandbox. Run 'gnosys sandbox start' manually.");
+    }
+  }
+
+  // Wait for socket to become available
+  const start = Date.now();
+  while (Date.now() - start < 5000) {
+    try { await send("ping"); _ensured = true; return; } catch { /* retry */ }
+    await new Promise(r => setTimeout(r, 200));
+  }
+  throw new Error("Sandbox started but not responding. Check ~/.gnosys/sandbox/sandbox.log");
+}
+
+// ─── Public API ───────────────────────────────────────────────────────────
+
+export const gnosys = {
+  /** Add a memory to the Gnosys brain */
+  async add(content: string, opts?: {
+    title?: string;
+    category?: string;
+    tags?: string[];
+    scope?: "project" | "user" | "global";
+  }): Promise<{ id: string; title: string }> {
+    await ensureRunning();
+    const res = await send("add", {
+      content,
+      ...opts,
+      tags: opts?.tags ? JSON.stringify(opts.tags) : undefined,
+      project_id: opts?.scope === "global" ? undefined : PROJECT_ID,
+    });
+    if (!res.ok) throw new Error(res.error || "add failed");
+    return res.result as { id: string; title: string };
+  },
+
+  /** Recall memories relevant to a query */
+  async recall(query: string, opts?: {
+    limit?: number;
+  }): Promise<Array<{
+    id: string;
+    title: string;
+    content: string;
+    category: string;
+    confidence: number;
+    score: number;
+  }>> {
+    await ensureRunning();
+    const res = await send("recall", {
+      query,
+      limit: opts?.limit,
+      project_id: PROJECT_ID,
+    });
+    if (!res.ok) throw new Error(res.error || "recall failed");
+    return res.result as any[];
+  },
+
+  /** Reinforce a memory (boost its confidence and visibility) */
+  async reinforce(idOrQuery: string): Promise<{
+    id: string;
+    reinforcement_count: number;
+    confidence: number;
+  }> {
+    await ensureRunning();
+    const isId = idOrQuery.startsWith("mem-") || /^[a-z]+-\\d+/.test(idOrQuery);
+    const params = isId ? { id: idOrQuery } : { query: idOrQuery };
+    const res = await send("reinforce", params);
+    if (!res.ok) throw new Error(res.error || "reinforce failed");
+    return res.result as any;
+  },
+
+  /** List memories (optionally filtered) */
+  async list(opts?: {
+    category?: string;
+    limit?: number;
+  }): Promise<Array<{
+    id: string;
+    title: string;
+    category: string;
+    confidence: number;
+  }>> {
+    await ensureRunning();
+    const res = await send("list", {
+      ...opts,
+      project_id: PROJECT_ID,
+    });
+    if (!res.ok) throw new Error(res.error || "list failed");
+    return res.result as any[];
+  },
+
+  /** Get database stats */
+  async stats(): Promise<{
+    active: number;
+    archived: number;
+    total: number;
+    categories: string[];
+    projects: number;
+  }> {
+    await ensureRunning();
+    const res = await send("stats");
+    if (!res.ok) throw new Error(res.error || "stats failed");
+    return res.result as any;
+  },
+
+  /** Reflect on an outcome — updates confidence, adds relationships, creates a reflection memory */
+  async reflect(outcome: string, opts?: {
+    memory_ids?: string[];
+    success?: boolean;
+    notes?: string;
+    confidence_delta?: number;
+  }): Promise<{
+    reflection_id: string;
+    outcome: "success" | "failure";
+    memories_updated: Array<{ id: string; confidence: number; reinforcement_count: number }>;
+    relationships_created: number;
+    confidence_delta: number;
+  }> {
+    await ensureRunning();
+    const res = await send("reflect", {
+      outcome,
+      memory_ids: opts?.memory_ids ? JSON.stringify(opts.memory_ids) : undefined,
+      success: opts?.success,
+      notes: opts?.notes,
+      confidence_delta: opts?.confidence_delta,
+    });
+    if (!res.ok) throw new Error(res.error || "reflect failed");
+    return res.result as any;
+  },
+
+  /** Traverse relationship chains starting from a memory (BFS, depth-limited) */
+  async traverse(id: string, opts?: {
+    depth?: number;
+    rel_types?: string[];
+  }): Promise<{
+    root: string;
+    depth: number;
+    nodes: Array<{
+      id: string;
+      title: string;
+      category: string;
+      confidence: number;
+      depth: number;
+      via_rel: string | null;
+      via_from: string | null;
+    }>;
+    total: number;
+  }> {
+    await ensureRunning();
+    const res = await send("traverse", {
+      id,
+      depth: opts?.depth,
+      rel_types: opts?.rel_types ? JSON.stringify(opts.rel_types) : undefined,
+    });
+    if (!res.ok) throw new Error(res.error || "traverse failed");
+    return res.result as any;
+  },
+};
+
+export default gnosys;
+`;
+}
+/**
+ * Write the helper library file to the specified directory.
+ */
+export async function generateHelper(targetDir) {
+    // Try to detect the project identity
+    let projectId = null;
+    try {
+        const identity = await findProjectIdentity(targetDir);
+        projectId = identity?.identity.projectId || null;
+    }
+    catch {
+        // No project identity found — that's fine
+    }
+    const source = generateHelperSource(projectId);
+    const outputPath = path.join(targetDir, "gnosys-helper.ts");
+    fs.writeFileSync(outputPath, source, "utf8");
+    return outputPath;
+}
+//# sourceMappingURL=helper-template.js.map