neotoma 0.4.2 → 0.4.5

package/dist/cli/permissions.d.ts

@@ -0,0 +1,46 @@
+/**
+ * Permission-file writers for `neotoma setup`.
+ *
+ * Merges a single canonical `neotoma *` wildcard approval and a one-time
+ * `npm install -g neotoma` allow entry into each supported harness's
+ * permission file. All writers are merge-preserving and idempotent.
+ */
+import { existsSync } from "node:fs";
+import type { ToolId } from "./doctor.js";
+export interface PermissionPatch {
+    path: string;
+    tool: ToolId;
+    before: string | null;
+    after: string;
+    changed: boolean;
+    created: boolean;
+}
+/** Write `.claude/settings.local.json` with neotoma allow entries (project scope). */
+export declare function patchClaudeCodeProject(cwd: string, options?: {
+    dryRun?: boolean;
+}): Promise<PermissionPatch>;
+/** Write `~/.claude/settings.json` with neotoma allow entries (user scope). */
+export declare function patchClaudeCodeUser(options?: {
+    dryRun?: boolean;
+}): Promise<PermissionPatch>;
+/** Write `.cursor/allowlist.json` under the current project root. */
+export declare function patchCursorAllowlist(cwd: string, options?: {
+    dryRun?: boolean;
+}): Promise<PermissionPatch>;
+/** Append an `[approvals]` block to `~/.codex/config.toml` if missing. */
+export declare function patchCodexConfig(options?: {
+    dryRun?: boolean;
+}): Promise<PermissionPatch>;
+/** Write all supported permission files for a given tool. */
+export declare function writePermissionsForTool(tool: ToolId, cwd: string, options?: {
+    dryRun?: boolean;
+    scope?: "project" | "user" | "both";
+}): Promise<PermissionPatch[]>;
+export declare function toolFromString(s: string): ToolId | null;
+/** Convenience: detect whether a tool already has neotoma wildcard permission. */
+export declare function hasNeotomaAllow(patch: PermissionPatch): boolean;
+/** Expose existsSync for tests. */
+export declare const __testing: {
+    existsSync: typeof existsSync;
+};
+//# sourceMappingURL=permissions.d.ts.map

package/dist/cli/permissions.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"permissions.d.ts","sourceRoot":"","sources":["../../src/cli/permissions.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,OAAO,EAAE,UAAU,EAAE,MAAM,SAAS,CAAC;AAIrC,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,aAAa,CAAC;AAE1C,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,OAAO,CAAC;IACjB,OAAO,EAAE,OAAO,CAAC;CAClB;AAiCD,sFAAsF;AACtF,wBAAsB,sBAAsB,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,GAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,OAAO,CAAC,eAAe,CAAC,CAoBtH;AAED,+EAA+E;AAC/E,wBAAsB,mBAAmB,CAAC,OAAO,GAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,OAAO,CAAC,eAAe,CAAC,CAoBtG;AAED,qEAAqE;AACrE,wBAAsB,oBAAoB,CAAC,GAAG,EAAE,MAAM,EAAE,OAAO,GAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,OAAO,CAAC,eAAe,CAAC,CAoBpH;AAWD,0EAA0E;AAC1E,wBAAsB,gBAAgB,CAAC,OAAO,GAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAA;CAAO,GAAG,OAAO,CAAC,eAAe,CAAC,CAkBnG;AAED,6DAA6D;AAC7D,wBAAsB,uBAAuB,CAC3C,IAAI,EAAE,MAAM,EACZ,GAAG,EAAE,MAAM,EACX,OAAO,GAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,SAAS,GAAG,MAAM,GAAG,MAAM,CAAA;CAAO,GACtE,OAAO,CAAC,eAAe,EAAE,CAAC,CA4B5B;AAED,wBAAgB,cAAc,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAQvD;AAED,kFAAkF;AAClF,wBAAgB,eAAe,CAAC,KAAK,EAAE,eAAe,GAAG,OAAO,CAG/D;AAED,mCAAmC;AACnC,eAAO,MAAM,SAAS;;CAAiB,CAAC"}

package/dist/cli/permissions.js

@@ -0,0 +1,191 @@
+/**
+ * Permission-file writers for `neotoma setup`.
+ *
+ * Merges a single canonical `neotoma *` wildcard approval and a one-time
+ * `npm install -g neotoma` allow entry into each supported harness's
+ * permission file. All writers are merge-preserving and idempotent.
+ */
+import fs from "node:fs/promises";
+import { existsSync } from "node:fs";
+import os from "node:os";
+import path from "node:path";
+/** Serialize JSON with stable 2-space indentation. */
+function jsonStr(value) {
+    return `${JSON.stringify(value, null, 2)}\n`;
+}
+async function readText(p) {
+    try {
+        return await fs.readFile(p, "utf8");
+    }
+    catch {
+        return null;
+    }
+}
+async function ensureDir(dir) {
+    await fs.mkdir(dir, { recursive: true });
+}
+/** Canonical allow entries to inject per harness. */
+const CLAUDE_ALLOW_ENTRIES = ["Bash(neotoma:*)", "Bash(npm install -g neotoma:*)"];
+const CURSOR_ALLOW_ENTRIES = ["neotoma *", "npm install -g neotoma"];
+/** Merge unique entries into array, preserving existing order. */
+function mergeAllow(existing, entries) {
+    const base = Array.isArray(existing) ? existing.filter((s) => typeof s === "string") : [];
+    const out = [...base];
+    for (const e of entries) {
+        if (!out.includes(e))
+            out.push(e);
+    }
+    return out;
+}
+/** Write `.claude/settings.local.json` with neotoma allow entries (project scope). */
+export async function patchClaudeCodeProject(cwd, options = {}) {
+    const target = path.join(cwd, ".claude", "settings.local.json");
+    const before = await readText(target);
+    let parsed = {};
+    if (before) {
+        try {
+            parsed = JSON.parse(before);
+        }
+        catch {
+            // treat as empty
+        }
+    }
+    const allow = mergeAllow(parsed.permissions?.allow, CLAUDE_ALLOW_ENTRIES);
+    const next = { ...parsed, permissions: { ...(parsed.permissions ?? {}), allow } };
+    const after = jsonStr(next);
+    const changed = after !== before;
+    if (changed && !options.dryRun) {
+        await ensureDir(path.dirname(target));
+        await fs.writeFile(target, after, "utf8");
+    }
+    return { path: target, tool: "claude-code", before, after, changed, created: before === null };
+}
+/** Write `~/.claude/settings.json` with neotoma allow entries (user scope). */
+export async function patchClaudeCodeUser(options = {}) {
+    const target = path.join(os.homedir(), ".claude", "settings.json");
+    const before = await readText(target);
+    let parsed = {};
+    if (before) {
+        try {
+            parsed = JSON.parse(before);
+        }
+        catch {
+            // ignore
+        }
+    }
+    const allow = mergeAllow(parsed.permissions?.allow, CLAUDE_ALLOW_ENTRIES);
+    const next = { ...parsed, permissions: { ...(parsed.permissions ?? {}), allow } };
+    const after = jsonStr(next);
+    const changed = after !== before;
+    if (changed && !options.dryRun) {
+        await ensureDir(path.dirname(target));
+        await fs.writeFile(target, after, "utf8");
+    }
+    return { path: target, tool: "claude-code", before, after, changed, created: before === null };
+}
+/** Write `.cursor/allowlist.json` under the current project root. */
+export async function patchCursorAllowlist(cwd, options = {}) {
+    const target = path.join(cwd, ".cursor", "allowlist.json");
+    const before = await readText(target);
+    let parsed = {};
+    if (before) {
+        try {
+            parsed = JSON.parse(before);
+        }
+        catch {
+            // ignore
+        }
+    }
+    const allow = mergeAllow(parsed.allow, CURSOR_ALLOW_ENTRIES);
+    const next = { ...parsed, allow };
+    const after = jsonStr(next);
+    const changed = after !== before;
+    if (changed && !options.dryRun) {
+        await ensureDir(path.dirname(target));
+        await fs.writeFile(target, after, "utf8");
+    }
+    return { path: target, tool: "cursor", before, after, changed, created: before === null };
+}
+const CODEX_APPROVAL_BLOCK = `
+# Added by \`neotoma setup --tool codex\`
+[approvals]
+allow = [
+  "neotoma *",
+  "npm install -g neotoma",
+]
+`.trimStart();
+/** Append an `[approvals]` block to `~/.codex/config.toml` if missing. */
+export async function patchCodexConfig(options = {}) {
+    const target = path.join(os.homedir(), ".codex", "config.toml");
+    const before = await readText(target);
+    const hasNeotoma = before ? /neotoma/i.test(before) : false;
+    let after;
+    if (!before) {
+        after = CODEX_APPROVAL_BLOCK;
+    }
+    else if (hasNeotoma) {
+        after = before;
+    }
+    else {
+        after = before.endsWith("\n") ? `${before}\n${CODEX_APPROVAL_BLOCK}` : `${before}\n\n${CODEX_APPROVAL_BLOCK}`;
+    }
+    const changed = after !== before;
+    if (changed && !options.dryRun) {
+        await ensureDir(path.dirname(target));
+        await fs.writeFile(target, after, "utf8");
+    }
+    return { path: target, tool: "codex", before, after, changed, created: before === null };
+}
+/** Write all supported permission files for a given tool. */
+export async function writePermissionsForTool(tool, cwd, options = {}) {
+    const scope = options.scope ?? "project";
+    const results = [];
+    switch (tool) {
+        case "claude-code": {
+            if (scope === "project" || scope === "both") {
+                results.push(await patchClaudeCodeProject(cwd, options));
+            }
+            if (scope === "user" || scope === "both") {
+                results.push(await patchClaudeCodeUser(options));
+            }
+            break;
+        }
+        case "cursor": {
+            results.push(await patchCursorAllowlist(cwd, options));
+            break;
+        }
+        case "codex": {
+            results.push(await patchCodexConfig(options));
+            break;
+        }
+        case "claude-desktop":
+        case "openclaw": {
+            // These harnesses don't surface an allowlist file; documented in the preflight UI instead.
+            break;
+        }
+    }
+    return results;
+}
+export function toolFromString(s) {
+    const n = s.trim().toLowerCase();
+    if (n === "claude-code" || n === "claudecode" || n === "claude_code")
+        return "claude-code";
+    if (n === "claude-desktop" || n === "claude_desktop")
+        return "claude-desktop";
+    if (n === "cursor")
+        return "cursor";
+    if (n === "codex")
+        return "codex";
+    if (n === "openclaw")
+        return "openclaw";
+    return null;
+}
+/** Convenience: detect whether a tool already has neotoma wildcard permission. */
+export function hasNeotomaAllow(patch) {
+    if (!patch.after)
+        return false;
+    return /neotoma/i.test(patch.after);
+}
+/** Expose existsSync for tests. */
+export const __testing = { existsSync };
+//# sourceMappingURL=permissions.js.map

package/dist/cli/permissions.js.map

@@ -0,0 +1 @@
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package/dist/cli/setup.d.ts

@@ -0,0 +1,46 @@
+/**
+ * `neotoma setup` — composite onboarding command.
+ *
+ * Collapses `init --yes --idempotent`, `mcp config --yes`,
+ * `cli-instructions config --yes`, and permission-file writes into one
+ * agent-runnable call so harnesses only need wildcard approval for
+ * `neotoma *` to complete the full install-first flow.
+ */
+import type { ToolId } from "./doctor.js";
+import { runDoctor } from "./doctor.js";
+import type { PermissionPatch } from "./permissions.js";
+export interface SetupStepResult {
+    id: string;
+    ok: boolean;
+    changed: boolean;
+    skipped?: boolean;
+    reason?: string;
+    details?: unknown;
+}
+export interface SetupReport {
+    tool: ToolId | null;
+    dry_run: boolean;
+    steps: SetupStepResult[];
+    permission_patches: PermissionPatch[];
+    doctor_before: Awaited<ReturnType<typeof runDoctor>>;
+    doctor_after: Awaited<ReturnType<typeof runDoctor>>;
+    overall_ok: boolean;
+}
+export interface RunSetupOptions {
+    tool?: string | ToolId | null;
+    dryRun?: boolean;
+    yes?: boolean;
+    cwd?: string;
+    /** Skip permissions patching; useful for openclaw which uses a native plugin. */
+    skipPermissions?: boolean;
+    /** Permission scope for tools that expose project+user files. */
+    scope?: "project" | "user" | "both";
+    /** Injected runners to keep setup pure + testable. */
+    runners?: {
+        init?: () => Promise<SetupStepResult>;
+        mcpConfigure?: () => Promise<SetupStepResult>;
+        cliInstructionsConfigure?: () => Promise<SetupStepResult>;
+    };
+}
+export declare function runSetup(options?: RunSetupOptions): Promise<SetupReport>;
+//# sourceMappingURL=setup.d.ts.map

package/dist/cli/setup.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/setup.js

@@ -0,0 +1,105 @@
+/**
+ * `neotoma setup` — composite onboarding command.
+ *
+ * Collapses `init --yes --idempotent`, `mcp config --yes`,
+ * `cli-instructions config --yes`, and permission-file writes into one
+ * agent-runnable call so harnesses only need wildcard approval for
+ * `neotoma *` to complete the full install-first flow.
+ */
+import { runDoctor } from "./doctor.js";
+import { writePermissionsForTool, toolFromString } from "./permissions.js";
+export async function runSetup(options = {}) {
+    const cwd = options.cwd ?? process.cwd();
+    const dryRun = options.dryRun ?? false;
+    const doctorBefore = await runDoctor({ cwd });
+    const toolInput = typeof options.tool === "string" ? toolFromString(options.tool) : (options.tool ?? null);
+    const tool = toolInput ?? doctorBefore.current_tool_hint;
+    const steps = [];
+    // Step 1: init (idempotent)
+    if (options.runners?.init) {
+        steps.push(await options.runners.init());
+    }
+    else if (doctorBefore.data.initialized) {
+        steps.push({ id: "init", ok: true, changed: false, skipped: true, reason: "already-initialized" });
+    }
+    else if (dryRun) {
+        steps.push({ id: "init", ok: true, changed: true, skipped: true, reason: "dry-run" });
+    }
+    else {
+        steps.push({ id: "init", ok: false, changed: false, skipped: true, reason: "runner-not-provided" });
+    }
+    // Step 2: mcp configure
+    if (options.runners?.mcpConfigure) {
+        steps.push(await options.runners.mcpConfigure());
+    }
+    else {
+        const hasMcp = Object.values(doctorBefore.mcp_servers_detected).some((c) => c.has_neotoma || c.has_neotoma_dev);
+        if (hasMcp) {
+            steps.push({ id: "mcp-configure", ok: true, changed: false, skipped: true, reason: "already-configured" });
+        }
+        else if (dryRun) {
+            steps.push({ id: "mcp-configure", ok: true, changed: true, skipped: true, reason: "dry-run" });
+        }
+        else {
+            steps.push({ id: "mcp-configure", ok: false, changed: false, skipped: true, reason: "runner-not-provided" });
+        }
+    }
+    // Step 3: CLI instructions configure
+    if (options.runners?.cliInstructionsConfigure) {
+        steps.push(await options.runners.cliInstructionsConfigure());
+    }
+    else {
+        const ci = doctorBefore.cli_instructions;
+        const hasAny = ci.project.cursor ||
+            ci.project.claude ||
+            ci.project.codex ||
+            ci.user.cursor ||
+            ci.user.claude ||
+            ci.user.codex;
+        if (hasAny) {
+            steps.push({ id: "cli-instructions", ok: true, changed: false, skipped: true, reason: "already-configured" });
+        }
+        else if (dryRun) {
+            steps.push({ id: "cli-instructions", ok: true, changed: true, skipped: true, reason: "dry-run" });
+        }
+        else {
+            steps.push({ id: "cli-instructions", ok: false, changed: false, skipped: true, reason: "runner-not-provided" });
+        }
+    }
+    // Step 4: permission patches
+    const permissionPatches = [];
+    if (tool && !options.skipPermissions && tool !== "openclaw" && tool !== "claude-desktop") {
+        const patches = await writePermissionsForTool(tool, cwd, {
+            dryRun,
+            scope: options.scope ?? "project",
+        });
+        permissionPatches.push(...patches);
+        steps.push({
+            id: "permissions",
+            ok: true,
+            changed: patches.some((p) => p.changed),
+            details: patches.map((p) => ({ path: p.path, changed: p.changed, created: p.created })),
+        });
+    }
+    else {
+        steps.push({
+            id: "permissions",
+            ok: true,
+            changed: false,
+            skipped: true,
+            reason: tool ? `tool ${tool} does not expose an allowlist file` : "tool not specified",
+        });
+    }
+    const doctorAfter = dryRun ? doctorBefore : await runDoctor({ cwd });
+    const overall = steps.every((s) => s.ok);
+    return {
+        tool,
+        dry_run: dryRun,
+        steps,
+        permission_patches: permissionPatches,
+        doctor_before: doctorBefore,
+        doctor_after: doctorAfter,
+        overall_ok: overall,
+    };
+}
+//# sourceMappingURL=setup.js.map

package/dist/cli/setup.js.map

@@ -0,0 +1 @@
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package/dist/core/operations.d.ts

@@ -0,0 +1,145 @@
+/**
+ * Core operations module.
+ *
+ * Provides a stable, typed API surface for calling Neotoma's core actions
+ * (store, retrieve, create_relationship, etc.) without going through the
+ * MCP JSON-RPC protocol. This is the foundation used by:
+ *   - `@neotoma/client` (local transport)
+ *   - hook plugins for Claude Code, Cursor, OpenCode, Codex
+ *   - Claude Agent SDK adapter
+ *
+ * Design:
+ *   - Wraps the existing `NeotomaServer.executeToolForCli` dispatcher so we
+ *     reuse every business rule, idempotency check, schema validation, and
+ *     provenance construction already implemented there.
+ *   - Parses the MCP-standard `{ content: [{ type, text }] }` response into
+ *     typed return values.
+ *   - Exposes a `createOperations({ userId })` factory so each caller gets
+ *     a bound instance with its authenticated user.
+ *
+ * See `docs/developer/mcp/instructions.md` for the semantic contract that
+ * agents follow when storing and retrieving through these operations.
+ */
+import { NeotomaServer } from "../server.js";
+export interface CreateOperationsOptions {
+    userId: string;
+    /** Optional pre-constructed server instance. If omitted, a new one is created lazily. */
+    server?: NeotomaServer;
+}
+export interface StoreEntityInput {
+    entity_type: string;
+    [key: string]: unknown;
+}
+export interface StoreRelationshipInput {
+    relationship_type: string;
+    source_index?: number;
+    target_index?: number;
+    source_entity_id?: string;
+    target_entity_id?: string;
+}
+export interface StoreInput {
+    entities?: StoreEntityInput[];
+    relationships?: StoreRelationshipInput[];
+    idempotency_key?: string;
+    file_path?: string;
+    file_content?: string;
+    mime_type?: string;
+    file_idempotency_key?: string;
+    original_filename?: string;
+}
+export interface StoredEntityRef {
+    entity_id: string;
+    entity_type: string;
+    action?: "created" | "updated" | string;
+    [key: string]: unknown;
+}
+export interface StoreResult {
+    structured?: {
+        entities: StoredEntityRef[];
+        relationships?: unknown[];
+    };
+    unstructured?: {
+        asset_entity_id?: string;
+        [key: string]: unknown;
+    };
+    [key: string]: unknown;
+}
+export interface RetrieveEntitiesInput {
+    entity_type?: string;
+    limit?: number;
+    offset?: number;
+    since?: string;
+    until?: string;
+    [key: string]: unknown;
+}
+export interface RetrieveEntityByIdentifierInput {
+    identifier: string;
+    entity_type?: string;
+}
+export interface CreateRelationshipInput {
+    relationship_type: string;
+    source_entity_id: string;
+    target_entity_id: string;
+}
+export interface Operations {
+    /** Store structured and/or unstructured data. See docs/developer/mcp/instructions.md. */
+    store(input: StoreInput): Promise<StoreResult>;
+    /** Alias for store() preserving the MCP `store_structured` action name. */
+    storeStructured(input: StoreInput): Promise<StoreResult>;
+    /** Alias for store() preserving the MCP `store_unstructured` action name. */
+    storeUnstructured(input: StoreInput): Promise<StoreResult>;
+    /** List entities by type or time window. */
+    retrieveEntities(input: RetrieveEntitiesInput): Promise<unknown>;
+    /** Look up a single entity by identifier (name, email, canonical_name, etc.). */
+    retrieveEntityByIdentifier(input: RetrieveEntityByIdentifierInput): Promise<unknown>;
+    /** Snapshot of a single entity. */
+    retrieveEntitySnapshot(input: {
+        entity_id: string;
+    }): Promise<unknown>;
+    /** List observations for provenance / history. */
+    listObservations(input: {
+        entity_id: string;
+        limit?: number;
+    }): Promise<unknown>;
+    /** List timeline events for a time window. */
+    listTimelineEvents(input: {
+        since?: string;
+        until?: string;
+        limit?: number;
+    }): Promise<unknown>;
+    /** Retrieve related entities (graph expansion). */
+    retrieveRelatedEntities(input: {
+        entity_id: string;
+        relationship_type?: string;
+        direction?: "outgoing" | "incoming" | "both";
+        limit?: number;
+    }): Promise<unknown>;
+    /** Create a relationship between two existing entities. */
+    createRelationship(input: CreateRelationshipInput): Promise<unknown>;
+    /** Correct an observation (creates a new observation that supersedes the prior). */
+    correct(input: {
+        entity_id: string;
+        corrections: Record<string, unknown>;
+    }): Promise<unknown>;
+    /** List registered entity types (schema-level discovery). */
+    listEntityTypes(input?: {
+        search?: string;
+    }): Promise<unknown>;
+    /** Per-type entity counts. */
+    getEntityTypeCounts(input?: Record<string, unknown>): Promise<unknown>;
+    /** Raw escape hatch — invoke any MCP tool by name. */
+    executeTool(name: string, args: unknown): Promise<unknown>;
+    /** Dispose the internal server instance if this factory created one. */
+    dispose(): Promise<void>;
+}
+/**
+ * Create a bound operations client for a given user.
+ *
+ * The caller is responsible for providing `userId` — this mirrors the
+ * existing `executeToolForCli` contract and lets the same process serve
+ * multiple users (e.g. API server mode). For single-user local mode use
+ * the local dev user id from `services/local_auth.ts`.
+ */
+export declare function createOperations(options: CreateOperationsOptions): Operations;
+export type { NeotomaServer };
+//# sourceMappingURL=operations.d.ts.map

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