@oxagen/cli 0.6.0 → 0.6.2

package/dist/commands/mcp.check.js

@@ -1,114 +0,0 @@
-/**
- * `oxagen mcp check` — Health check all configured MCP servers.
- *
- * Probes each enabled server and reports connectivity status.
- * For HTTP servers: attempts a connection and tool list.
- * For stdio servers: attempts to spawn the command.
- */
-import { Command } from "commander";
-import { resolveSettings, findProjectRoot } from "@oxagen/mcp-config/resolve";
-import { resolveCredential } from "@oxagen/mcp-config/credentials";
-import { loadManagedConfig, getManagedServers } from "@oxagen/mcp-config/managed";
-async function checkServer(name, config) {
-    const transport = config.transport;
-    if ("disabled" in config && config.disabled) {
-        return { name, transport, status: "disabled" };
-    }
-    if (transport === "stdio") {
-        // For stdio, just verify the command exists (don't spawn it)
-        const { execSync } = await import("node:child_process");
-        try {
-            execSync(`which ${config.command}`, { stdio: "ignore" });
-            return { name, transport, status: "healthy" };
-        }
-        catch {
-            return { name, transport, status: "unreachable", error: `command "${config.command}" not found` };
-        }
-    }
-    // HTTP-based transports: resolve credentials and attempt connection
-    const cred = await resolveCredential({ serverName: name, config });
-    if (cred.source === "none" && "auth" in config && config.auth !== "none") {
-        return { name, transport, status: "auth_required", error: "no credentials configured" };
-    }
-    if (cred.expired) {
-        return { name, transport, status: "auth_required", error: "token expired" };
-    }
-    // Attempt HTTP probe
-    const url = "url" in config ? config.url : "";
-    const start = Date.now();
-    try {
-        const headers = { accept: "application/json" };
-        if (cred.token)
-            headers["authorization"] = `Bearer ${cred.token}`;
-        if (cred.headers)
-            Object.assign(headers, cred.headers);
-        const res = await fetch(url, {
-            method: "GET",
-            headers,
-            signal: AbortSignal.timeout(10_000),
-        });
-        const latencyMs = Date.now() - start;
-        if (res.status === 401 || res.status === 403) {
-            return { name, transport, status: "auth_required", latencyMs, error: `HTTP ${res.status}` };
-        }
-        // Any response (even 404/405) means the server is reachable
-        return { name, transport, status: "healthy", latencyMs };
-    }
-    catch (err) {
-        const latencyMs = Date.now() - start;
-        const error = err instanceof Error ? err.message : String(err);
-        return { name, transport, status: "unreachable", latencyMs, error };
-    }
-}
-export const mcpCheckCommand = new Command("check")
-    .description("Health check all configured MCP servers")
-    .option("--json", "Output results as JSON")
-    .option("--server <name>", "Check only this server")
-    .action(async (options) => {
-    const projectRoot = findProjectRoot();
-    const { settings } = resolveSettings({ projectRoot });
-    const managed = loadManagedConfig();
-    const managedServers = getManagedServers(managed);
-    // Merge all servers
-    const allServers = {
-        ...(settings.mcpServers ?? {}),
-        ...managedServers,
-    };
-    // Filter if --server specified
-    const targets = options.server
-        ? Object.fromEntries(Object.entries(allServers).filter(([name]) => name === options.server))
-        : allServers;
-    if (Object.keys(targets).length === 0) {
-        if (options.server) {
-            console.error(`Error: server "${options.server}" not found`);
-        }
-        else {
-            console.log("No MCP servers configured.");
-        }
-        process.exit(options.server ? 1 : 0);
-    }
-    const results = [];
-    for (const [name, config] of Object.entries(targets)) {
-        const result = await checkServer(name, config);
-        results.push(result);
-    }
-    if (options.json) {
-        console.log(JSON.stringify(results, null, 2));
-        return;
-    }
-    // Pretty print
-    console.log("MCP Server Health:\n");
-    for (const r of results) {
-        const icon = r.status === "healthy" ? "●"
-            : r.status === "disabled" ? "○"
-                : r.status === "auth_required" ? "◐"
-                    : "✕";
-        const latency = r.latencyMs ? ` (${r.latencyMs}ms)` : "";
-        const error = r.error ? ` — ${r.error}` : "";
-        console.log(`  ${icon} ${r.name}: ${r.status}${latency}${error}`);
-    }
-    const healthy = results.filter((r) => r.status === "healthy").length;
-    const total = results.filter((r) => r.status !== "disabled").length;
-    console.log(`\n  ${healthy}/${total} servers healthy`);
-});
-//# sourceMappingURL=mcp.check.js.map

package/dist/commands/mcp.check.js.map

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package/dist/commands/mcp.list.d.ts

@@ -1,9 +0,0 @@
-/**
- * `oxagen mcp list` — List effective MCP servers (merged across all scopes).
- *
- * Shows each server with its transport, source scope, and auth status.
- * If --verbose, also shows the file paths being loaded and any warnings.
- */
-import { Command } from "commander";
-export declare const mcpListLocalCommand: Command;
-//# sourceMappingURL=mcp.list.d.ts.map

package/dist/commands/mcp.list.d.ts.map

@@ -1 +0,0 @@
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package/dist/commands/mcp.list.js

@@ -1,93 +0,0 @@
-/**
- * `oxagen mcp list` — List effective MCP servers (merged across all scopes).
- *
- * Shows each server with its transport, source scope, and auth status.
- * If --verbose, also shows the file paths being loaded and any warnings.
- */
-import { Command } from "commander";
-import { resolveSettings, getSettingsPaths, findProjectRoot } from "@oxagen/mcp-config/resolve";
-import { loadManagedConfig, getManagedServers } from "@oxagen/mcp-config/managed";
-import { readCredential } from "@oxagen/mcp-config/credentials";
-export const mcpListLocalCommand = new Command("list")
-    .description("List effective MCP servers from file-based configuration")
-    .option("--verbose", "Show file paths and detailed configuration")
-    .option("--json", "Output as JSON")
-    .action(async (options) => {
-    const projectRoot = findProjectRoot();
-    const { settings, serverSources } = resolveSettings({ projectRoot });
-    // Inject managed servers
-    const managed = loadManagedConfig();
-    const managedServers = getManagedServers(managed);
-    // Build unified server list
-    const allServers = {};
-    // File-based servers
-    for (const [name, config] of Object.entries(settings.mcpServers ?? {})) {
-        const cred = readCredential(name);
-        let authStatus = "none";
-        if ("auth" in config && config.auth !== "none") {
-            if (cred?.accessToken) {
-                const expired = cred.expiresAt ? new Date(cred.expiresAt).getTime() < Date.now() : false;
-                authStatus = expired ? "expired" : "authenticated";
-            }
-            else {
-                authStatus = "not configured";
-            }
-        }
-        allServers[name] = {
-            config,
-            scope: serverSources[name] ?? "unknown",
-            managed: false,
-            authStatus,
-        };
-    }
-    // Managed servers (override file-based)
-    for (const [name, config] of Object.entries(managedServers)) {
-        allServers[name] = {
-            config,
-            scope: "managed",
-            managed: true,
-            authStatus: "org-managed",
-        };
-    }
-    if (options.json) {
-        console.log(JSON.stringify(allServers, null, 2));
-        return;
-    }
-    // Pretty print
-    const entries = Object.entries(allServers);
-    if (entries.length === 0) {
-        console.log("No MCP servers configured.");
-        if (options.verbose) {
-            const paths = getSettingsPaths(projectRoot);
-            console.log("\nSearched:");
-            console.log(`  User:    ${paths.user}`);
-            console.log(`  Project: ${paths.project}`);
-            console.log(`  Local:   ${paths.local}`);
-        }
-        return;
-    }
-    console.log("MCP Servers:\n");
-    // Calculate column widths
-    const nameWidth = Math.max(...entries.map(([n]) => n.length), 4);
-    const transportWidth = 16;
-    console.log(`  ${"NAME".padEnd(nameWidth)}  ${"TRANSPORT".padEnd(transportWidth)}  ${"SCOPE".padEnd(10)}  AUTH`);
-    console.log(`  ${"─".repeat(nameWidth)}  ${"─".repeat(transportWidth)}  ${"─".repeat(10)}  ${"─".repeat(16)}`);
-    for (const [name, info] of entries) {
-        const config = info.config;
-        const transport = config["transport"] ?? "unknown";
-        const disabled = config["disabled"] === true;
-        const prefix = disabled ? "  (disabled) " : "  ";
-        console.log(`${prefix}${name.padEnd(nameWidth)}  ${transport.padEnd(transportWidth)}  ${info.scope.padEnd(10)}  ${info.authStatus}`);
-    }
-    if (options.verbose) {
-        const paths = getSettingsPaths(projectRoot);
-        console.log("\nSettings files:");
-        console.log(`  User:    ${paths.user}`);
-        console.log(`  Project: ${paths.project}`);
-        console.log(`  Local:   ${paths.local}`);
-        if (managed) {
-            console.log(`  Managed: synced ${managed._syncedAt} (org: ${managed._orgId})`);
-        }
-    }
-});
-//# sourceMappingURL=mcp.list.js.map

package/dist/commands/mcp.list.js.map

@@ -1 +0,0 @@
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package/dist/commands/mcp.permit.d.ts

@@ -1,12 +0,0 @@
-/**
- * `oxagen mcp permit <server>` — Set permission rules for an MCP server.
- *
- * Writes allow/deny rules to the specified scope file.
- * Examples:
- *   oxagen mcp permit github --allow-all --deny delete_repository
- *   oxagen mcp permit internal-api --allow "query_*,get_*" --deny "delete_*"
- *   oxagen mcp permit filesystem --default allow
- */
-import { Command } from "commander";
-export declare const mcpPermitCommand: Command;
-//# sourceMappingURL=mcp.permit.d.ts.map

package/dist/commands/mcp.permit.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"mcp.permit.d.ts","sourceRoot":"","sources":["../../src/commands/mcp.permit.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA4BpC,eAAO,MAAM,gBAAgB,SA6FzB,CAAC"}

package/dist/commands/mcp.permit.js

@@ -1,117 +0,0 @@
-/**
- * `oxagen mcp permit <server>` — Set permission rules for an MCP server.
- *
- * Writes allow/deny rules to the specified scope file.
- * Examples:
- *   oxagen mcp permit github --allow-all --deny delete_repository
- *   oxagen mcp permit internal-api --allow "query_*,get_*" --deny "delete_*"
- *   oxagen mcp permit filesystem --default allow
- */
-import { Command } from "commander";
-import { readFileSync, writeFileSync, existsSync, mkdirSync } from "node:fs";
-import { join, dirname } from "node:path";
-import { homedir } from "node:os";
-import { findProjectRoot } from "@oxagen/mcp-config/resolve";
-function getSettingsPath(scope, projectRoot) {
-    switch (scope) {
-        case "user":
-            return join(homedir(), ".config", "oxagen", "settings.json");
-        case "project":
-            return join(projectRoot, ".oxagen", "settings.json");
-        case "local":
-            return join(projectRoot, ".oxagen", "settings.local.json");
-    }
-}
-function readOrCreateSettings(filePath) {
-    if (!existsSync(filePath))
-        return {};
-    try {
-        return JSON.parse(readFileSync(filePath, "utf8"));
-    }
-    catch {
-        return {};
-    }
-}
-export const mcpPermitCommand = new Command("permit")
-    .description("Set permission rules for an MCP server's tools")
-    .argument("<server>", "Server name to configure permissions for")
-    .option("--allow <patterns>", "Glob patterns for tools to allow (comma-separated)")
-    .option("--deny <patterns>", "Glob patterns for tools to deny (comma-separated)")
-    .option("--allow-all", "Set defaultPolicy to allow for this server")
-    .option("--deny-all", "Set defaultPolicy to deny for this server")
-    .option("--ask-all", "Set defaultPolicy to ask for this server (reset to default)")
-    .option("--default <policy>", "Set server defaultPolicy: allow, deny, ask")
-    .option("--scope <scope>", "Config scope: user, project, local", "project")
-    .option("--clear", "Remove all permission rules for this server")
-    .action(async (server, options) => {
-    const scope = options.scope;
-    const projectRoot = findProjectRoot();
-    const filePath = getSettingsPath(scope, projectRoot);
-    const dir = dirname(filePath);
-    if (!existsSync(dir)) {
-        mkdirSync(dir, { recursive: true });
-    }
-    const settings = readOrCreateSettings(filePath);
-    // Ensure permissions structure exists
-    if (!settings["permissions"]) {
-        settings["permissions"] = {};
-    }
-    const permissions = settings["permissions"];
-    if (!permissions["mcpServers"]) {
-        permissions["mcpServers"] = {};
-    }
-    const mcpServers = permissions["mcpServers"];
-    if (options.clear) {
-        delete mcpServers[server];
-        writeFileSync(filePath, JSON.stringify(settings, null, 2) + "\n", "utf8");
-        console.log(`Cleared all permission rules for "${server}" in ${scope} scope`);
-        return;
-    }
-    // Build the permission entry
-    if (!mcpServers[server]) {
-        mcpServers[server] = {};
-    }
-    const serverPerms = mcpServers[server];
-    // Default policy
-    if (options.allowAll) {
-        serverPerms["defaultPolicy"] = "allow";
-    }
-    else if (options.denyAll) {
-        serverPerms["defaultPolicy"] = "deny";
-    }
-    else if (options.askAll) {
-        serverPerms["defaultPolicy"] = "ask";
-    }
-    else if (options.default) {
-        if (!["allow", "deny", "ask"].includes(options.default)) {
-            console.error("Error: --default must be allow, deny, or ask");
-            process.exit(1);
-        }
-        serverPerms["defaultPolicy"] = options.default;
-    }
-    // Allow patterns (append to existing)
-    if (options.allow) {
-        const existing = serverPerms["allow"] ?? [];
-        const newPatterns = options.allow.split(",").map((p) => p.trim());
-        serverPerms["allow"] = [...new Set([...existing, ...newPatterns])];
-    }
-    // Deny patterns (append to existing)
-    if (options.deny) {
-        const existing = serverPerms["deny"] ?? [];
-        const newPatterns = options.deny.split(",").map((p) => p.trim());
-        serverPerms["deny"] = [...new Set([...existing, ...newPatterns])];
-    }
-    writeFileSync(filePath, JSON.stringify(settings, null, 2) + "\n", "utf8");
-    // Print summary
-    const parts = [];
-    if (serverPerms["defaultPolicy"])
-        parts.push(`default: ${serverPerms["defaultPolicy"]}`);
-    if (serverPerms["allow"])
-        parts.push(`allow: ${serverPerms["allow"].join(", ")}`);
-    if (serverPerms["deny"])
-        parts.push(`deny: ${serverPerms["deny"].join(", ")}`);
-    console.log(`Updated permissions for "${server}" in ${scope} scope`);
-    if (parts.length > 0)
-        console.log(`  ${parts.join(" | ")}`);
-});
-//# sourceMappingURL=mcp.permit.js.map

package/dist/commands/mcp.permit.js.map

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package/dist/commands/mcp.remove.d.ts

@@ -1,9 +0,0 @@
-/**
- * `oxagen mcp remove <name>` — Remove an MCP server from file-based configuration.
- *
- * Removes the server entry from the specified scope. Managed servers cannot
- * be removed. Also deletes stored credentials unless --keep-credentials.
- */
-import { Command } from "commander";
-export declare const mcpRemoveCommand: Command;
-//# sourceMappingURL=mcp.remove.d.ts.map

package/dist/commands/mcp.remove.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"mcp.remove.d.ts","sourceRoot":"","sources":["../../src/commands/mcp.remove.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAqBpC,eAAO,MAAM,gBAAgB,SA8CzB,CAAC"}

package/dist/commands/mcp.remove.js

@@ -1,65 +0,0 @@
-/**
- * `oxagen mcp remove <name>` — Remove an MCP server from file-based configuration.
- *
- * Removes the server entry from the specified scope. Managed servers cannot
- * be removed. Also deletes stored credentials unless --keep-credentials.
- */
-import { Command } from "commander";
-import { readFileSync, writeFileSync, existsSync } from "node:fs";
-import { join } from "node:path";
-import { homedir } from "node:os";
-import { loadManagedConfig, isManagedServer } from "@oxagen/mcp-config/managed";
-import { deleteCredential } from "@oxagen/mcp-config/credentials";
-import { findProjectRoot } from "@oxagen/mcp-config/resolve";
-function getSettingsPath(scope, projectRoot) {
-    switch (scope) {
-        case "user":
-            return join(homedir(), ".config", "oxagen", "settings.json");
-        case "project":
-            return join(projectRoot, ".oxagen", "settings.json");
-        case "local":
-            return join(projectRoot, ".oxagen", "settings.local.json");
-    }
-}
-export const mcpRemoveCommand = new Command("remove")
-    .description("Remove an MCP server from file-based configuration")
-    .argument("<name>", "Server name to remove")
-    .option("--scope <scope>", "Config scope to remove from: user, project, local", "project")
-    .option("--keep-credentials", "Do not delete stored credentials for this server")
-    .action(async (name, options) => {
-    const scope = options.scope;
-    const projectRoot = findProjectRoot();
-    // Cannot remove managed servers
-    const managed = loadManagedConfig();
-    if (isManagedServer(name, managed)) {
-        console.error(`Error: "${name}" is a managed server provisioned by your organization and cannot be removed.`);
-        process.exit(1);
-    }
-    const filePath = getSettingsPath(scope, projectRoot);
-    if (!existsSync(filePath)) {
-        console.error(`Error: no settings file found at ${filePath}`);
-        process.exit(1);
-    }
-    let settings;
-    try {
-        settings = JSON.parse(readFileSync(filePath, "utf8"));
-    }
-    catch {
-        console.error(`Error: failed to parse ${filePath}`);
-        process.exit(1);
-    }
-    const mcpServers = (settings["mcpServers"] ?? {});
-    if (!(name in mcpServers)) {
-        console.error(`Error: server "${name}" not found in ${scope} scope (${filePath})`);
-        process.exit(1);
-    }
-    delete mcpServers[name];
-    settings["mcpServers"] = mcpServers;
-    writeFileSync(filePath, JSON.stringify(settings, null, 2) + "\n", "utf8");
-    // Clean up credentials unless --keep-credentials
-    if (!options.keepCredentials) {
-        deleteCredential(name);
-    }
-    console.log(`Removed MCP server "${name}" from ${scope} scope (${filePath})`);
-});
-//# sourceMappingURL=mcp.remove.js.map

package/dist/commands/mcp.remove.js.map

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package/dist/commands/mermaid.generate.d.ts

@@ -1,3 +0,0 @@
-import { Command } from "commander";
-export declare const mermaidGenerateCommand: Command;
-//# sourceMappingURL=mermaid.generate.d.ts.map

package/dist/commands/mermaid.generate.d.ts.map

@@ -1 +0,0 @@
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package/dist/commands/mermaid.generate.js

@@ -1,33 +0,0 @@
-import { Command } from "commander";
-import { apiRequest } from "../lib/api-client.js";
-import * as fs from "fs";
-export const mermaidGenerateCommand = new Command("generate")
-    .description("Generate a Mermaid diagram artifact")
-    .requiredOption("-d, --diagram <source>", "Mermaid diagram source text")
-    .requiredOption("-t, --title <title>", "Diagram title")
-    .option("--theme <theme>", "Mermaid theme: default | dark | neutral | forest (default: default)", "default")
-    .option("-o, --output <path>", "Write the diagram source to a file")
-    .action(async (options) => {
-    try {
-        const result = await apiRequest("/mermaid/generate", {
-            method: "POST",
-            body: JSON.stringify({
-                title: options.title,
-                diagram: options.diagram,
-                theme: options.theme,
-            }),
-        });
-        if (options.output) {
-            fs.writeFileSync(String(options.output), result.source);
-            console.log(`Diagram source written to ${options.output}`);
-        }
-        else {
-            console.log(JSON.stringify(result, null, 2));
-        }
-    }
-    catch (error) {
-        console.error("Failed to generate Mermaid diagram:", error);
-        process.exit(1);
-    }
-});
-//# sourceMappingURL=mermaid.generate.js.map

package/dist/commands/mermaid.generate.js.map

@@ -1 +0,0 @@
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package/dist/commands/notifications.list.d.ts

@@ -1,3 +0,0 @@
-import { Command } from "commander";
-export declare const notificationsListCommand: Command;
-//# sourceMappingURL=notifications.list.d.ts.map

package/dist/commands/notifications.list.d.ts.map

@@ -1 +0,0 @@
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package/dist/commands/notifications.list.js

@@ -1,33 +0,0 @@
-import { Command } from "commander";
-import { apiRequest, requireAuth, ApiError } from "../lib/api-client.js";
-export const notificationsListCommand = new Command("list")
-    .description("List notifications")
-    .option("--unread", "Show only unread notifications")
-    .option("--limit <n>", "Maximum results", "20")
-    .action(async (options) => {
-    requireAuth();
-    try {
-        const qs = new URLSearchParams();
-        if (options.unread)
-            qs.set("filter", "unread");
-        if (options.limit)
-            qs.set("limit", options.limit);
-        const data = await apiRequest(`/notifications?${qs}`);
-        const items = data.notifications ?? data.data ?? [];
-        if (items.length === 0) {
-            console.log("No notifications.");
-            return;
-        }
-        console.log("Notifications:");
-        for (const n of items) {
-            const status = n.readAt ? "  " : "• ";
-            console.log(`${status}${n.publicId ?? n.id ?? "unknown"}  ${n.title ?? n.type ?? "notification"}`);
-        }
-    }
-    catch (err) {
-        const _msg = err instanceof ApiError ? err.message : String(err);
-        console.error(`Error: ${_msg}`);
-        process.exit(1);
-    }
-});
-//# sourceMappingURL=notifications.list.js.map

package/dist/commands/notifications.list.js.map

@@ -1 +0,0 @@
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package/dist/commands/notifications.mark.d.ts

@@ -1,3 +0,0 @@
-import { Command } from "commander";
-export declare const notificationsMarkCommand: Command;
-//# sourceMappingURL=notifications.mark.d.ts.map

package/dist/commands/notifications.mark.d.ts.map

@@ -1 +0,0 @@
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package/dist/commands/notifications.mark.js

@@ -1,23 +0,0 @@
-import { Command } from "commander";
-import { apiRequest, requireAuth, ApiError } from "../lib/api-client.js";
-export const notificationsMarkCommand = new Command("mark")
-    .description("Mark a notification as read or unread")
-    .argument("<id>", "Notification public ID")
-    .option("--unread", "Mark as unread instead")
-    .action(async (id, options) => {
-    requireAuth();
-    try {
-        await apiRequest(`/notifications/${id}/mark`, {
-            method: "POST",
-            body: JSON.stringify({ read: !options.unread }),
-        });
-        const state = options.unread ? "unread" : "read";
-        console.log(`✓ Notification ${id} marked as ${state}`);
-    }
-    catch (err) {
-        const _msg = err instanceof ApiError ? err.message : String(err);
-        console.error(`Error: ${_msg}`);
-        process.exit(1);
-    }
-});
-//# sourceMappingURL=notifications.mark.js.map

package/dist/commands/notifications.mark.js.map

@@ -1 +0,0 @@
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package/dist/commands/ontology.neighbors.d.ts

@@ -1,3 +0,0 @@
-import { Command } from "commander";
-export declare const ontologyNeighborsCommand: Command;
-//# sourceMappingURL=ontology.neighbors.d.ts.map

package/dist/commands/ontology.neighbors.d.ts.map

@@ -1 +0,0 @@
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