Fix: core cli to work with core repo (#26)

* Fix: core cli to work with core repo

* Fix: cli working and mcp proxy

.env.example

@@ -12,7 +12,7 @@ POSTGRES_PASSWORD=docker
 POSTGRES_DB=core
 
 LOGIN_ORIGIN=http://localhost:3033
-DATABASE_URL="postgresql://${POSTGRES_USER}:${POSTGRES_PASSWORD}@postgres:5432/${POSTGRES_DB}?schema=core"
+DATABASE_URL=postgresql://${POSTGRES_USER}:${POSTGRES_PASSWORD}@postgres:5432/${POSTGRES_DB}?schema=core"
 
 # This sets the URL used for direct connections to the database and should only be needed in limited circumstances
 # See: https://www.prisma.io/docs/reference/api-reference/prisma-schema-reference#fields:~:text=the%20shadow%20database.-,directUrl,-No
@@ -22,6 +22,8 @@ REMIX_APP_PORT=3033
 APP_ENV=production
 NODE_ENV=${APP_ENV}
 APP_ORIGIN=http://localhost:3033
+API_BASE_URL=${APP_ORIGIN}
+
 
 SESSION_SECRET=27192e6432564f4788d55c15131bd5ac
 ENCRYPTION_KEY=27192e6432564f4788d55c15131bd5ac
@@ -48,8 +50,8 @@ MAGIC_LINK_SECRET=27192e6432564f4788d55c15131bd5ac
 NEO4J_AUTH=neo4j/27192e6432564f4788d55c15131bd5ac
 OLLAMA_URL=http://ollama:11434
 
-EMBEDDING_MODEL=GPT41
-MODEL=GPT41
+EMBEDDING_MODEL=text-embedding-3-small
+MODEL=gpt-4.1-2025-04-14
 
 ## Trigger ##
 TRIGGER_PROJECT_ID=

apps/webapp/app/components/logo/logo.tsx

@@ -1,14 +1,9 @@
-import React from "react";
-import { Theme, useTheme } from "remix-themes";
-
 export interface LogoProps {
   width: number;
   height: number;
 }
 
 export default function StaticLogo({ width, height }: LogoProps) {
-  const [theme] = useTheme();
-
   return (
     <svg
       width={width}

apps/webapp/app/components/logs/logs-filters.tsx

@@ -51,7 +51,7 @@ export function LogsFilters({
   const handleBack = () => setStep("main");
 
   return (
-    <div className="mb-4 flex items-center gap-2">
+    <div className="mb-4 flex w-full items-center justify-start gap-2">
       <Popover
         open={popoverOpen}
         onOpenChange={(open) => {

apps/webapp/app/components/logs/virtual-logs-list.tsx

@@ -153,7 +153,7 @@ export function VirtualLogsList({
   const itemCount = hasMore ? logs.length + 1 : logs.length;
 
   return (
-    <div className="h-[calc(100vh_-_132px)] overflow-hidden rounded-lg">
+    <div className="h-full grow overflow-hidden rounded-lg">
       <AutoSizer className="h-full">
         {({ width, height: autoHeight }) => (
           <InfiniteLoader

apps/webapp/app/entry.server.tsx

@@ -6,13 +6,21 @@
 
 import { PassThrough } from "node:stream";
 
-import { type AppLoadContext, type EntryContext , createReadableStreamFromReadable } from "@remix-run/node";
+import {
+  type AppLoadContext,
+  type EntryContext,
+  createReadableStreamFromReadable,
+} from "@remix-run/node";
 import { RemixServer } from "@remix-run/react";
 import { isbot } from "isbot";
 import { renderToPipeableStream } from "react-dom/server";
+import { initializeStartupServices } from "./utils/startup";
 
 const ABORT_DELAY = 5_000;
 
+// Initialize startup services once per server process
+await initializeStartupServices();
+
 export default function handleRequest(
   request: Request,
   responseStatusCode: number,
@@ -21,20 +29,20 @@ export default function handleRequest(
   // This is ignored so we can keep it in the template for visibility.  Feel
   // free to delete this parameter in your app if you're not using it!
   // eslint-disable-next-line @typescript-eslint/no-unused-vars
-  loadContext: AppLoadContext
+  loadContext: AppLoadContext,
 ) {
   return isbot(request.headers.get("user-agent") || "")
     ? handleBotRequest(
         request,
         responseStatusCode,
         responseHeaders,
-        remixContext
+        remixContext,
       )
     : handleBrowserRequest(
         request,
         responseStatusCode,
         responseHeaders,
-        remixContext
+        remixContext,
       );
 }
 
@@ -42,7 +50,7 @@ function handleBotRequest(
   request: Request,
   responseStatusCode: number,
   responseHeaders: Headers,
-  remixContext: EntryContext
+  remixContext: EntryContext,
 ) {
   return new Promise((resolve, reject) => {
     let shellRendered = false;
@@ -64,7 +72,7 @@ function handleBotRequest(
             new Response(stream, {
               headers: responseHeaders,
               status: responseStatusCode,
-            })
+            }),
           );
 
           pipe(body);
@@ -81,7 +89,7 @@ function handleBotRequest(
             console.error(error);
           }
         },
-      }
+      },
     );
 
     setTimeout(abort, ABORT_DELAY);
@@ -92,7 +100,7 @@ function handleBrowserRequest(
   request: Request,
   responseStatusCode: number,
   responseHeaders: Headers,
-  remixContext: EntryContext
+  remixContext: EntryContext,
 ) {
   return new Promise((resolve, reject) => {
     let shellRendered = false;
@@ -114,7 +122,7 @@ function handleBrowserRequest(
             new Response(stream, {
               headers: responseHeaders,
               status: responseStatusCode,
-            })
+            }),
           );
 
           pipe(body);
@@ -131,7 +139,7 @@ function handleBrowserRequest(
             console.error(error);
           }
         },
-      }
+      },
     );
 
     setTimeout(abort, ABORT_DELAY);

apps/webapp/app/root.tsx

@@ -4,7 +4,6 @@ import {
   Outlet,
   Scripts,
   ScrollRestoration,
-  useLoaderData,
 } from "@remix-run/react";
 import type {
   LinksFunction,
@@ -41,7 +40,6 @@ import {
   useTheme,
 } from "remix-themes";
 import clsx from "clsx";
-import { initNeo4jSchemaOnce } from "./lib/neo4j.server";
 
 export const links: LinksFunction = () => [{ rel: "stylesheet", href: styles }];
 
@@ -50,8 +48,6 @@ export const loader = async ({ request }: LoaderFunctionArgs) => {
   const toastMessage = session.get("toastMessage") as ToastMessage;
   const { getTheme } = await themeSessionResolver(request);
 
-  await initNeo4jSchemaOnce();
-
   const posthogProjectKey = env.POSTHOG_PROJECT_KEY;
 
   return typedjson(
@@ -138,7 +134,6 @@ function App() {
 // `specifiedTheme` is the stored theme in the session storage.
 // `themeAction` is the action name that's used to change the theme in the session storage.
 export default function AppWithProviders() {
-  const data = useLoaderData<typeof loader>();
   return (
     <ThemeProvider specifiedTheme={Theme.LIGHT} themeAction="/action/set-theme">
       <App />

apps/webapp/app/routes/api.v1.mcp.$slug.tsx

@@ -4,6 +4,9 @@ import { getIntegrationDefinitionWithSlug } from "~/services/integrationDefiniti
 import { proxyRequest } from "~/utils/proxy.server";
 import { z } from "zod";
 import { getIntegrationAccount } from "~/services/integrationAccount.server";
+import { createMCPStdioProxy } from "@core/mcp-proxy";
+import { randomUUID } from "node:crypto";
+import { configureStdioMCPEnvironment } from "~/trigger/utils/mcp";
 
 export const integrationSlugSchema = z.object({
   slug: z.string(),
@@ -48,7 +51,7 @@ const { action, loader } = createActionApiRoute(
 
       const spec = integrationDefinition.spec as any;
 
-      if (!spec.mcpAuth) {
+      if (!spec.mcp) {
         return new Response(
           JSON.stringify({
             error: "MCP auth configuration not found for this integration",
@@ -60,7 +63,7 @@ const { action, loader } = createActionApiRoute(
         );
       }
 
-      const { serverUrl } = spec.mcpAuth;
+      const { url, type } = spec.mcp;
 
       // Find the integration account for this user and integration
       const integrationAccount = await getIntegrationAccount(
@@ -68,29 +71,66 @@ const { action, loader } = createActionApiRoute(
         authentication.userId,
       );
 
-      const integrationConfig =
-        integrationAccount?.integrationConfiguration as any;
+      if (type === "http") {
+        const integrationConfig =
+          integrationAccount?.integrationConfiguration as any;
 
-      if (!integrationAccount || !integrationConfig || !integrationConfig.mcp) {
-        return new Response(
-          JSON.stringify({
-            error: "No integration account with mcp config",
-          }),
-          {
-            status: 400,
-            headers: { "Content-Type": "application/json" },
-          },
+        if (
+          !integrationAccount ||
+          !integrationConfig ||
+          !integrationConfig.mcp
+        ) {
+          return new Response(
+            JSON.stringify({
+              error: "No integration account with mcp config",
+            }),
+            {
+              status: 400,
+              headers: { "Content-Type": "application/json" },
+            },
+          );
+        }
+
+        // Proxy the request to the serverUrl
+        return await proxyRequest(
+          request,
+          url,
+          integrationConfig.mcp.tokens.access_token,
         );
-      }
+      } else {
+        if (!integrationAccount) {
+          return new Response(
+            JSON.stringify({
+              error: "No integration account found",
+            }),
+            {
+              status: 400,
+              headers: { "Content-Type": "application/json" },
+            },
+          );
+        }
 
-      // Proxy the request to the serverUrl
-      return await proxyRequest(
-        request,
-        serverUrl,
-        integrationConfig.mcp.tokens.access_token,
-      );
+        // Configure environment variables using the utility function
+        const { env, args } = configureStdioMCPEnvironment(
+          spec,
+          integrationAccount,
+        );
+
+        // Get session_id from headers (case-insensitive), or generate a new uuid if not present
+        const sessionId =
+          request.headers.get("mcp-session-id") ||
+          request.headers.get("Mcp-Session-Id") ||
+          randomUUID();
+
+        // Use the saved local file instead of command
+        const executablePath = `./integrations/${slug}/main`;
+
+        return createMCPStdioProxy(request, executablePath, args, {
+          env,
+          sessionId,
+        });
+      }
     } catch (error: any) {
-      console.error("MCP Proxy Error:", error);
       return new Response(JSON.stringify({ error: error.message }), {
         status: 500,
         headers: { "Content-Type": "application/json" },

apps/webapp/app/routes/api.v1.oauth.callback.mcp.tsx

@@ -53,14 +53,14 @@ export async function loader({ request }: LoaderFunctionArgs) {
 
     const spec = integrationDefinition.spec as any;
 
-    if (!spec.mcpAuth) {
+    if (!spec.mcp) {
       throw new Error("MCP auth configuration not found for this integration");
     }
 
-    const { transportStrategy, serverUrl } = spec.mcpAuth;
+    const { transportStrategy, url } = spec.mcp;
 
     const authClient = createMCPAuthClient({
-      serverUrl,
+      serverUrl: url,
       transportStrategy: transportStrategy || "sse-first",
       redirectUrl: MCP_CALLBACK_URL,
     });

apps/webapp/app/routes/home.integration.$slug.tsx

@@ -137,7 +137,9 @@ export default function IntegrationDetail() {
   );
   const hasApiKey = !!specData?.auth?.api_key;
   const hasOAuth2 = !!specData?.auth?.OAuth2;
-  const hasMCPAuth = !!specData?.mcpAuth;
+  const hasMCPAuth = !!(
+    specData?.mcp.type === "url" && specData?.mcp.needsAuth
+  );
   const Component = getIcon(integration.icon as IconType);
 
   return (

apps/webapp/app/routes/home.logs.activity.tsx

@@ -75,9 +75,9 @@ export default function LogsActivity() {
             )}
 
             {/* Logs List */}
-            <div className="space-y-4">
+            <div className="flex h-full w-full space-y-4">
               {logs.length === 0 ? (
-                <Card>
+                <Card className="bg-background-2 w-full">
                   <CardContent className="bg-background-2 flex items-center justify-center py-16">
                     <div className="text-center">
                       <Activity className="text-muted-foreground mx-auto mb-4 h-12 w-12" />

apps/webapp/app/routes/home.logs.all.tsx

@@ -45,7 +45,7 @@ export default function LogsAll() {
           },
         ]}
       />
-      <div className="flex h-[calc(100vh_-_56px)] flex-col items-center space-y-6 p-4 px-5">
+      <div className="flex h-[calc(100vh_-_56px)] w-full flex-col items-center space-y-6 p-4 px-5">
         {isInitialLoad ? (
           <>
             <LoaderCircle className="text-primary h-4 w-4 animate-spin" />{" "}
@@ -64,10 +64,10 @@ export default function LogsAll() {
               />
             )}
             {/* Logs List */}
-            <div className="space-y-4">
+            <div className="flex h-full w-full space-y-4">
               {logs.length === 0 ? (
-                <Card>
-                  <CardContent className="bg-background-2 flex items-center justify-center py-16">
+                <Card className="bg-background-2 w-full">
+                  <CardContent className="bg-background-2 flex w-full items-center justify-center py-16">
                     <div className="text-center">
                       <Database className="text-muted-foreground mx-auto mb-4 h-12 w-12" />
                       <h3 className="mb-2 text-lg font-semibold">

apps/webapp/app/routes/login.magic.tsx

@@ -158,7 +158,8 @@ export default function LoginMagicLinkPage() {
 
               <Fieldset className="flex w-full flex-col items-center gap-y-2 px-2">
                 <FormButtons
-                  cancelButton={
+                  cancelButton={<></>}
+                  confirmButton={
                     <Button
                       type="submit"
                       name="action"
@@ -169,7 +170,6 @@ export default function LoginMagicLinkPage() {
                       Re-enter email
                     </Button>
                   }
-                  confirmButton={<></>}
                 />
               </Fieldset>
             </Card>

apps/webapp/app/routes/oauth.authorize.tsx

@@ -199,13 +199,13 @@ export default function OAuthAuthorize() {
 
             <p className="text-muted-foreground mb-2 text-sm">Permissions</p>
             <ul className="text-muted-foreground text-sm">
-              {params.scope?.split(",").map((scope, index, arr) => {
+              {params.scope?.split(" ").map((scope, index, arr) => {
                 const isFirst = index === 0;
                 const isLast = index === arr.length - 1;
                 return (
                   <li
                     key={index}
-                    className={`border-border flex items-center gap-2 border-x border-t p-2 ${isLast ? "border-b" : ""} ${isFirst ? "rounded-tl-md rounded-tr-md" : ""} ${isLast ? "rounded-br-md rounded-bl-md" : ""} `}
+                    className={`flex items-center gap-2 border-x border-t border-gray-300 p-2 ${isLast ? "border-b" : ""} ${isFirst ? "rounded-tl-md rounded-tr-md" : ""} ${isLast ? "rounded-br-md rounded-bl-md" : ""} `}
                   >
                     <div>{getIcon(scope)}</div>
                     <div>

apps/webapp/app/services/integrationAccount.server.ts

@@ -10,6 +10,9 @@ export const getIntegrationAccount = async (
       integratedById: userId,
       isActive: true,
     },
+    include: {
+      integrationDefinition: true,
+    },
   });
 };
 

apps/webapp/app/services/oauth/oauth.server.ts

@@ -278,14 +278,14 @@ export async function getRedirectURLForMCP(
 
   const spec = integrationDefinition.spec as any;
 
-  if (!spec.mcpAuth) {
+  if (!spec.mcp) {
     throw new Error("MCP auth configuration not found for this integration");
   }
 
-  const { serverUrl, transportStrategy } = spec.mcpAuth;
+  const { url, transportStrategy } = spec.mcp;
 
   const authClient = createMCPAuthClient({
-    serverUrl,
+    serverUrl: url,
     transportStrategy: transportStrategy || "sse-first",
     redirectUrl: MCP_CALLBACK_URL,
   });

apps/webapp/app/trigger/utils/mcp.ts

@@ -1,9 +1,69 @@
 /* eslint-disable @typescript-eslint/no-explicit-any */
 import { logger } from "@trigger.dev/sdk/v3";
 import { jsonSchema, tool, type ToolSet } from "ai";
+import * as fs from "fs";
+import * as path from "path";
 
 import { type MCPTool } from "./types";
 import { StreamableHTTPClientTransport } from "@modelcontextprotocol/sdk/client/streamableHttp.js";
+import { prisma } from "~/db.server";
+
+export const configureStdioMCPEnvironment = (
+  spec: any,
+  account: any,
+): { env: Record<string, string>; args: any[] } => {
+  if (!spec.mcp) {
+    return { env: {}, args: [] };
+  }
+
+  const mcpSpec = spec.mcp;
+  const configuredMCP = { ...mcpSpec };
+
+  // Replace config placeholders in environment variables
+  if (configuredMCP.env) {
+    for (const [key, value] of Object.entries(configuredMCP.env)) {
+      if (typeof value === "string" && value.includes("${config:")) {
+        // Extract the config key from the placeholder
+        const configKey = value.match(/\$\{config:(.*?)\}/)?.[1];
+        if (
+          configKey &&
+          account.integrationConfiguration &&
+          // eslint-disable-next-line @typescript-eslint/no-explicit-any
+          (account.integrationConfiguration as any)[configKey]
+        ) {
+          configuredMCP.env[key] = value.replace(
+            `\${config:${configKey}}`,
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            (account.integrationConfiguration as any)[configKey],
+          );
+        }
+      }
+
+      if (typeof value === "string" && value.includes("${integrationConfig:")) {
+        // Extract the config key from the placeholder
+        const configKey = value.match(/\$\{integrationConfig:(.*?)\}/)?.[1];
+        if (
+          configKey &&
+          account.integrationDefinition.config &&
+          // eslint-disable-next-line @typescript-eslint/no-explicit-any
+          (account.integrationDefinition.config as any)[configKey]
+        ) {
+          configuredMCP.env[key] = value.replace(
+            `\${integrationConfig:${configKey}}`,
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            (account.integrationDefinition.config as any)[configKey],
+          );
+        }
+      }
+    }
+  }
+
+  return {
+    env: configuredMCP.env || {},
+    args: Array.isArray(configuredMCP.args) ? configuredMCP.args : [],
+  };
+};
+
 export class MCP {
   private Client: any;
   private clients: Record<string, any> = {};
@@ -133,3 +193,135 @@ export class MCP {
     }
   }
 }
+
+export const getIntegrationStdioFile = async (
+  integrationDefinitionSlug: string,
+) => {
+  // If the file is in public/integrations/[slug]/main, it is served at /integrations/[slug]/main
+  return `/integrations/${integrationDefinitionSlug}/main`;
+};
+
+export const fetchAndSaveStdioIntegrations = async () => {
+  try {
+    logger.info("Starting stdio integrations fetch and save process");
+
+    // Get all integration definitions
+    const integrationDefinitions =
+      await prisma.integrationDefinitionV2.findMany({
+        where: {
+          deleted: null, // Only active integrations
+        },
+      });
+
+    logger.info(
+      `Found ${integrationDefinitions.length} integration definitions`,
+    );
+
+    for (const integration of integrationDefinitions) {
+      try {
+        const spec = integration.spec as any;
+
+        // Check if this integration has MCP config and is stdio type
+        if (spec?.mcp?.type === "stdio" && spec?.mcp?.url) {
+          logger.info(`Processing stdio integration: ${integration.slug}`);
+
+          const integrationDir = path.join(
+            process.cwd(),
+            "integrations",
+            integration.slug,
+          );
+          const targetFile = path.join(integrationDir, "main");
+
+          // Create directory if it doesn't exist
+          if (!fs.existsSync(integrationDir)) {
+            fs.mkdirSync(integrationDir, { recursive: true });
+            logger.info(`Created directory: ${integrationDir}`);
+          }
+
+          // Skip if file already exists
+          if (fs.existsSync(targetFile)) {
+            logger.info(
+              `Integration ${integration.slug} already exists, skipping`,
+            );
+            continue;
+          }
+
+          const urlOrPath = spec.mcp.url;
+
+          // If urlOrPath looks like a URL, use fetch, otherwise treat as local path
+          let isUrl = false;
+          try {
+            // Try to parse as URL
+            const parsed = new URL(urlOrPath);
+            isUrl = ["http:", "https:"].includes(parsed.protocol);
+          } catch {
+            isUrl = false;
+          }
+
+          if (isUrl) {
+            // Fetch the URL content
+            logger.info(`Fetching content from URL: ${urlOrPath}`);
+            const response = await fetch(urlOrPath);
+
+            if (!response.ok) {
+              logger.error(
+                `Failed to fetch ${urlOrPath}: ${response.status} ${response.statusText}`,
+              );
+              continue;
+            }
+
+            const content = await response.text();
+
+            // Save the content to the target file
+            fs.writeFileSync(targetFile, content);
+
+            // Make the file executable if it's a script
+            if (process.platform !== "win32") {
+              fs.chmodSync(targetFile, "755");
+            }
+
+            logger.info(
+              `Successfully saved stdio integration: ${integration.slug} to ${targetFile}`,
+            );
+          } else {
+            // Treat as local file path
+            const sourcePath = path.isAbsolute(urlOrPath)
+              ? urlOrPath
+              : path.join(process.cwd(), urlOrPath);
+
+            logger.info(`Copying content from local path: ${sourcePath}`);
+
+            if (!fs.existsSync(sourcePath)) {
+              logger.error(`Source file does not exist: ${sourcePath}`);
+              continue;
+            }
+
+            fs.copyFileSync(sourcePath, targetFile);
+
+            // Make the file executable if it's a script
+            if (process.platform !== "win32") {
+              fs.chmodSync(targetFile, "755");
+            }
+
+            logger.info(
+              `Successfully copied stdio integration: ${integration.slug} to ${targetFile}`,
+            );
+          }
+        } else {
+          logger.debug(
+            `Skipping integration ${integration.slug}: not a stdio type or missing URL`,
+          );
+        }
+      } catch (error) {
+        logger.error(`Error processing integration ${integration.slug}:`, {
+          error,
+        });
+      }
+    }
+
+    logger.info("Completed stdio integrations fetch and save process");
+  } catch (error) {
+    logger.error("Failed to fetch and save stdio integrations:", { error });
+    throw error;
+  }
+};

apps/webapp/app/utils/oauth2-middleware.ts

@@ -24,11 +24,14 @@ export interface OAuth2Context {
 
 export async function requireOAuth2(request: Request): Promise<OAuth2Context> {
   const authHeader = request.headers.get("authorization");
-  
+
   if (!authHeader || !authHeader.startsWith("Bearer ")) {
     throw json(
-      { error: "invalid_token", error_description: "Missing or invalid authorization header" },
-      { status: 401 }
+      {
+        error: "invalid_token",
+        error_description: "Missing or invalid authorization header",
+      },
+      { status: 401 },
     );
   }
 
@@ -36,7 +39,7 @@ export async function requireOAuth2(request: Request): Promise<OAuth2Context> {
 
   try {
     const accessToken = await oauth2Service.validateAccessToken(token);
-    
+
     return {
       user: {
         id: accessToken.user.id,
@@ -59,13 +62,18 @@ export async function requireOAuth2(request: Request): Promise<OAuth2Context> {
     };
   } catch (error) {
     throw json(
-      { error: "invalid_token", error_description: "Invalid or expired access token" },
-      { status: 401 }
+      {
+        error: "invalid_token",
+        error_description: "Invalid or expired access token",
+      },
+      { status: 401 },
     );
   }
 }
 
-export async function getOAuth2Context(request: Request): Promise<OAuth2Context | null> {
+export async function getOAuth2Context(
+  request: Request,
+): Promise<OAuth2Context | null> {
   try {
     return await requireOAuth2(request);
   } catch (error) {
@@ -73,20 +81,31 @@ export async function getOAuth2Context(request: Request): Promise<OAuth2Context
   }
 }
 
-export function hasScope(context: OAuth2Context, requiredScope: string): boolean {
+export function hasScope(
+  context: OAuth2Context,
+  requiredScope: string,
+): boolean {
   if (!context.token.scope) {
     return false;
   }
-  
-  const scopes = context.token.scope.split(' ');
+
+  const scopes = context.token.scope.split(" ");
   return scopes.includes(requiredScope);
 }
 
-export function requireScope(context: OAuth2Context, requiredScope: string): void {
+export function requireScope(
+  context: OAuth2Context,
+  requiredScope: string,
+): void {
   if (!hasScope(context, requiredScope)) {
     throw json(
-      { error: "insufficient_scope", error_description: `Required scope: ${requiredScope}` },
-      { status: 403 }
+      {
+        error: "insufficient_scope",
+        error_description: `Required scope: ${requiredScope}`,
+      },
+      { status: 403 },
     );
   }
-}
+}
+
+export function getEnvForCommand() {}

apps/webapp/app/utils/startup.ts

@@ -0,0 +1,34 @@
+import { logger } from "~/services/logger.service";
+import { fetchAndSaveStdioIntegrations } from "~/trigger/utils/mcp";
+import { initNeo4jSchemaOnce } from "~/lib/neo4j.server";
+
+// Global flag to ensure startup only runs once per server process
+let startupInitialized = false;
+
+/**
+ * Initialize all startup services once per server process
+ * Safe to call multiple times - will only run initialization once
+ */
+export async function initializeStartupServices() {
+  if (startupInitialized) {
+    return;
+  }
+
+  try {
+    logger.info("Starting application initialization...");
+
+    // Initialize Neo4j schema
+    await initNeo4jSchemaOnce();
+    logger.info("Neo4j schema initialization completed");
+
+    await fetchAndSaveStdioIntegrations();
+    logger.info("Stdio integrations initialization completed");
+
+    startupInitialized = true;
+    logger.info("Application initialization completed successfully");
+  } catch (error) {
+    logger.error("Failed to initialize startup services:", { error });
+    // Don't mark as initialized if there was an error, allow retry
+    throw error;
+  }
+}

apps/webapp/package.json

@@ -10,8 +10,8 @@
     "lint:fix": "eslint --fix --ignore-path .gitignore --cache --cache-location ./node_modules/.cache/eslint .",
     "start": "remix-serve ./build/server/index.js",
     "typecheck": "tsc",
-    "trigger:dev": "pnpm dlx trigger.dev@v4-beta dev",
-    "trigger:deploy": "pnpm dlx trigger.dev@v4-beta deploy"
+    "trigger:dev": "pnpm dlx trigger.dev@4.0.0-v4-beta.22 dev",
+    "trigger:deploy": "pnpm dlx trigger.dev@4.0.0-v4-beta.22 deploy"
   },
   "dependencies": {
     "@ai-sdk/anthropic": "^1.2.12",

apps/webapp/server.mjs

@@ -47,6 +47,7 @@ async function init() {
   // handle SSR requests
   app.all("*", remixHandler);
 
+
   const port = process.env.REMIX_APP_PORT || 3000;
   app.listen(port, () =>
     console.log(`Express server listening at http://localhost:${port}`),

apps/webapp/trigger.config.ts

@@ -27,8 +27,16 @@ export default defineConfig({
   build: {
     extensions: [
       syncEnvVars(() => ({
-        DATABASE_URL: process.env.DATABASE_URL as string,
+        ANTHROPIC_API_KEY: process.env.ANTHROPIC_API_KEY as string,
         API_BASE_URL: process.env.API_BASE_URL as string,
+        DATABASE_URL: process.env.DATABASE_URL as string,
+        EMBEDDING_MODEL: process.env.EMBEDDING_MODEL as string,
+        ENCRYPTION_KEY: process.env.ENCRYPTION_KEY as string,
+        MODEL: process.env.MODEL ?? "gpt-4.1-2025-04-14",
+        NEO4J_PASSWORD: process.env.NEO4J_PASSWORD as string,
+        NEO4J_URI: process.env.NEO4J_URI as string,
+        NEO4J_USERNAME: process.env.NEO4J_USERNAME as string,
+        OPENAI_API_KEY: process.env.OPENAI_API_KEY as string,
       })),
       prismaExtension({
         schema: "prisma/schema.prisma",

apps/webapp/tsconfig.json

@@ -7,7 +7,8 @@
     "**/*.tsx",
     "tailwind.config.js",
     "tailwind.config.js",
-    "trigger.config.ts"
+    "trigger.config.ts",
+    "server.mjs"
   ],
   "compilerOptions": {
     "types": ["@remix-run/node", "vite/client"],

docker-compose.yaml

@@ -40,7 +40,7 @@ services:
 
   postgres:
     container_name: core-postgres
-    image: redplanethq/postgres:0.1.0
+    image: redplanethq/postgres:0.1.2
     environment:
       - POSTGRES_USER=${POSTGRES_USER}
       - POSTGRES_PASSWORD=${POSTGRES_PASSWORD}

integrations/linear/spec.json

@@ -12,9 +12,9 @@
       "label": "Linear API Key"
     }
   },
-  "mcpAuth": {
-    "serverUrl": "https://mcp.linear.app/sse",
-    "transportStrategy": "sse-first",
-    "needsSeparateAuth": true
+  "mcp": {
+    "type": "http",
+    "url": "https://mcp.linear.app/mcp",
+    "needsAuth": true
   }
 }

integrations/slack/spec.json

@@ -4,12 +4,11 @@
   "description": "Connect your workspace to Slack. Run your workflows from slack bookmarks",
   "icon": "slack",
   "mcp": {
-    "command": "npx",
-    "args": ["-y", "@modelcontextprotocol/server-slack"],
+    "type": "stdio",
+    "url": "",
+    "args": [ ],
     "env": {
-      "SLACK_BOT_TOKEN": "${config:access_token}",
-      "SLACK_TEAM_ID": "${config:team_id}",
-      "SLACK_CHANNEL_IDS": "${config:channel_ids}"
+      "SLACK_MCP_XOXP_TOKEN": "${config:access_token}"
     }
   },
   "auth": {

packages/core-cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@redplanethq/core",
-  "version": "0.1.1",
+  "version": "0.1.3",
   "description": "A Command-Line Interface for Core",
   "type": "module",
   "license": "MIT",
@@ -89,6 +89,7 @@
     "commander": "^9.4.1",
     "defu": "^6.1.4",
     "dotenv": "^16.4.5",
+    "dotenv-expand": "^12.0.2",
     "esbuild": "^0.23.0",
     "eventsource": "^3.0.2",
     "evt": "^2.4.13",

packages/core-cli/src/commands/init.ts

@@ -1,10 +1,13 @@
 import { intro, outro, text, confirm, spinner, note, log } from "@clack/prompts";
 import { fileExists, updateEnvFile } from "../utils/file.js";
 import { checkPostgresHealth } from "../utils/docker.js";
-import { executeDockerCommandInteractive } from "../utils/docker-interactive.js";
+import { executeCommandInteractive } from "../utils/docker-interactive.js";
 import { printCoreBrainLogo } from "../utils/ascii.js";
 import { setupEnvFile } from "../utils/env.js";
 import { hasTriggerConfig } from "../utils/env-checker.js";
+import { getDockerCompatibleEnvVars } from "../utils/env-docker.js";
+import { handleDockerLogin } from "../utils/docker-login.js";
+import { deployTriggerTasks } from "../utils/trigger-deploy.js";
 import path from "path";
 
 export async function initCommand() {
@@ -14,20 +17,29 @@ export async function initCommand() {
   intro("🚀 Core Development Environment Setup");
 
   // Step 1: Confirm this is the Core repository
-  note("Please ensure you have:\n• Docker and Docker Compose installed\n• Git installed\n• pnpm package manager installed\n• You are in the Core repository directory", "📋 Prerequisites");
-  
+  note(
+    "Please ensure you have:\n• Docker and Docker Compose installed\n• Git installed\n• pnpm package manager installed\n• You are in the Core repository directory",
+    "📋 Prerequisites"
+  );
+
   const isCoreRepo = await confirm({
     message: "Are you currently in the Core repository directory?",
   });
 
   if (!isCoreRepo) {
-    note("Please clone the Core repository first:\n\ngit clone https://github.com/redplanethq/core.git\ncd core\n\nThen run 'core init' again.", "📥 Clone Repository");
+    note(
+      "Please clone the Core repository first:\n\ngit clone https://github.com/redplanethq/core.git\ncd core\n\nThen run 'core init' again.",
+      "📥 Clone Repository"
+    );
     outro("❌ Setup cancelled. Please navigate to the Core repository first.");
     process.exit(1);
   }
 
   const rootDir = process.cwd();
   const triggerDir = path.join(rootDir, "trigger");
+  const webappDir = path.join(rootDir, "apps", "webapp");
+  const databaseDir = path.join(rootDir, "packages", "database");
+  const typesDir = path.join(rootDir, "packages", "types");
 
   try {
     // Step 2: Setup .env file in root
@@ -51,7 +63,7 @@ export async function initCommand() {
 
     // Step 3: Docker compose up -d in root
     try {
-      await executeDockerCommandInteractive("docker compose up -d", {
+      await executeCommandInteractive("docker compose up -d", {
         cwd: rootDir,
         message: "Starting Docker containers in root...",
         showOutput: true,
@@ -103,7 +115,7 @@ export async function initCommand() {
 
     // Step 6: Docker compose up for trigger
     try {
-      await executeDockerCommandInteractive("docker compose up -d", {
+      await executeCommandInteractive("docker compose up -d", {
         cwd: triggerDir,
         message: "Starting Trigger.dev containers...",
         showOutput: true,
@@ -175,6 +187,16 @@ export async function initCommand() {
         },
       });
 
+      const openaiApiKey = await text({
+        message: "Enter your OpenAI API Key:",
+        validate: (value) => {
+          if (!value || value.length === 0) {
+            return "OpenAI API Key is required";
+          }
+          return;
+        },
+      });
+
       // Step 11: Update .env with project details
       const s6 = spinner();
       s6.start("Updating .env with Trigger.dev configuration...");
@@ -182,6 +204,7 @@ export async function initCommand() {
       try {
         await updateEnvFile(envPath, "TRIGGER_PROJECT_ID", projectId as string);
         await updateEnvFile(envPath, "TRIGGER_SECRET_KEY", secretKey as string);
+        await updateEnvFile(envPath, "OPENAI_API_KEY", openaiApiKey as string);
         s6.stop("✅ Updated .env with Trigger.dev configuration");
       } catch (error: any) {
         s6.stop("❌ Failed to update .env file");
@@ -190,13 +213,13 @@ export async function initCommand() {
 
       // Step 12: Restart root docker-compose with new configuration
       try {
-        await executeDockerCommandInteractive("docker compose down", {
+        await executeCommandInteractive("docker compose down", {
           cwd: rootDir,
           message: "Stopping Core services...",
           showOutput: true,
         });
 
-        await executeDockerCommandInteractive("docker compose up -d", {
+        await executeCommandInteractive("docker compose up -d", {
           cwd: rootDir,
           message: "Starting Core services with new Trigger.dev configuration...",
           showOutput: true,
@@ -206,73 +229,12 @@ export async function initCommand() {
       }
     }
 
-    // Step 13: Show docker login instructions
+    // Step 13: Handle Docker login
     note("Run the following command to login to Docker registry:", "🐳 Docker Registry Login");
-
-    try {
-      // Read env file to get docker registry details
-      const envContent = await import("fs").then((fs) =>
-        fs.promises.readFile(triggerEnvPath, "utf8")
-      );
-      const envLines = envContent.split("\n");
-
-      const getEnvValue = (key: string) => {
-        const line = envLines.find((l) => l.startsWith(`${key}=`));
-        return line ? line.split("=")[1] : "";
-      };
-
-      const dockerRegistryUrl = getEnvValue("DOCKER_REGISTRY_URL");
-      const dockerRegistryUsername = getEnvValue("DOCKER_REGISTRY_USERNAME");
-      const dockerRegistryPassword = getEnvValue("DOCKER_REGISTRY_PASSWORD");
-
-      log.info(
-        `docker login ${dockerRegistryUrl} -u ${dockerRegistryUsername} -p ${dockerRegistryPassword}`
-      );
-    } catch (error) {
-      log.info("docker login <REGISTRY_URL> -u <USERNAME> -p <PASSWORD>");
-    }
-
-    const dockerLoginConfirmed = await confirm({
-      message: "Have you completed the Docker login successfully?",
-    });
-
-    if (!dockerLoginConfirmed) {
-      outro("❌ Setup cancelled. Please complete Docker login first and run the command again.");
-      process.exit(1);
-    }
+    await handleDockerLogin(triggerEnvPath);
 
     // Step 14: Deploy Trigger.dev tasks
-    note(
-      "We'll now deploy the trigger tasks to your Trigger.dev instance.",
-      "🚀 Deploying Trigger.dev tasks"
-    );
-
-    try {
-      // Login to trigger.dev CLI
-      await executeDockerCommandInteractive(
-        "npx -y trigger.dev@v4-beta login -a http://localhost:8030",
-        {
-          cwd: rootDir,
-          message: "Logging in to Trigger.dev CLI...",
-          showOutput: true,
-        }
-      );
-
-      // Deploy trigger tasks
-      await executeDockerCommandInteractive("pnpm trigger:deploy", {
-        cwd: rootDir,
-        message: "Deploying Trigger.dev tasks...",
-        showOutput: true,
-      });
-
-      log.success("Trigger.dev tasks deployed successfully!");
-    } catch (error: any) {
-      log.warning("Failed to deploy Trigger.dev tasks:");
-      note(
-        `${error.message}\n\nYou can deploy them manually later with:\n1. npx trigger.dev@v4-beta login -a http://localhost:8030\n2. pnpm trigger:deploy`,
-        "Manual Deployment"
-      );
-    }
+    await deployTriggerTasks(rootDir);
 
     // Step 15: Final instructions
     outro("🎉 Setup Complete!");

packages/core-cli/src/commands/start.ts

@@ -1,50 +1,55 @@
-import { intro, outro, note, log, confirm } from '@clack/prompts';
-import { executeDockerCommandInteractive } from '../utils/docker-interactive.js';
-import { printCoreBrainLogo } from '../utils/ascii.js';
-import path from 'path';
+import { intro, outro, note, log, confirm } from "@clack/prompts";
+import { executeCommandInteractive } from "../utils/docker-interactive.js";
+import { printCoreBrainLogo } from "../utils/ascii.js";
+import path from "path";
 
 export async function startCommand() {
   // Display the CORE brain logo
   printCoreBrainLogo();
-  
-  intro('🚀 Starting Core Development Environment');
+
+  intro("🚀 Starting Core Development Environment");
 
   // Step 1: Confirm this is the Core repository
   const isCoreRepo = await confirm({
-    message: 'Are you currently in the Core repository directory?',
+    message: "Are you currently in the Core repository directory?",
   });
 
   if (!isCoreRepo) {
-    note('Please navigate to the Core repository first:\n\ngit clone https://github.com/redplanethq/core.git\ncd core\n\nThen run "core start" again.', '📥 Core Repository Required');
-    outro('❌ Please navigate to the Core repository first.');
+    note(
+      'Please navigate to the Core repository first:\n\ngit clone https://github.com/redplanethq/core.git\ncd core\n\nThen run "core start" again.',
+      "📥 Core Repository Required"
+    );
+    outro("❌ Please navigate to the Core repository first.");
     process.exit(1);
   }
 
   const rootDir = process.cwd();
-  const triggerDir = path.join(rootDir, 'trigger');
+  const triggerDir = path.join(rootDir, "trigger");
 
   try {
     // Start main services
-    await executeDockerCommandInteractive('docker compose up -d', {
+    await executeCommandInteractive("docker compose up -d", {
       cwd: rootDir,
-      message: 'Starting Core services...',
-      showOutput: true
+      message: "Starting Core services...",
+      showOutput: true,
     });
 
     // Start trigger services
-    await executeDockerCommandInteractive('docker compose up -d', {
+    await executeCommandInteractive("docker compose up -d", {
       cwd: triggerDir,
-      message: 'Starting Trigger.dev services...',
-      showOutput: true
+      message: "Starting Trigger.dev services...",
+      showOutput: true,
     });
 
     // Final success message
-    outro('🎉 Core Development Environment Started!');
-    note('• Core Application: http://localhost:3033\n• Trigger.dev: http://localhost:8030\n• PostgreSQL: localhost:5432', '🌐 Your services are now running');
-    log.success('Happy coding!');
-
+    outro("🎉 Core Development Environment Started!");
+    note(
+      "• Core Application: http://localhost:3033\n• Trigger.dev: http://localhost:8030\n• PostgreSQL: localhost:5432",
+      "🌐 Your services are now running"
+    );
+    log.success("Happy coding!");
   } catch (error: any) {
     outro(`❌ Failed to start services: ${error.message}`);
     process.exit(1);
   }
-}
+}

packages/core-cli/src/commands/stop.ts

@@ -1,50 +1,52 @@
-import { intro, outro, log, confirm, note } from '@clack/prompts';
-import { executeDockerCommandInteractive } from '../utils/docker-interactive.js';
-import { printCoreBrainLogo } from '../utils/ascii.js';
-import path from 'path';
+import { intro, outro, log, confirm, note } from "@clack/prompts";
+import { executeCommandInteractive } from "../utils/docker-interactive.js";
+import { printCoreBrainLogo } from "../utils/ascii.js";
+import path from "path";
 
 export async function stopCommand() {
   // Display the CORE brain logo
   printCoreBrainLogo();
-  
-  intro('🛑 Stopping Core Development Environment');
+
+  intro("🛑 Stopping Core Development Environment");
 
   // Step 1: Confirm this is the Core repository
   const isCoreRepo = await confirm({
-    message: 'Are you currently in the Core repository directory?',
+    message: "Are you currently in the Core repository directory?",
   });
 
   if (!isCoreRepo) {
-    note('Please navigate to the Core repository first:\n\ngit clone https://github.com/redplanethq/core.git\ncd core\n\nThen run "core stop" again.', '📥 Core Repository Required');
-    outro('❌ Please navigate to the Core repository first.');
+    note(
+      'Please navigate to the Core repository first:\n\ngit clone https://github.com/redplanethq/core.git\ncd core\n\nThen run "core stop" again.',
+      "📥 Core Repository Required"
+    );
+    outro("❌ Please navigate to the Core repository first.");
     process.exit(1);
   }
 
   const rootDir = process.cwd();
-  const triggerDir = path.join(rootDir, 'trigger');
+  const triggerDir = path.join(rootDir, "trigger");
 
   try {
     // Stop trigger services first
-    await executeDockerCommandInteractive('docker compose down', {
+    await executeCommandInteractive("docker compose down", {
       cwd: triggerDir,
-      message: 'Stopping Trigger.dev services...',
-      showOutput: true
+      message: "Stopping Trigger.dev services...",
+      showOutput: true,
     });
 
     // Stop main services
-    await executeDockerCommandInteractive('docker compose down', {
+    await executeCommandInteractive("docker compose down", {
       cwd: rootDir,
-      message: 'Stopping Core services...',
-      showOutput: true
+      message: "Stopping Core services...",
+      showOutput: true,
     });
 
     // Final success message
-    outro('🎉 Core Development Environment Stopped!');
-    log.success('All services have been stopped.');
+    outro("🎉 Core Development Environment Stopped!");
+    log.success("All services have been stopped.");
     log.info('Run "core start" to start services again.');
-
   } catch (error: any) {
     outro(`❌ Failed to stop services: ${error.message}`);
     process.exit(1);
   }
-}
+}

packages/core-cli/src/utils/docker-interactive.ts

@@ -1,46 +1,45 @@
-import { spawn, ChildProcess } from 'child_process';
-import { spinner } from '@clack/prompts';
+import { spawn, ChildProcess } from "child_process";
+import { spinner } from "@clack/prompts";
 
-export interface DockerCommandOptions {
+export interface CommandOptions {
   cwd: string;
   message: string;
   showOutput?: boolean;
+  env?: Record<string, string>;
 }
 
-export function executeDockerCommandInteractive(
-  command: string, 
-  options: DockerCommandOptions
-): Promise<void> {
+export function executeCommandInteractive(command: string, options: CommandOptions): Promise<void> {
   return new Promise((resolve, reject) => {
     const s = spinner();
     s.start(options.message);
 
     // Split command into parts
-    const parts = command.split(' ');
+    const parts = command.split(" ");
     const cmd = parts[0];
     const args = parts.slice(1);
-    
+
     if (!cmd) {
-      reject(new Error('Invalid command'));
+      reject(new Error("Invalid command"));
       return;
     }
 
     const child: ChildProcess = spawn(cmd, args, {
       cwd: options.cwd,
-      stdio: options.showOutput ? ['ignore', 'pipe', 'pipe'] : 'ignore',
-      detached: false
+      stdio: options.showOutput ? ["ignore", "pipe", "pipe"] : "ignore",
+      detached: false,
+      env: options.env ? { ...process.env, ...options.env } : { ...process.env },
     });
 
-    let output = '';
+    let output = "";
 
     // Handle stdout
     if (child.stdout && options.showOutput) {
-      child.stdout.on('data', (data: Buffer) => {
+      child.stdout.on("data", (data: Buffer) => {
         const text = data.toString();
         output += text;
-        
+
         // Update spinner with latest output line
-        const lines = text.trim().split('\n');
+        const lines = text.trim().split("\n");
         const lastLine = lines[lines.length - 1];
         if (lastLine && lastLine.trim()) {
           s.message(`${options.message}\n${lastLine.trim()}`);
@@ -50,12 +49,13 @@ export function executeDockerCommandInteractive(
 
     // Handle stderr
     if (child.stderr && options.showOutput) {
-      child.stderr.on('data', (data: Buffer) => {
+      child.stderr.on("data", (data: Buffer) => {
         const text = data.toString();
         output += text;
-        
+        // console.log(text);
+
         // Update spinner with error output
-        const lines = text.trim().split('\n');
+        const lines = text.trim().split("\n");
         const lastLine = lines[lines.length - 1];
         if (lastLine && lastLine.trim()) {
           s.message(`${options.message}\n❌ ${lastLine.trim()}`);
@@ -64,14 +64,14 @@ export function executeDockerCommandInteractive(
     }
 
     // Handle process exit
-    child.on('exit', (code: number | null) => {
+    child.on("exit", (code: number | null) => {
       if (code === 0) {
-        s.stop(`✅ ${options.message.replace(/\.\.\.$/, '')} completed`);
+        s.stop(`✅ ${options.message.replace(/\.\.\.$/, "")} completed`);
         resolve();
       } else {
-        s.stop(`❌ ${options.message.replace(/\.\.\.$/, '')} failed (exit code: ${code})`);
+        s.stop(`❌ ${options.message.replace(/\.\.\.$/, "")} failed (exit code: ${code})`);
         if (options.showOutput && output) {
-          console.log('\nOutput:');
+          console.log("\nOutput:");
           console.log(output);
         }
         reject(new Error(`Command failed with exit code ${code}`));
@@ -79,30 +79,30 @@ export function executeDockerCommandInteractive(
     });
 
     // Handle errors
-    child.on('error', (error: Error) => {
-      s.stop(`❌ ${options.message.replace(/\.\.\.$/, '')} failed`);
+    child.on("error", (error: Error) => {
+      s.stop(`❌ ${options.message.replace(/\.\.\.$/, "")} failed`);
       reject(error);
     });
 
     // Handle Ctrl+C
     const handleSigint = () => {
-      s.stop(`⏹️  ${options.message.replace(/\.\.\.$/, '')} interrupted`);
-      child.kill('SIGTERM');
-      
+      s.stop(`⏹️  ${options.message.replace(/\.\.\.$/, "")} interrupted`);
+      child.kill("SIGTERM");
+
       // Give the process time to clean up
       setTimeout(() => {
         if (child.killed === false) {
-          child.kill('SIGKILL');
+          child.kill("SIGKILL");
         }
         process.exit(130); // Standard exit code for SIGINT
       }, 5000);
     };
 
-    process.on('SIGINT', handleSigint);
+    process.on("SIGINT", handleSigint);
 
     // Clean up event listener when done
-    child.on('exit', () => {
-      process.off('SIGINT', handleSigint);
+    child.on("exit", () => {
+      process.off("SIGINT", handleSigint);
     });
   });
-}
+}

packages/core-cli/src/utils/docker-login.ts

@@ -0,0 +1,63 @@
+import { confirm, log } from "@clack/prompts";
+import path from "path";
+import os from "os";
+import fs from "fs";
+
+export async function handleDockerLogin(triggerEnvPath: string): Promise<void> {
+  // Check if Docker is already logged in to localhost:5000
+  let dockerLoginNeeded = true;
+  try {
+    const dockerConfigPath = process.env.DOCKER_CONFIG
+      ? path.join(process.env.DOCKER_CONFIG, "config.json")
+      : path.join(os.homedir(), ".docker", "config.json");
+
+    if (fs.existsSync(dockerConfigPath)) {
+      const configContent = await fs.promises.readFile(dockerConfigPath, "utf8");
+      const config = JSON.parse(configContent);
+      if (
+        config &&
+        config.auths &&
+        Object.prototype.hasOwnProperty.call(config.auths, "localhost:5000")
+      ) {
+        dockerLoginNeeded = false;
+      }
+    }
+  } catch (error) {
+    // Ignore errors, will prompt for login below
+  }
+
+  if (dockerLoginNeeded) {
+    try {
+      // Read env file to get docker registry details
+      const envContent = await fs.promises.readFile(triggerEnvPath, "utf8");
+      const envLines = envContent.split("\n");
+
+      const getEnvValue = (key: string) => {
+        const line = envLines.find((l) => l.startsWith(`${key}=`));
+        return line ? line.split("=")[1] : "";
+      };
+
+      const dockerRegistryUrl = getEnvValue("DOCKER_REGISTRY_URL");
+      const dockerRegistryUsername = getEnvValue("DOCKER_REGISTRY_USERNAME");
+      const dockerRegistryPassword = getEnvValue("DOCKER_REGISTRY_PASSWORD");
+
+      log.info(
+        `docker login -u ${dockerRegistryUsername} -p ${dockerRegistryPassword} ${dockerRegistryUrl} `
+      );
+    } catch (error) {
+      log.info("docker login -u <USERNAME> -p <PASSWORD> <REGISTRY_URL>");
+    }
+  } else {
+    log.info("✅ Docker is already logged in to localhost:5000, skipping login prompt.");
+  }
+
+  const dockerLoginConfirmed = await confirm({
+    message: "Have you completed the Docker login successfully?",
+  });
+
+  if (!dockerLoginConfirmed) {
+    throw new Error(
+      "Docker login required. Please complete Docker login first and run the command again."
+    );
+  }
+}

packages/core-cli/src/utils/env-docker.ts

@@ -0,0 +1,48 @@
+import path from "path";
+import fs from "fs";
+import dotenv from "dotenv";
+import dotenvExpand from "dotenv-expand";
+
+/**
+ * Reads environment variables from .env file and replaces localhost URLs with host.docker.internal
+ * for Docker container compatibility
+ */
+export async function getDockerCompatibleEnvVars(rootDir: string): Promise<Record<string, string>> {
+  const envPath = path.join(rootDir, ".env");
+
+  try {
+    // Use dotenv to parse and expand variables
+
+    const envVarsExpand =
+      dotenvExpand.expand(dotenv.config({ path: envPath, processEnv: {} })).parsed || {};
+
+    const getEnvValue = (key: string): string => {
+      return envVarsExpand[key] || "";
+    };
+
+    const replaceLocalhostWithDockerHost = (value: string): string => {
+      return value
+        .replace(/localhost/g, "host.docker.internal")
+        .replace(/127\.0\.0\.1/g, "host.docker.internal");
+    };
+
+    // Get all required environment variables
+    const envVars = {
+      ANTHROPIC_API_KEY: getEnvValue("ANTHROPIC_API_KEY"),
+      API_BASE_URL: replaceLocalhostWithDockerHost(getEnvValue("API_BASE_URL")),
+      DATABASE_URL: replaceLocalhostWithDockerHost(getEnvValue("DATABASE_URL")),
+      EMBEDDING_MODEL: getEnvValue("EMBEDDING_MODEL"),
+      ENCRYPTION_KEY: getEnvValue("ENCRYPTION_KEY"),
+      MODEL: getEnvValue("MODEL") || "gpt-4.1-2025-04-14",
+      NEO4J_PASSWORD: getEnvValue("NEO4J_PASSWORD"),
+      NEO4J_URI: replaceLocalhostWithDockerHost(getEnvValue("NEO4J_URI")),
+      NEO4J_USERNAME: getEnvValue("NEO4J_USERNAME"),
+      OPENAI_API_KEY: getEnvValue("OPENAI_API_KEY"),
+      TRIGGER_PROJECT_ID: getEnvValue("TRIGGER_PROJECT_ID"),
+    };
+
+    return envVars;
+  } catch (error) {
+    throw new Error(`Failed to read .env file: ${error}`);
+  }
+}

packages/core-cli/src/utils/trigger-deploy.ts

@@ -0,0 +1,66 @@
+import { note, log } from "@clack/prompts";
+import { executeCommandInteractive } from "./docker-interactive.js";
+import { getDockerCompatibleEnvVars } from "./env-docker.js";
+import path from "path";
+
+export async function deployTriggerTasks(rootDir: string): Promise<void> {
+  const webappDir = path.join(rootDir, "apps", "webapp");
+  const databaseDir = path.join(rootDir, "packages", "database");
+  const typesDir = path.join(rootDir, "packages", "types");
+
+  note(
+    "We'll now deploy the trigger tasks to your Trigger.dev instance.",
+    "🚀 Deploying Trigger.dev tasks"
+  );
+
+  try {
+    // Login to trigger.dev CLI
+    await executeCommandInteractive(
+      "npx -y trigger.dev@4.0.0-v4-beta.22 login -a http://localhost:8030",
+      {
+        cwd: rootDir,
+        message: "Logging in to Trigger.dev CLI...",
+        showOutput: true,
+      }
+    );
+
+    await executeCommandInteractive("pnpm install", {
+      cwd: rootDir,
+      message: "Running package installation",
+      showOutput: true,
+    });
+
+    const envVars = await getDockerCompatibleEnvVars(rootDir);
+
+    await executeCommandInteractive("pnpm build", {
+      cwd: databaseDir,
+      message: "Building @core/database...",
+      showOutput: true,
+      env: {
+        DATABASE_URL: envVars.DATABASE_URL as string,
+      },
+    });
+
+    await executeCommandInteractive("pnpm build", {
+      cwd: typesDir,
+      message: "Building @core/types...",
+      showOutput: true,
+    });
+
+    // Deploy trigger tasks
+    await executeCommandInteractive("pnpm run trigger:deploy", {
+      cwd: webappDir,
+      message: "Deploying Trigger.dev tasks...",
+      showOutput: true,
+      env: envVars,
+    });
+
+    log.success("Trigger.dev tasks deployed successfully!");
+  } catch (error: any) {
+    log.warning("Failed to deploy Trigger.dev tasks:");
+    note(
+      `${error.message}\n\nYou can deploy them manually later with:\n1. npx trigger.dev@v4-beta login -a http://localhost:8030\n2. pnpm trigger:deploy`,
+      "Manual Deployment"
+    );
+  }
+}

packages/database/package.json

@@ -21,7 +21,7 @@
     "db:studio": "prisma studio",
     "db:reset": "prisma migrate reset",
     "typecheck": "tsc --noEmit",
-    "build": "pnpm run clean && tsc --noEmit false --outDir dist --declaration",
+    "build": "pnpm run generate && pnpm run clean && tsc --noEmit false --outDir dist --declaration",
     "dev": "tsc --noEmit false --outDir dist --declaration --watch"
   }
 }

packages/mcp-proxy/src/core/mcp-remote-client.ts

@@ -1,6 +1,7 @@
 import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { SSEClientTransport } from "@modelcontextprotocol/sdk/client/sse.js";
 import { StreamableHTTPClientTransport } from "@modelcontextprotocol/sdk/client/streamableHttp.js";
+import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js";
 import {
   MCPRemoteClientConfig,
   AuthenticationResult,
@@ -153,7 +154,7 @@ export function createMCPProxy(
     redirectUrl: string,
     transportStrategy: TransportStrategy = "sse-first",
     clientHeaders?: { sessionId?: string | null; lastEventId?: string | null }
-  ): Promise<SSEClientTransport | StreamableHTTPClientTransport> {
+  ): Promise<SSEClientTransport | StreamableHTTPClientTransport | StdioClientTransport> {
     // Create auth provider with stored credentials using common factory
     const authProvider = await createAuthProviderForProxy(serverUrl, credentials, redirectUrl);
 
@@ -173,9 +174,16 @@ export function createMCPProxy(
     }
 
     // Create transport based on strategy (don't start yet)
-    let transport: SSEClientTransport | StreamableHTTPClientTransport;
+    let transport: SSEClientTransport | StreamableHTTPClientTransport | StdioClientTransport;
 
     switch (transportStrategy) {
+      case "stdio":
+        // For stdio transport, serverUrl should contain the command to execute
+        // This is mainly for completeness - prefer using createMCPStdioProxy directly
+        throw new Error(
+          "Stdio transport not supported in createRemoteTransport. Use createMCPStdioProxy instead."
+        );
+
       case "sse-only":
         transport = new SSEClientTransport(url, {
           authProvider,
@@ -227,6 +235,257 @@ export function createMCPProxy(
   }
 }
 
+/**
+ * Creates an MCP proxy that forwards requests to a stdio process.
+ * Maintains a mapping of sessionId -> StdioClientTransport for reuse.
+ * If sessionId is provided, it is returned in the response header as mcp_session_id.
+ * @param request The incoming HTTP request
+ * @param command The command to execute for the stdio process
+ * @param args Arguments for the command
+ * @param options Optional configuration for the proxy
+ * @param sessionId Optional session id for transport reuse
+ * @returns Promise that resolves to the HTTP response
+ */
+// Track both the transport and its last used timestamp
+type StdioTransportEntry = {
+  transport: StdioClientTransport;
+  lastUsed: number; // ms since epoch
+};
+
+const stdioTransports: Map<string, StdioTransportEntry> = new Map();
+
+/**
+ * Cleans up any stdio transports that have not been used in the last 5 minutes.
+ * Closes and removes them from the map.
+ */
+function cleanupOldStdioTransports() {
+  const now = Date.now();
+  const FIVE_MINUTES = 5 * 60 * 1000;
+  for (const [sessionId, entry] of stdioTransports.entries()) {
+    if (now - entry.lastUsed > FIVE_MINUTES) {
+      try {
+        entry.transport.close?.();
+      } catch (err) {
+        // ignore
+      }
+      stdioTransports.delete(sessionId);
+    }
+  }
+}
+
+export function createMCPStdioProxy(
+  request: Request,
+  command: string,
+  args?: string[],
+  options?: {
+    /** Enable debug logging */
+    debug?: boolean;
+    /** Environment variables to pass to the process */
+    env?: Record<string, string>;
+    /** Custom header-to-environment variable mapping */
+    headerMapping?: Record<string, string>;
+    /** Optional session id for transport reuse */
+    sessionId?: string;
+  }
+): Promise<Response> {
+  return new Promise<Response>(async (resolve) => {
+    let bridge: any = null;
+    let serverTransport: StdioClientTransport | undefined;
+    let sessionId: string | undefined =
+      options?.sessionId || request.headers.get("Mcp-Session-Id") || undefined;
+
+    // Clean up old transports before handling new connection
+    cleanupOldStdioTransports();
+
+    try {
+      // Extract headers from the incoming request and convert to environment variables
+      const env = createEnvironmentFromRequest(
+        request,
+        options?.env || {},
+        options?.headerMapping || {}
+      );
+
+      // If sessionId is provided, try to reuse the transport
+      let entry: StdioTransportEntry | undefined;
+      if (sessionId) {
+        entry = stdioTransports.get(sessionId);
+        if (entry) {
+          serverTransport = entry.transport;
+          entry.lastUsed = Date.now();
+        }
+      }
+
+      // If no transport exists for this sessionId, create a new one and store it
+      if (!serverTransport) {
+        serverTransport = new StdioClientTransport({
+          command,
+          args: args || [],
+          env,
+        });
+        await serverTransport.start();
+        if (sessionId) {
+          stdioTransports.set(sessionId, {
+            transport: serverTransport,
+            lastUsed: Date.now(),
+          });
+        }
+      }
+
+      // Create Remix transport (converts HTTP to MCP messages)
+      // We need to wrap resolve to inject the sessionId header if present
+      const resolveWithSessionId = (response: Response) => {
+        if (sessionId) {
+          // Clone the response and add the mcp_session_id header
+          const headers = new Headers(response.headers);
+          headers.set("mcp-session-id", sessionId);
+          resolve(
+            new Response(response.body, {
+              status: response.status,
+              statusText: response.statusText,
+              headers,
+            })
+          );
+        } else {
+          resolve(response);
+        }
+      };
+
+      const clientTransport = new RemixMCPTransport(request, resolveWithSessionId);
+
+      // Bridge the transports
+      const bridgeOptions: any = {
+        debug: options?.debug || false,
+        onError: (error: Error, source: string) => {
+          console.error(`[MCP Stdio Bridge] ${source} error:`, error);
+        },
+      };
+
+      if (options?.debug) {
+        bridgeOptions.onMessage = (direction: string, message: any) => {
+          console.log(`[MCP Stdio Bridge] ${direction}:`, message.method || message.id);
+        };
+      }
+
+      bridge = createMCPTransportBridge(
+        clientTransport as any,
+        serverTransport as any,
+        bridgeOptions
+      );
+
+      // Start only the client transport (server is already started)
+      await clientTransport.start();
+    } catch (error) {
+      console.error("MCP Stdio Proxy Error:", error);
+
+      if (bridge) {
+        bridge.close().catch(console.error);
+      }
+
+      const errorMessage = error instanceof Error ? error.message : String(error);
+      // Always include mcp_session_id header if sessionId is present
+      const headers: Record<string, string> = { "Content-Type": "application/json" };
+      if (sessionId) {
+        headers["mcp-session-id"] = sessionId;
+      }
+      resolve(
+        new Response(
+          JSON.stringify({
+            error: `Stdio proxy error: ${errorMessage}`,
+          }),
+          {
+            status: 500,
+            headers,
+          }
+        )
+      );
+    }
+  });
+}
+
+/**
+ * Creates environment variables from request headers
+ */
+function createEnvironmentFromRequest(
+  request: Request,
+  baseEnv: Record<string, string>,
+  headerMapping: Record<string, string>
+): Record<string, string> {
+  // Start with base environment (inherit safe environment variables)
+  const env: Record<string, string> = {
+    ...getDefaultEnvironment(),
+    ...baseEnv,
+  };
+
+  // Add standard MCP headers as environment variables
+  const sessionId = request.headers.get("Mcp-Session-Id");
+  const lastEventId = request.headers.get("Last-Event-Id");
+  const contentType = request.headers.get("Content-Type");
+  const userAgent = request.headers.get("User-Agent");
+
+  if (sessionId) {
+    env["MCP_SESSION_ID"] = sessionId;
+  }
+  if (lastEventId) {
+    env["MCP_LAST_EVENT_ID"] = lastEventId;
+  }
+  if (contentType) {
+    env["MCP_CONTENT_TYPE"] = contentType;
+  }
+  if (userAgent) {
+    env["MCP_USER_AGENT"] = userAgent;
+  }
+
+  // Apply custom header-to-environment variable mapping
+  for (const [headerName, envVarName] of Object.entries(headerMapping)) {
+    const headerValue = request.headers.get(headerName);
+    if (headerValue) {
+      env[envVarName] = headerValue;
+    }
+  }
+
+  return env;
+}
+
+/**
+ * Returns a default environment object including only environment variables deemed safe to inherit.
+ */
+function getDefaultEnvironment(): Record<string, string> {
+  const DEFAULT_INHERITED_ENV_VARS =
+    process.platform === "win32"
+      ? [
+          "APPDATA",
+          "HOMEDRIVE",
+          "HOMEPATH",
+          "LOCALAPPDATA",
+          "PATH",
+          "PROCESSOR_ARCHITECTURE",
+          "SYSTEMDRIVE",
+          "SYSTEMROOT",
+          "TEMP",
+          "USERNAME",
+          "USERPROFILE",
+        ]
+      : ["HOME", "LOGNAME", "PATH", "SHELL", "TERM", "USER"];
+
+  const env: Record<string, string> = {};
+
+  for (const key of DEFAULT_INHERITED_ENV_VARS) {
+    const value = process.env[key];
+    if (value === undefined) {
+      continue;
+    }
+
+    if (value.startsWith("()")) {
+      // Skip functions, which are a security risk.
+      continue;
+    }
+
+    env[key] = value;
+  }
+
+  return env;
+}
+
 export class MCPAuthenticationClient {
   private serverUrlHash: string;
   private authProvider: NodeOAuthClientProvider | null = null;

packages/mcp-proxy/src/index.ts

@@ -5,6 +5,7 @@ export * from "./types/index.js";
 export {
   createMCPAuthClient,
   createMCPProxy,
+  createMCPStdioProxy,
   MCPAuthenticationClient,
 } from "./core/mcp-remote-client.js";
 

packages/mcp-proxy/src/types/remote-client.ts

@@ -51,7 +51,7 @@ export interface ProxyConnectionConfig {
 /**
  * Transport strategy options
  */
-export type TransportStrategy = "sse-only" | "http-only" | "sse-first" | "http-first";
+export type TransportStrategy = "sse-only" | "http-only" | "sse-first" | "http-first" | "stdio";
 
 /**
  * Static OAuth client metadata

packages/mcp-proxy/src/utils/mcp-transport-bridge.ts

@@ -23,7 +23,7 @@ export function createMCPTransportBridge(
 
   // Forward messages from client to server
   clientTransport.onmessage = (message: any, extra: any) => {
-    console.log(JSON.stringify(message));
+    console.log(message);
     log("[Client→Server]", message.method || message.id);
     onMessage?.("client-to-server", message);
 
@@ -41,6 +41,7 @@ export function createMCPTransportBridge(
 
   // Forward messages from server to client
   serverTransport.onmessage = (message: any, extra: any) => {
+    console.log(message);
     console.log(JSON.stringify(message), JSON.stringify(extra));
     log("[Server→Client]", message.method || message.id);
     onMessage?.("server-to-client", message);

packages/mcp-proxy/src/utils/mcp-transport.ts

@@ -34,13 +34,24 @@ export class RemixMCPTransport implements Transport {
         throw new Error("Invalid JSON-RPC message");
       }
 
-      // Emit the message to handler
-      if (this.onmessage) {
-        try {
-          this.onmessage(message);
-        } catch (error) {
-          if (this.onerror) {
-            this.onerror(error as Error);
+      if (message.method.includes("notifications")) {
+        this.send({});
+        return;
+      }
+
+      console.log(message, "message");
+
+      if (Object.keys(message).length === 0) {
+        this.send({});
+      } else {
+        // Emit the message to handler
+        if (this.onmessage) {
+          try {
+            this.onmessage(message);
+          } catch (error) {
+            if (this.onerror) {
+              this.onerror(error as Error);
+            }
           }
         }
       }

pnpm-lock.yaml

@@ -568,6 +568,9 @@ importers:
       dotenv:
         specifier: ^16.4.5
         version: 16.5.0
+      dotenv-expand:
+        specifier: ^12.0.2
+        version: 12.0.2
       esbuild:
         specifier: ^0.23.0
         version: 0.23.1
@@ -6315,6 +6318,10 @@ packages:
     resolution: {integrity: sha512-GopVGCpVS1UKH75VKHGuQFqS1Gusej0z4FyQkPdwjil2gNIv+LNsqBlboOzpJFZKVT95GkCyWJbBSdFEFUWI2A==}
     engines: {node: '>=12'}
 
+  dotenv-expand@12.0.2:
+    resolution: {integrity: sha512-lXpXz2ZE1cea1gL4sz2Ipj8y4PiVjytYr3Ij0SWoms1PGxIv7m2CRKuRuCRtHdVuvM/hNJPMxt5PbhboNC4dPQ==}
+    engines: {node: '>=12'}
+
   dotenv@16.0.3:
     resolution: {integrity: sha512-7GO6HghkA5fYG9TYnNxi14/7K9f5occMlp3zXAuSxn7CKCxt9xbNWG7yF8hTCSUchlfWSe3uLmlPfigevRItzQ==}
     engines: {node: '>=12'}
@@ -17106,6 +17113,10 @@ snapshots:
 
   dotenv-expand@10.0.0: {}
 
+  dotenv-expand@12.0.2:
+    dependencies:
+      dotenv: 16.5.0
+
   dotenv@16.0.3: {}
 
   dotenv@16.4.7: {}

trigger/.env.example

@@ -31,7 +31,7 @@ POSTGRES_USER=docker
 POSTGRES_PASSWORD=docker
 TRIGGER_DB=trigger
 
-DB_HOST=localhost
+DB_HOST=host.docker.internal
 DB_PORT=5432
 DB_SCHEMA=sigma
 

trigger/auth.htpasswd

@@ -0,0 +1 @@
+registry-user:$2y$05$6ingYqw0.3j13dxHY4w3neMSvKhF3pvRmc0AFifScWsVA9JpuLwNK

trigger/docker-compose.yaml

@@ -146,7 +146,7 @@ services:
       - webapp
     volumes:
       # registry-user:very-secure-indeed
-      - ../registry/auth.htpasswd:/auth/htpasswd:ro
+      - ./auth.htpasswd:/auth/htpasswd:ro
     environment:
       REGISTRY_AUTH: htpasswd
       REGISTRY_AUTH_HTPASSWD_REALM: Registry Realm

turbo.json

@@ -52,6 +52,7 @@
     "SESSION_SECRET",
     "APP_ORIGIN",
     "LOGIN_ORIGIN",
+    "API_BASE_URL",
     "POSTHOG_PROJECT_KEY",
     "AUTH_GOOGLE_CLIENT_ID",
     "AUTH_GOOGLE_CLIENT_SECRET",