auto generated tools docs, added stdio transport, added additional mcp config and permissions

app/src/modules/permissions/index.ts

@@ -7,3 +7,4 @@ export const configReadSecrets = new Permission("system.config.read.secrets");
 export const configWrite = new Permission("system.config.write");
 export const schemaRead = new Permission("system.schema.read");
 export const build = new Permission("system.build");
+export const mcp = new Permission("system.mcp");