Code marked as undefined or unused

I have problem with latest PHPstorm that markings are not set on code correctly, like unmarks defined vairables or unused

This happened after I installed ubuntu 18.04 from scratch, invalidating cache, syncrhronize, restart of phpstorm or restart of ubuntu doesnt help

DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=18.04
DISTRIB_CODENAME=bionic
DISTRIB_DESCRIPTION="Ubuntu 18.04.1 LTS"

PhpStorm 2018.2.2
Build #PS-182.4129.45, built on August 22, 2018
JRE: 1.8.0_152-release-1248-b8 amd64
JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o
Linux 4.15.0-33-generic

Get this error aswell when starting phpstorm:
07:21 Can't analyse webpack.config.js: coding assistance will ignore module resolution rules in this file.
Possible reasons: this file is not a valid webpack configuration file or its format is not currently supported by the IDE.
Error details: Encore.addLoader() cannot be called yet because the runtime environment doesn't appear to be configured. Make sure you're using the encore executable or call Encore.configureRuntimeEnvironment() first if you're purposely not calling Encore directly.

But that I got when using Ubuntu 16.04 aswell and there the code marking worked