What I did:
1. removed/disabled all plugins
2. removed folder .idea
3. ran invalidate and restart many times
4. checked scopes, show excluded files
5. updated phpstorm
6. read a bunch of advice about vue-for-idea
We in PhpStorm with a colleague from WebStorm thought and no entries were decided, comes to mind only Show Excluded Files.
For fun, you can try to start with a clean configuration file (rename the %USERPROFILE%\.PhpStorm2018.3 and start the Storm without importing settings), open the project and see how it will be.
If it is good, then it somehow in the config.
If it is bad, you can try some newly created c project node_modules.
If still bad, then we will think again.