What are the proper settings for the new directory structure?
Translations is now translations, easy.
Web directory is now public, easy.
App directory is now what exactly? this one is a bit hard to change to the right folder....
App directory is the whole src directory.
Basically the previous app directory now doesn't exist anymore and all is moved to src (due to the removing of support for bundles - only the ones that are not reusable).

Service id resolving is still not working. I have cleared PHPStorm's cache and restarted IDE already
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1118 is still not fixed, it's been months since symfony 4 was released and now it is stable ( 4.1.1 ), yet this is still a bug :)