Eventually I solved it by moving my app/
folder and my wp/
folder into a subfolder, which becomes the web root.
Something like this:
my_project
|
\--vendor <-- folder for composer packages
| |
| \...
|
\--wordpress <-- Web Root
| |
| \--app <-- custom wp-content folder
| | |
| | \--mu-plugins
| | \--plugins
| | \--themes
| |
| \--core <-- WordPress core code
|
|--all the other stuff like config, environment variables, SASS, Grunt, etc... outside the web root
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