PR tested locally, works like a charm. The critical feature this PR provides is decoupling recipes. As explained in the description, the current recipes are broken because they make too many assumptions.

Note that this PR introduces a new bootstrap.php file that should be used to setup both the autoload and load .env files.
In order to reduce duplication while still providing decoupling of recipes, this PR uses symbolic links to ship the bootstrap.php in several recipes.
Works transparently with the flex server.

PR ready. Votes pending.

for anyone running paratest, this will break your tests.
src/.bootstrap.php is loaded by paratest before <env name="APP_ENV" value="test" /> is read in phpunit.xml.dist, so the wrong .env files are read.

Still looking for a solution.

You need to define APP_ENV=test before running paratest.
Dunno how this can be achieved when using paratest.
A different bootstrap file would do it of course:

// tests/bootstrap.php
putenv('APP_ENV='.$_SERVER['APP_ENV'] = $_ENV['APP_ENV'] = 'test');
require dirname(__DIR__).'/src/.bootstrap.php');

Yep - lovely, thankyou. Have submitted an issue to paratest.

@nicolas-grekas is there a bug in bin/console here?

These two should be equivalent, shouldn't they?

> APP_ENV=prod APP_DEBUG=0 bin/console cache:clear --no-warmup
> bin/console cache:clear --no-warmup --env=prod --no-debug

The 2nd will result in

Fatal error: Uncaught RuntimeException: The "APP_ENV" environment variable is not set to "prod". Please run "composer require symfony/dotenv" to load the ".env" files configuring the application. in project/src/.bootstrap.php on line 13

Edit:

Reproducer:

> composer create-project symfony/skeleton skeleton 
> cd skeleton
> rm -rf vendor
> composer install --no-dev #error will be here too.
> bin/console cache:clear --no-warmup --env=prod --no-debug