Remove `include` of application configuration

Per #24, `include` can be problematic on applications that use ENV variables or
constants inside their `application.config.php`. This patch removes the
`include` in favor of doing static analysis via regexp; it's far from perfect,
but will work in the majority of use cases.

`include` is still required, however, if you want to selectively enable modules.

CS fixes
- Updated php-cs-fixer
- php-cs-fixer is being too aggressive on `include` statements; moved include
  out of constructor call to prevent fixer changes in the future.