Allow runtime configuration #4128
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By loading the configuration before bootstrap we can also change the configuration of extensions. This allows us add more configuration into the guides packages when they are started.
This simple example project shows how to configure phpdocumentor and render markdown files.
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Before we loaded the configuration after the application was bootstrapped, but when we introduced extensions is was already less applicable. Now I moved the configuration loading into the start of the application. This allows me to enable features on guides when the user configures particular settings. A first example is the option for auto menus when using markdown format.
Fixes #3892