Package - overwrite block (templates)

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I'm creating a package that contains a theme, some blocks and an autonav block with a template that contains the html structure for bootstrap.

The autonav template is not triggered when I use setup 1. If I copy it directly in the root blocks folder than it does. When I use setup 2 it does work. The difference is that the template php file is directly in the templates folder. Both setups are valid when used directly in the root blocks folder.

Setup 1 is how i would like to get it working so that I can include javascript and css (view.js / view.css). Is this possible from a package?

Setup 1 (does not work)
|- autonav
   |-- templates
      |-- bootstrap
          |-- view.php

Setup 2 (does work)
|- autonav
   |-- templates
       |-- bootstrap.php


The BlockType gets installed via the controller.

BlockType::installBlockTypeFromPackage('autonav', $pkg); //custom template


Thanks,

Rge