Manipulating theme module paths means that the paths you author are not the ones used at runtime. This can lead to some very unexpected behavior and potential module name clashes. It also meant that the refactor in 16c6ab8661 was unable to correctly match up theme connector js/templates.
While this could technically be a breaking change, I think it is reasonably safe because:
1. Themes are already forced to use relative paths when referencing their own modules (since they're namespaced based on the site-specific id). The only time this might be problematic is when theme tests reference modules in the theme's main `javascripts` directory
2. For things like components/services/controllers/etc. our custom Ember resolver works backwards from the end of the path, so adding `discourse/` in the middle will not affect resolution.
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