In mojito 0.4.x due to the automatic inclusion of the mojito-assets-addon, when executing the loop on line 124 it calls the metaMergeInto of the assets addon which makes the config to merge.
Since we dont have that automatic, we will need to do it by default.
If you add the assets addon as a dependencie, due to the implementation of metaMerge will not duplicate assets. So is just a small overhead on computation in that case.
This is a must merge to Shaker.