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Freestyle loading unneeded collections
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Description

System Information
Operating system: Windows 10 64-bit
Graphics card: NVIDIA Geforce GTX 960M

Blender Version
Broken: 2.80 ad707115d5bc 2019-01-17
Worked: (Cannot be solved by the user)

Blender 2.80 loads unneeded collections, which are marked as set indirect only and set holdout to the view layer.

Exact steps for others to reproduce the error
This file has view layer A and collection B, C, D in it. C and D are made up of millions of polygons and is very heavy. B is very light and low-poly.
In View Layer A, I marked collection C as set indirect only and D as set holdout inside the outliner editor. However at the final part of the rendering, freestyle was loading mesh for a very long time and it turned out that the freestyle was trying to load B, C, D instead of just B.

Set exclude works fine with freestyle. It doesn't load collections marked as set exclude. However it does load set indirect and set holdout collections, which is obviously unnecessary and takes up our precious time. Sometimes like this it makes blender unresponsive if the unnecessary mesh is too heavy.

This needs to be fixed since some of us users are using workflow that is related to cartoons and have to draw lines on only parts of the scene.