@Luigi: if I manually add "create spatial index" often, this very much 
"pollutes" the model.

I agree with Ujaval, that it would be a better user experience if QGIS would do 
the indexing automatically (on intermediate layers) for operations where the 
input doesn't have an index and the algorithm would potentially benefit from an 
index.

This is a fair enough request -- we could keep the index generation as
a "lazy" thing which is only done when a step in the model indicates
that it's about to benefit from it. I can't see any technical
blockers/disadvantages to this.

Ok - great. If this requires funding - we will suggest / vote for
several grant proposals from the QGIS-CH user group early next year. I
would like to invest in "data quality" tools/improvements - also, but
not limited, to Processing.
Next to automatic indexing I would think that "auto-repairs" for errors that 
processing algorithms introduce would be good to have, e.g. remove double vertices, 
remove empty geometries, empty holes/rings, self-intersections. etc.. If this is 
potentially dangerous, we can do opt-in with central threshold values, and only if the 
analysis is 2d only. I understand that for 3D analysis automatic cleaning is not always 
possible.

There's some discussion on this here:
https://github.com/qgis/QGIS/pull/39891#issuecomment-734676128

Ok - great - thanks for being involved here!
Or maybe a switch to GEOS 3.9 with the "fixed precision model" enabled would 
remove all these errors previously introduced by processing?

I'll open a separate thread for this discussion.
Andreas
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