Geometry fixer fixes

[olivierdalang]

Description

This PR adds some fixes in the topology fixer logic (that is hidden by default, but used in the plugins) :

• fixes an issue where trying to fix gaps would have no effect (happened when the gap was defined by a non-shared vertex on the edge or inside a neighbouring polygon)
• fixed an issue where trying to fix overlaps would have no effect (happened because the tolerance used when first finding the overlap wasn't the same than when fixing the overlap, so that the initial overlap polygon wouldn't be found when fixing it)
• fixed an issue where all points of a geometry would be "snapped to grid" when fixing an overlap, even points far away from the overlap (happened because the tolerance set to detect the overlaps was also used to modify the geometry)

There's many more issues (just look at the tracker :-) ) including in the provided overlap fixer test, where a sliver is left after fixing the overlap.
It's not easy to fix if we want to keep the ability to fix each part of an overlap independently (as an overlap part has shared edges with the base geom). But I'm not really sure of the current state of the geometry/topology checker plugin VS core feature, so I suggest to treat that separately (in what we shall call a geometry fixer fixes fix PR :-) )

[nyalldawson]

Looks good to me!

@m-kuhn I'd appreciate your review here too, you know this code better than I do...

[stale]

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